Manual de Microbiologie

INTRODUCTION
PREFACE
This laboratory manual has evolved over the years to meet the needs of students taking microbiology at the
Catonsville Campus of The Community College of Baltimore County. The intention is to provide the student with
an organized, user-friendly tool to better enable him or her to understand laboratory aspects of microbiology as
well as to hopefully make learning laboratory material and preparing for lab quizzes a bit easier.
Each lab exercise is set up as a complete module that demonstrates some microbiological principle or
technique. Each exercise begins with a detailed Discussion that provides all the information needed to
understand that lab and has key words and phrases presented in boldface. The discussion section is followed by
a detailed step-by-step Procedure, again with key elements presented in boldface. The Results section of each
exercise is where the student records important results and conclusions that will enable him or her to prepare for
the practical portion of each lab quiz. This WWW version of the manual has the advantage of providing students
with a complete set of color photographs and photomicrographs of the results for each laboratory
exercise to use in reviewing and studying for quizzes. The URL is
http://student.ccbcmd.edu/~gkaiser/goshp.html .
Finally, each lab exercise ends with a set of Performance Objectives that tells the student exactly what he or
she is responsible for on lab quizzes.
The lab exercises are designed to give the student "hands-on" laboratory experience to better reinforce certain
topics discussed in lecture as well as to present a number of selected microbiological principles not covered in
lecture. The first several labs enable the student to master techniques essential in working with and studying
microorganisms. The next series covers microbial morphology. A number of labs deal with the laboratory isolation
and identification of common opportunistic and pathogenic microorganisms as well as other techniques used in
the diagnosis of infectious diseases. Several of the labs pertain to the control of microorganisms.
I hope you enjoy this laboratory manual and also hope it makes your study of microbiology a bit easier. Keep in
mind that the labs are meant to be informal and your instructor is more than willing to answer any questions on
either lab or lecture topics.
G.E.K.
2007
INTRODUCTION
ACKNOWLEDGEMENTS
I would like to extend my deepest thanks to my co-worker and treasured friend Dr. David R. Jeffrey, for his
many comments and suggestions during the various editions of this manual, and for the many hours he has spent
in editing. Also special thanks for encouraging me over these many years I have known him to maintain some
degree of sanity in this sometimes crazy world.
Many thanks to my co-worker and friend Mr. Jeffrey D. Smith for his countless hours spent editing the early
editions of this manual.
Continuous thanks to another friend and co-worker Mr. Robert L. Hudson whose efforts and ability assure that
the microbiology labs always run smoothly and whose friendship and daily conversations help me to usually run
smoothly.
Thanks to Dr. Donna H. Linksz, Associate Dean for Mathematics, Science, and Engineering for her continued
encouragement and support in all my efforts to devise and write teaching aids for my students.
A special thanks to Ms. Karen Miller for her great cover to this lab manual.
A big thanks to you, the students in my microbiology classes, who always seem to make coming to work a
pleasure.
Also, my complete love and heartfelt thanks to my wonderful wife and colleague Dr. Sonja Schmitz. You are my
dream-maker!
Finally, thanks to microorganisms everywhere --- for without their existence, I'd be out of a job and forced to join
the "real world."
Gary E. Kaiser
Copyright Gary E. Kaiser 1979, 1984, 1986, 1989, 1994, 1999, 2002, 2005, 2007, 2008
ii
INTRODUCTION
TABLE OF CONTENTS
INTRODUCTION
i
I
ii
iii
vii
vii
viii
ix
ix
x
Preface
Acknowledgements
Table of Contents
Using Performance Objectives
Laboratory Rules
General Directions
Binomial Nomenclature
Metric Length
Using the Microscope
LAB 1: INTRODUCTION TO THE MICROSCOPE

AND COMPARISON OF SIZES AND SHAPES OF
MICROORGANISMS
Bacterial Shapes and Arrangements
Yeasts
Measurement of Microorganisms
Focusing With Oil Immersion
1
1
3
3
5
LAB 2: ASEPTIC TECHNIQUE AND TRANSFER OF

MICROORGANISMS
Aseptic Technique
Forms of Culture Medium
Oxygen Requirements for Growth
Temperature Requirements for Growth
Colony Morphology and Pigmentation
13
13
15
21
21
22
LAB 3: OBTAINING PURE CULTURES FROM A MIXED

POPULATION
Streak Plate Method
Pour Plate and Spin Plate Methods
Use of Specialized Media
29
29
29
30
LAB 4: ENUMERATION OF MICROORGANISMS

Plate Count
Direct Microscopic Method
Turbidity
37
37
38
39
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INTRODUCTION
LAB 5: DIRECT STAIN AND INDIRECT STAIN

Introduction to Staining
Direct Stain
Indirect Stain
47
47
49
50
LAB 6: GRAM STAIN AND CAPSULE STAIN
55
Gram Stain
Capsule Stain
55
58
LAB 7: ENDOSPORE STAIN AND BACTERIAL MOTILITY

Endospore Stain
Bacterial Motility
63
63
66
LAB 8: IDENTIFICATION OF BACTERIA THROUGH

BIOCHEMICAL TESTING
75
Introduction
Starch Hydrolysis
Protein Hydrolysis
Fermentation of Carbohydrates
Indole and Hydrogen Sulfide Production
Catalase Activity
75
76
77
78
80
81
LAB 9: FUNGI PART 1 - THE YEASTS
87
LAB 10: FUNGI PART 2 - THE MOLDS
95
Non-pathogenic Molds
Dermatophytes
Dimorphic Fungi
96
99
99
LAB 11: VIRUSES - THE BACTERIOPHAGES
107
LAB 12: ISOLATION AND IDENTIFICATION OF

ENTEROBACTERIACEAE AND PSEUDOMONAS,
PART 1
119
The Enterobacteriaceae: Fermentative,

Gram-Negative, Enteric Bacilli
Pseudomonas and Other Non-fermentative,
Gram-Negative Bacilli
Isolation of Enterobacteriaceae and
Pseudomonas
Differentiating Between the Enterobacteriaceae
and Pseudomonas
Identifying the Enterobacteriaceae
119
122
123
123
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INTRODUCTION
Using the EnterotubeII
124

ENTEROBACTERIACEAE AND PSEUDOMONAS,
PART 2
The Oxidase Test
The Gram Stain
Isolation of Enterobacteriaceae on
XLD Agar
Isolation and Identification of Pseudomonas
on Pseudosel Agar
Identifying Members of the Enterobacteriaceae
Using the EnterotubeII
Bacteriological Examination of Water:
Coliform Counts
129
129
129
129
130
131
133

STREPTOCOCCI
The Beta Streptococci (Groups A,B,C,F,G)
The Pneumococcus (Streptococcus pneumoniae)
The Viridans Streptococci
The Enterococci
143
144
149
150
148

STAPHYLOCOCCI
157

NEISSERIAE, MYCOBACTERIA, AND OBLIGATE
ANAEROBES
167
The Neisseriae (Neisseria gonorrhoeae and

Neisseria meningitidis)
The Mycobacteria (Mycobacterium tuberculosis)
The Obligate Anaerobes (Clostridium perfringens)
167
170
172
LAB 17: SEROLOGY, PART 1: DIRECT SEROLOGIC

TESTING
181
Introduction to Serological Testing

Using Antigen-Antibody Reactions in the
Laboratory to Identify Unknown Antigens
such as Microorganisms
Examples of Serologic Tests to Identify
Unknown Antigens
181
184
187
INTRODUCTION
LAB 18: SEROLOGY, PART 2: INDIRECT SEROLOGIC

TESTING
Using Antigen-Antibody Reactions in the Laboratory
to Indirectly Diagnose Disease by Detecting
Antibodies in a Person's Serum
Examples of Indirect Serologic Tests to Detect
Antibodies in the Patient's Serum
LAB 19: USING PHYSICAL AGENTS TO CONTROL

MICROORGANISMS
Introduction to Control of Microorganisms
Temperature
Desiccation
Osmotic Pressure
Radiation
Bacteriological Filtration
195
195
197
209
209
210
211
211
212
214
LAB 20: USING DISINFECTANTS AND ANTISEPTICS

TO CONTROL MICROORGANISMS
Disinfectants and Antiseptics
Evaluation of Disinfectants and Antiseptics
Effectiveness of Hand Washing
221
221
223
223
LAB 21: USING ANTIMICROBIAL CHEMOTHERAPEUTIC

AGENTS TO CONTROL MICROORGANISMS
Antimicrobial Chemotherapeutic Agents
Microbial Resistance to Antimicrobial
Chemotherapeutic Agents
Antibiotic Susceptibility Testing
229
229
234
235
LAB 22: PARASITOLOGY
249
Parasitic Protozoa
Parasitic Helminths
249
253
APPENDIX A: Bacterial Growth on an Agar Surface
271
APPENDIX B: Scientific Notation and Dilutions
275
APPENDIX C: The Acid-Fast Stain
279
APPENDIX D: Bacteriological Examination of Water

(Coliform Counts)
280
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INTRODUCTION
INTRODUCTION
A. Using Performance Objectives
B. Laboratory Rules
C. General Directions
D. Binomial Nomenclature
E. Metric Length
F. Using the Microscope
A. Using Performance Objectives

This manual contains performance objectives for each of the 22 lab exercises covered in BIOL 230. The
objectives tell exactly what you are expected to perform after the completion of each lab exercise.
When verbs such as "define," "state," "discuss," "describe," or "differentiate" are used in the objective, you will
be expected to "perform" that objective by way of short answer, multiple choice, or matching questions on a
pre-announced quiz. When verbs such as "demonstrate" or "perform" are used, you will be expected to
demonstrate a particular technique or procedure to the instructor during the course of the laboratory exercise.
When verbs such as "recognize" or "interpret" are used, you will be expected to give a written interpretation of the
results of an experiment when given these results in either a written form or a practical form.
As a general rule, when the objective falls under the discussion sections of a lab exercise, it will be tested by
means of short answer, multiple choice, or matching questions. When an objective falls under the procedure
section of a lab exercise, it represents a procedure or technique that must be mastered during the course of the
lab period. Finally, when an objective is found under the results section of an exercise, it will most likely be tested
for by a practical question.
B. Laboratory Rules
For the safety and convenience of everyone working in the laboratory, it is important that the following
laboratory rules are observed at all times:
1. Place only those materials needed for the day's laboratory exercise on the bench tops. Purses,
coats, extra books, etc., should be placed in the lab bench storage areas or under the lab benches in
order to avoid damage or contamination.
2. Since some of the microorganisms used in this class are pathogenic or potentially pathogenic
(opportunistic), it is essential to always follow proper aseptic technique in handling and transferring
all organisms. Aseptic technique will be learned in Laboratory 2.
3. No smoking, eating, drinking, or any other hand to mouth activity while in the lab. If you need a
short break, wash or sanitize your hands and leave the room.
4. If you should spill a culture, observe the following procedures:
a. Immediately place the culture tube in the plastic baskets found in the hood in the back
of the room so no one else touches the contaminated tube.
b. Have your partner spray isopropyl alcohol liberally over the spill. Be sure your Bunsen
burner is turned off before you spray any alcohol! After a few minutes, use paper towels to
dry the area.
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INTRODUCTION
c. Both you and your partner wash your hands with disinfectant soap and sanitize your
hands.
d. Notify your instructor of the spill.
5. Report any cuts, burns, or other injuries to your instructor.
6. Using a wax marker, properly label all inoculated culture tubes or Petri plates with the name or the
initials of the microorganism you are growing, your initials or a group symbol, and any other
pertinent information. It is important to know what microorganisms are growing in each tube or on each
plate.
7. Place all inoculated material only on your assigned incubator shelf, the shelf corresponding to
your lab section. Culture tubes should be stored upright in plastic beakers, while Petri plates should
be stacked and incubated upside-down (lid on the bottom.
8. After completing an experiment, dispose of all material properly:
a. Place all culture tubes upright in the plastic baskets found in the disposal hood. Lay them
in the basket carefully so they do not tip over and spill.
b. Place Petri plates in the plastic bag-lined buckets found in the disposal hood.
c. Put all used pipettes, swabs and microscope slides in the biohazard disposal containers
located in the front of the room and under the hood
9. Handle all glassware carefully. Notify your instructor of any broken glassware (culture tubes, flasks,
beakers, etc.) or microscope slides. DO NOT PICK UP BROKEN GLASSWARE WITH YOUR HANDS!
Use the dust pan and brush. All broken glassware must be disposed of in the sharps/biowaste
container in room D-202S.
10. Use caution around the Bunsen burners. In a crowded lab it is easy to lean over a burner and
ignite your hair or clothing.
11. Always clean the oil from of the oil immersion lens of the microscope with a piece of lens paper
at the completion of each microscopy lab.
12. Return all equipment, reagents, and other supplies to their proper places at the end of each lab
period.
13. Disinfect the bench top with isopropyl alcohol before and after each lab period. Be sure your
Bunsen burner is turned off before you spray any alcohol!
14. Always wash and/or sanitize your hands with disinfectant soap before leaving the laboratory.
15. Anyone working with hazardous chemicals should wear safety glasses or goggles.
16. You must wear shoes that cover the tops of your feet to prevent injury from broken glass, spilled
chemicals, and dropped objects. Sandals are not permitted in the lab!
17. Do not run in the laboratory. Avoid horseplay.
18. To avoid contamination and damage, do not use cell phones or other personal media devices in
the laboratory.
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INTRODUCTION
19. Please read the laboratory exercises and follow the laboratory directions carefully.
20. Do not place regular trash such as Kim wipes and paper towels in the biohazard containers.
21. If body fluids are used in a laboratory exercise, each student will work only with his or her own
sample. Remember, used swabs go directly into the biowaste container when you are finished with them.
IN CASE OF EMERGENCY, CONTACT CAMPUS SECURITY AT x4958 and describe the situation and your
location.
Students who engage in any actions that may damage college property, create an unsafe condition, injure
another person, or result in a disruption that interferes with learning may have any, or a combination of
the following sanctions imposed as determined by the instructor:
a. A verbal or written warning;
b. Being directed to leave the class for the remainder of the period;
c. A referral to either the Campus Ombudsman or the Department Chairperson;
d. Suspension from the class or the college.
Please see Code of Conduct in the most recent Student Handbook.
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INTRODUCTION
Biology Department
Safety Procedures Agreement
The instructor has reviewed the Safety Procedures with me and has provided the opportunity
to ask questions during the review. I read and understand the safety rules and policies of
CCBC; I agree to follow the Safety Policies.
I understand that failure to comply with the safety and laboratory guidelines may result in a
reduction of my final grade and/or I may be asked to leave the class.
_______________________________
Printed Name
_______________________________
Class and Section
_______________________________
Signature
_______________________________
Date
INTRODUCTION
C. General Directions
1. Always familiarize yourself in advance with the exercises to be performed.
2. Disinfect the bench tops with isopropyl alcohol before and after each lab.
3. The first part of each lab period will be used to complete and record the results of prior experiments.
When you come into the lab, always pull out and organize any culture tubes or petri plates you
have in the incubator from previous labs. We will always go over these results as a class. You may
wish to purchase a set of colored pencils to aid you in recording your results in the lab manual.
4. The latter part of each lab period will be used to begin new experiments. Preliminary instructions,
demonstrations, and any changes in procedure will be given by your instructor prior to starting each new
lab exercise.
5. After completing an experiment, dispose of all laboratory media and contaminated materials in the
designated areas as described above.
6. Wash your hands with disinfectant soap before leaving the lab.
D. Binomial Nomenclature
Microorganisms are given specific scientific names based on the binomial (two names) system of
nomenclature. The first name is referred to as the genus and the second name is termed the species. The
names usually come from Latin or Greek and describe some characteristic of the organism.
To correctly write the scientific name of a microorganism, the first letter of the genus should be capitalized while
the species name should be in lower case letters. Both the genus and species names are italicized or
underlined. Several examples are given below.
Bacillus subtilus
Bacillus: L. dim. noun Bacillum, a small rod
subtilus: L. adj. subtilus, slender
Escherichia coli
Escherichia: after discoverer, Prof. Escherich
coli: L. gen. noun coli, of the colon
Staphylococcus aureus
Staphylococcus: Gr. noun Staphyle, a bunch of grapes; Gr. noun coccus, berry
aureus: L. adj. aureus, golden
E. Metric Length and Fluid Volume

The study of microorganisms necessitates an understanding of the metric system of length. The basic unit of
length is the meter (m), which is approximately 39.37 inches. The basic unit for fluid volume is the liter (l), which
is approximately 1.06 quarts. The prefix placed in front of the basic unit indicates a certain fraction or multiple of
that unit. The most common prefixes we will be using are:
-2
centi = 10 or 1/100
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INTRODUCTION
-2
centimeter (cm) = 10 m or 1/100 m

-3
milli = 10 or 1/1000
-3
millimeter (mm) = 10 m or 1/1000 m
-3
milliliter (ml) = 10 l or 1/1000 l
-6
micro = 10 or 1/1,000,000
-6
micrometer ( m) = 10 m or 1/1,000,000 m
-6
microliter ( l) = 10 l or 1/1,000,000 l
-9
nano = 10 or 1/1,000,000,000
-9
nanometer (nm) = 10 m or 1/1,000,000,000 m
In microbiology, we deal with extremely small units of metric length (micrometer, nanometer). The main unit of
-6
length is the micrometer ( m) which is 10 (1/1,000,000) of a meter or approximately 1/25,400 of an inch.
The average size of a rod-shaped (cylindrical) bacterium (see Fig. 1) is 0.5-1.0 m wide by 1.0-4.0 m long. An
average coccus-shaped (spherical) bacterium (see Fig. 2) is about 0.5-1.0 m in diameter. A volume of one cubic
inch is sufficient to contain approximately nine trillion average-sized bacteria. It would take over 18,000,000
average-sized cocci lined up edge to edge to span the diameter of a dime!
In several labs we will be using pipettes to measure fluid volume in ml.
Fig. 1:
A Bacillus or Rod-Shaped Bacterium
Fig. 2:
A Coccus-Shaped Bacterium
Escherichia coli, a rod-shaped bacterium.
Staphylococcus aureus, a coccus-shaped bacterium.
F. Using the Microscope (Olympus Model CH-2 Microscope)

1. Moving and transporting the microscope
Grasp the arm of the microscope with one hand and support the base of the microscope with the other.
Handle the microscope gently, it costs over $1500.
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INTRODUCTION
2. Before you plug in the microscope, turn the voltage control dial on the right side of the base of the
microscope to 1 (see Fig. 3). Now plug in the microscope and use the on/off switch in the front of the
microscope on the base to turn it on. Make sure the entire cord is on the bench top and not hanging down
where it could be caught by a leg. Adjust the voltage control dial to 10 (see Fig. 3).
3. Adjusting the eyepieces
These microscopes are binocular, that is, they have 2 ocular lenses (eyepieces; see Fig. 4). To adjust
them, first find the proper distance between your eyes and the eyepieces by closing one eye and slowly
moving your head toward that eyepiece until you see the complete field of view - about 1 inch away. Keep
your head steady and both eyes in the same plane. Now open the other eye and gradually increase the
distance between the eyepieces until it matches the distance between your eyes. At the correct distance
you will see one circular field of view with both eyes.
4. Positioning the slide
Place the slide specimen-side-up on the stage so that the specimen lies over the opening for the light in
the middle of the stage. Secure the slide between - not under- the slide holder arms of the mechanical
stage (see Fig. 3). The slide can now be moved from place to place using the 2 control knobs located
under the stage on the right of the microscope (see Fig. 3).
5. Adjusting the illumination
a. Adjust the voltage by turning the voltage control dial located in the rear, right-hand side of
the microscope base (see Fig. 3).. For oil immersion microscopy (1000X) set the light on 9 or 10.
At lower magnifications less light will be needed.
b. Adjust the amount of light coming through the condenser using the iris diaphragm lever
located under the stage in the front of the microscope (see Fig. 3). Light adjustment using the iris
diaphragm lever is critical to obtaining proper contrast. For oil immersion microscopy (1000X), the
iris diaphragm lever should be set almost all the way open (to your left for maximum light). For
low powers such as 100X the iris diaphragm lever should be set mostly closed (to your right for
minimum light).
c. The condenser height control (the single knob under the stage on the left-hand side of the
microscope; see Fig. 4) should be set so the condenser is all the way up.
6. Obtaining different magnifications
The final magnification is a product of the 2 lenses being used. The eyepiece or ocular lens magnifies
10X. The objective lenses (see Fig. 3) are mounted on a turret near the stage. The small yellow-striped
lens magnifies 10X; the blue-striped lens magnifies 40X, and the white-striped oil immersion lens
magnifies 100X. Final magnifications are as follows:
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INTRODUCTION
ocular lens
X
objective lens =
magnification
10X
X
=
10X (yellow)
100X
10X
X
=
40 (blue)
400X
10X
X
=
100X (white)
1000X
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total
INTRODUCTION
Fig. 3: An Olympus CH-2 Microscope
Iris diaphragm lever: moving the lever to the left increases the light; moving the lever to the right
decreases the light.
Stage control "A": moves the mechanical stage holding the slide forward and backward.
Stage control "B": moves the mechanical stage holding the slide left and right.
Coarse focus: turning the knob away from you raises the stage; turning the knob towards you
lowers the stage.
Fine focus: turning the knob away from you raises the stage; turning the knob towards you
lowers the stage.
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INTRODUCTION
7. Focusing from lower power to higher power

a. Rotate the yellow-striped 10X objective until it locks into place (total magnification of 100X).
b. Turn the coarse focus control (larger knob; see Fig. 3) all the way away from you until it
stops.
c. Look through the eyepieces and turn the coarse focus control (larger knob) towards you
slowly until the specimen comes into focus.
d. Get the specimen into sharp focus using the fine focus control (smaller knob; see Fig. 3) and
adjust the light for optimum contrast using the iris diaphragm lever.
e. If higher magnification is desired, simply rotate the blue-striped 40X objective into place (total
magnification of 400X) and the specimen should still be in focus. (Minor adjustments in fine focus
and light contrast may be needed.)
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INTRODUCTION
f. For maximum magnification (1000X or oil immersion), rotate the blue-striped 40X objective
slightly out of position and place a drop of immersion oil on the slide. Now rotate the
white-striped 100X oil immersion objective into place. Again, the specimen should remain in
focus, although minor adjustments in fine focus and light contrast may be needed.
Directions for focusing directly with oil immersion (1000X) without first focusing using lower powers will be
given in Laboratory 1.
8. Cleaning the microscope
Clean the exterior lenses of the eyepiece and objective before and after each lab using lens paper
only. (Paper towel or kim-wipes may scratch the lens.) Remove any immersion oil from the oil
immersion lens before putting the microscope away.
9. Reason for using immersion oil
Normally, when light waves travel from one medium into another, they bend. Therefore, as the light
travels from the glass slide to the air, the light waves bend and are scattered similar to the "bent pencil"
effect when a pencil is placed in a glass of water. The microscope magnifies this distortion effect. Also, if
high magnification is to be used, more light is needed.
Immersion oil has the same refractive index as glass and, therefore, provides an optically
homogeneous path between the slide and the lens of the objective. Light waves thus travel from the glass
slide, into glass-like oil, into the glass lens without being scattered or distorting the image (Fig. 5). In other
words, the immersion oil "traps" the light and prevents the distortion effect that is seen as a result
of the bending of the light waves.
Fig. 5: The Oil Immersion Lens
The immersion oil has the same refractive index

as the glass lens and the glass slide. Because
the light waves follow a homogeneous path, there
is no distortion.
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INTRODUCTION
PERFORMANCE OBJECTIVES
INTRODUCTION
After completing this introduction, the student will be able to perform the following objectives:
A. USING PERFORMANCE OBJECTIVES

1. Answer all performance objectives as soon as possible after completing each laboratory exercise.
B. LABORATORY RULES
1. Follow all laboratory rules stated in the Introduction.
C. GENERAL DIRECTIONS
1. Follow all general directions stated in the Introduction.
D. BINOMIAL NOMENCLATURE
1. Define genus and species and state how to correctly write the scientific name of a microorganism.
2. Correctly write the scientific names of microorganisms.
E. METRIC LENGTH
1. Define and give the commonly used abbreviations for the following units of metric length and fluid
volume: centimeter, millimeter, micrometer, nanometer, milliliter, and microliter.
2. State the length and width of an average rod-shaped bacterium and the diameter of an average
coccus-shaped bacterium in micrometers.
F. USING THE MICROSCOPE

1. Correctly clean the eyepiece and the objective lenses before and after each lab.
2. Define ocular lens and objective lens.
3. Place a slide in the slide holder of a mechanical stage correctly.
4. Focus on a specimen using 10X, 40X, and 100X objectives.
5. Adjust the light using the iris diaphragm lever for optimum contrast after focusing.
6. State the reason for using immersion oil at 1000X.
7. Calculate the total magnification of a lens system when using a 10X, 40X, or 100X objective in
conjunction with a 10X eyepiece.
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LABORATORY 1:
INTRODUCTION TO THE MICROSCOPE AND COMPARISON OF SIZES AND SHAPES OF
MICROORGANISMS
LABORATORY 1
INTRODUCTION TO THE MICROSCOPE AND
COMPARISON OF SIZES AND SHAPES OF
MICROORGANISMS
A. Bacterial Shapes and Arrangements
B. Yeasts
C. Measurement of Microorganisms
D. Focusing Using Oil Immersion Microscopy
DISCUSSION
In this lab, you will become familiar with the use of the microscope (particularly oil immersion microscopy) and will
compare the relative size and shape of various microorganisms.
A. BACTERIAL SHAPES AND ARRANGEMENTS

Bacteria are unicellular prokaryotic microorganisms that divide by binary fission, a process by which one
bacterium splits into two. For a review of prokaryotic versus eukaryotic cellular characteristics, see Unit 1, section
IB in your Lecture Guide.
There are three common shapes of bacteria: the coccus, the bacillus, and the spiral.
1. Coccus
A coccus-shaped bacterium is usually spherical, although some appear oval, elongated, or flattened on
one side. Most cocci are approximately 0.5 1.0 micrometer ( m) in diameter and may be seen, based
on their planes of division and tendency to remain attached after replication, in one of the following
arrangements (see Fig. 1A):
a. Division in one plane produces either a diplococcus arrangement (cocci in pairs) or a
streptococcus arrangement (cocci in chains), as shown in Figs. 1A, 1E, and 1C.
b. Division in two planes produces a tetrad arrangement (cocci forming a square of four), as
shown in Fig. 1A.
c. Division in three planes produces a sarcina arrangement (cocci forming a cube of eight), as
shown in Figs. 1A and 1D.
d. Division in random planes produces a staphylococcus arrangement (cocci in irregular, often
grape-like clusters), as shown in Figs. 1A and 1B.
As you observe these different cocci, keep in mind that the procedures used in slide preparation may
cause some arrangements to break apart or clump together. The correct form, however, should
predominate. Also remember that each coccus in an arrangement represents a complete, individual, onecelled organism.
LABORATORY 1:
MICROORGANISMS
Fig. 1:
Arrangement of Cocci
A= Arrangement of cocci
B= Staphylococcus arrangement
C= Streptococcus arrangement
D= Sarcina arrangement
E= Diplococcus arrangement
2. Bacillus (rod)
A bacillus or rod is a hotdog-shaped bacterium having one of the following arrangements (see Fig. 2A):
a. Bacillus: a single bacillus (see Fig. 2B).
b. Streptobacillus: bacilli in chains (see Fig. 2C).
c. Coccobacillus: oval and similar to a coccus.
A single bacillus is typically 0.5-1.0 m wide and from 1-4 m long. Small bacilli or bacilli that have just
divided by binary fission may at first glance be confused for cocci so they must be observed carefully.
You will, however, be able to see bacilli that have not divided and are definitely rod-shaped as well as
bacilli in the process of dividing.
LABORATORY 1:
MICROORGANISMS
Fig. 2:
Arrangements of Bacilli
A= Arrangements of bacilli
B= Single bacillus
C= Streptobacillus
3. Spiral
Spiral-shaped bacteria occur in one of three forms (see Fig. 3A):
a. Vibrio: an incomplete spiral or comma-shaped (see Fig. 3D).
b. Spirillum: a thick, rigid spiral (see Fig. 3B).
c. Spirochete: a thin, flexible spiral (see Fig. 3C).
While some spirochetes are over 100 m in length, the spirals you will observe today range from 5 m to
40 m long.
B. YEASTS
Yeasts, such as the common baker's yeast Saccharomyces cerevisiae, are unicellular fungi. They usually
appear spherical and have a diameter of 3 - 5 m. Yeasts commonly reproduce asexually by a process called
budding (see Fig. 4). Unlike bacteria, which are prokaryotic, yeasts are eukaryotic. For a review of prokaryotic
versus eukaryotic cellular characteristics, see Unit 1, section IB in your Lecture Guide.
C. MEASUREMENT OF MICROORGANISMS
The approximate size of a microorganism can be determined using an ocular micrometer, an eyepiece that
contains a scale that will appear superimposed upon the focused specimen.
The ocular micrometers provided are calibrated so that when using 1000X oil immersion
microscopy, the distance between any two lines on the scale represents a length of approximately
one micrometer (see Fig. 5). Remember this does not hold true when using other magnifications.
LABORATORY 1:
MICROORGANISMS
Fig. 3:
Spiral Forms
A= Spiral forms
B= Spirillum
C= Spirochete (arrows) mixed with red blood cells
D= Vibrio
Fig. 4:
A Budding Yeast
Note budding (arrows).
LABORATORY 1:
MICROORGANISMS
Fig. 5:
Ocular Micrometer
When using oil immersion microscopy, the distance between any two
lines is one micrometer. The streptococcus seen here is five
micrometers long.
D. FOCUSING WITH OIL IMMERSION - Olympus CH-2 Microscope (see Fig. 7)

1. Before you plug in the microscope, turn the voltage control dial on the right-hand side of the base of
the microscope to 1 (see Fig. 6). Now plug in the microscope and turn it on (see Fig. 7).
2. Place the slide in the slide holder (see Fig. 6), center the slide using the two mechanical stage control
knobs under the stage on the right-hand side of the microscope, and place a rounded drop of immersion
oil on the area to be observed.
3. Rotate the white-striped 100X oil immersion objective until it is locked into place. This will give a
total magnification of 1000X.
4. Turn the voltage control dial on the right-hand side of the base of the microscope to 9 or 10 (see Fig.
6). Make sure the iris diaphragm lever in front under the stage (see Fig. 6) is almost wide open (toward
the left-hand side of the stage), and the knob under the stage on the left-hand side of the stage controlling
the height of the condenser is turned so the condenser is all the way up (see Fig. 7).
5. Watching the slide and objective lens carefully from the front of the microscope, lower the oil immersion
objective into the oil by raising the stage until the lens just touches the slide. Do this by turning the
coarse focus (larger knob; see Fig. 6) away from you until the spring-loaded objective lens just begins
to spring upward.
6. While looking through the eyepieces, turn the fine focus (smaller knob; see Fig. 6) towards you at a
slow steady speed until the specimen comes into focus. (If the specimen does not come into focus
within a few complete turns of the fine focus control and the lens is starting to come out of the oil, you
missed the specimen when it went through focus. Simply reverse direction and start turning the fine focus
away from you.)
7. Using the iris diaphragm lever, adjust the light to obtain optimum contrast (see Fig. 6).
LABORATORY 1:
MICROORGANISMS
8. When finished, wipe the oil off of the oil immersion objective with lens paper, turn the voltage
control dial back to 1, turn off the microscope, unplug the power cord, and wrap the cord around the
base of the microscope.
An alternate focusing technique is to first focus on the slide with the yellow-striped 10X objective using only the
coarse focus control and then without moving the stage, add immersion oil, rotate the white-striped 100X oil
immersion objective into place, and adjust the fine focus and the light as needed. This procedure is discussed in
the Introduction portion of the lab manual on p. xii.
iris diaphragm lever: moving the lever to the left increases the light; moving the lever to the right
decreases the light.
stage control "A": moves the mechanical stage holding the slide forward and backward.
stage control "B": moves the mechanical stage holding the slide left and right.
coarse focus: turning the knob away from you raises the stage; turning the knob towards you
lowers the stage.
fine focus: turning the knob away from you raises the stage; turning the knob towards you lowers
the stage.
LABORATORY 1:
MICROORGANISMS
Fig. 7: Olympus CH-2 Microscope
SPECIMENS
Prepared slides of the following bacteria:
Escherichia coli
Borrelia recurrentis or Borrelia burgdorferi
Spirillum species
On-line demonstration slides of the following bacteria:
Micrococcus luteus
Neisseria gonorrhoeae
Streptococcus pyogenes
Bacillus megaterium
Broth culture of Saccharomyces cerevisiae
Human hair
LABORATORY 1:
MICROORGANISMS
PROCEDURE
1. Using oil immersion microscopy (1000X), observe and measure the bacteria listed below.
TIPS FOR MICROSCOPIC OBSERVATIONS
Remember that in the process of making the slide, some of the coccal arrangements will clump together and
others will break apart. Move the slide around until you see an area representing the true arrangement of each
organism. Also remember that small bacilli (such as Escherichia coli) that have just divided by binary fission will
look similar to cocci. Look carefully for bacilli that are not dividing and are definitely rod-shaped as well as bacilli in
the process of dividing to confirm the true shape. Also, bacilli do not divide so as to form clusters. Any such
clusters you see are artifacts from preparing the slide. Finally, you will have to look carefully to see the
spirochetes as they are the thinnest of the bacteria. When seen microscopically, spirochetes resemble extremely
thin, wavy pencil lines.
a. Staphylococcus aureus: Staphylococcus species, as the genus name implies, have a staphylococcus
arrangement (cocci in irregular, often grape-like clusters). Measure the diameter of a single coccus.
b. Escherichia coli: Escherichia coli is a small bacillus. Measure the length and width of a typical rod.
c. Borrelia species: Borrelia species are spirochetes (thin, flexible spirals). You will observe either Borrelia
recurrentis or Borrelia burgdorferi.
Borrelia recurrentis: On this slide you are examining blood infected with Borrelia recurrentis, the
bacterium that causes relapsing fever. Measure the length and width of a typical spirochete and the
diameter of a red blood cell.
or
Borrelia burgdorferi: On this slide you are examining a direct stain of Borrelia burgdorferi, the bacterium
that causes Lyme disease. Measure the length and width of a typical spirochete.
d. Spirillum species: Spirillum species appear as thick, rigid spirals. Measure the length and width of a
typical spirillum.
When finished, remove the oil from the prepared slides using paper towel and return them to their proper tray.
2. Observe the on-line demonstration slides of the following bacteria:
a. Micrococcus luteus: Micrococcus luteus can appear in tetrads, cubes of 8, or in irregular clusters. This
strain usually exhibits a tetrad or a sarcina arrangement. Note the shape and arrangement.
b. Neisseria gonorrhoeae: Neisseria species usually have a diplococcus arrangement. Note the shape
and arrangement.
c. Streptococcus pyogenes: Streptococcus species, as the genus name implies, usually have a
streptococcus arrangement (cocci in chains). Note the shape and arrangement.
d. Bacillus megaterium: Bacillus megaterium appears as large bacilli in chains (a streptobacillus). Note
the shape and arrangement.
3. Prepare a wet mount of baker's yeast (Saccharomyces cerevisiae.
a. Using a pipette, put a small drop of the yeast culture on a microscope slide and place a cover slip over
the drop.
LABORATORY 1:
MICROORGANISMS
b. Using your iris diaphragm lever, reduce the light for improved contrast by moving the lever almost all
the way to the right.
c. Observe using oil immersion microscopy. Measure the diameter of a typical yeast cell.
d. When finished, wash the slide and use it again for step 4. Discard the coverslip in the biowaste
disposal containers at the front of the room and under the hood.
4. Prepare a wet mount of your hair.
a. Remove a small piece of a hair from your head and place it in a small drop of water on a slide.
b. Place a cover slip over the drop and observe using oil immersion microscopy.
c.
Measure the diameter of your hair and compare this with the size of each of the bacteria and the
yeast observed in steps 1-3.
d. Discard the slide and coverslip in the biowaste disposal containers at the front of the room and under
the hood.
5. At the completion of the lab, remove the oil from the oil immersion objective using lens paper and put your
microscope away.
LABORATORY 1:
MICROORGANISMS
RESULTS
1. Make drawings of several of the bacteria from each of the four prepared slides and indicate their approximate
size in micrometers.
Escherichia coli
Shape =
Shape =
Arrangement =
Length =
Width =
Diameter =
Borrelia recurrentis or
Borrelia burgdorferi
Spirillum species
Shape =
Shape =
Form =
Form =
Length =
Length =
Width =
Width =
Diameter of RBC =
10
LABORATORY 1:
MICROORGANISMS
2. Make drawings of several of the bacteria from each of the four demonstration slides and indicate their
approximate size in micrometers.
Micrococcus luteus
Shape =
Shape =
Arrangement =
Arrangement =
Streptococcus pyogenes
Bacillus megaterium
Shape =
Shape =
Arrangement =
Arrangement =
11
LABORATORY 1:
MICROORGANISMS
3. Make a drawing of several yeast cells and indicate their size in micrometers.
Saccharomyces cerevisiae
Diameter =
4. Make a drawing indicating the size of the bacteria and yeast observed above relative to the diameter of your
hair.
Hair
Diameter =
12
LABORATORY 1:
MICROORGANISMS
LABORATORY 1
After completing this lab, the student will be able to perform the following objectives:
DISCUSSION
1. State three basic shapes of bacteria.
2. State and describe five different arrangements of cocci.
3. State and describe three different arrangements of bacilli.
4. State and describe three different spiral forms.
5. Describe the appearance of a typical yeast cell.
RESULTS
1. When given an oil immersion microscope, a prepared slide of a microorganism, and an ocular
micrometer, determine the size of that organism in micrometers.
2. Using a microscope, identify different bacterial shapes and arrangements.
3. Differentiate a yeast cell from a coccus-shaped bacterium by its size.
4. Compare the size of the microorganisms observed in lab with the diameter of a hair when using oil
immersion microscopy.
13
LABORATORY 1:
MICROORGANISMS
14
LABORATORY 2:
ASEPTIC TECHNIQUE
LABORATORY 2
ASEPTIC TECHNIQUE AND TRANSFER OF
MICROORGANISMS
A. Aseptic Technique
B. Forms of Culture Media
C. Oxygen Requirements for Microbial Growth
D. Temperature Requirements
E. Colony Morphology and Pigmentation
DISCUSSION
In natural environments, microorganisms usually exist as mixed populations. However, if we are to study,
characterize, and identify microorganisms, we must have the organisms in the form of a pure culture. A pure
culture is one in which all organisms are descendants of the same organism. Techniques for obtaining pure
cultures from a mixed population will be described in Lab 3.
In working with microorganisms we must also have a sterile nutrient-containing medium in which to grow the
organisms. Anything in or on which we grow a microorganism is termed a medium. A sterile medium is one that
is free of all life forms. It is usually sterilized by heating it to a temperature at which all contaminating
microorganisms are destroyed.
Finally, in working with microorganisms, we must have a method of transferring growing organisms (called the
inoculum) from a pure culture to a sterile medium without introducing any unwanted outside contaminants. This
method of preventing unwanted microorganisms from gaining access is termed aseptic technique.
A. ASEPTIC TECHNIQUE (Figs. 1 & 2)

The procedure for aseptically transferring microorganisms is as follows:
1. Sterilize the inoculating loop (Fig. 1A).
The inoculating loop is sterilized by passing it at an angle through the flame of a gas burner until
the entire length of the wire becomes orange from the heat. In this way all contaminants on the wire
are incinerated. Never lay the loop down once it is sterilized or it may again become contaminated.
Allow the loop to cool a few seconds to avoid killing the inoculum.
2. Remove the inoculum.

a. Removing inoculum from a broth culture (organisms growing in a liquid medium):
1) Hold the culture tube in one hand and tap the bottom of the tube to resuspend the
organisms.
2) In your other hand, hold the sterilized inoculating loop as if it were a pencil.
15
LABORATORY 2:
ASEPTIC TECHNIQUE
3) Remove the cap of the pure culture tube with the little finger of your loop hand. Never
lay the cap down or it may become contaminated (FIG. 1B).
4) Very briefly pass the lip of the culture tube through the flame. This creates a
convection current which forces air out of the tube and preventing airborne contaminants
from entering the tube. The heat of the gas burner also causes the air around your work
area to rise, and this also reduces the chance of airborne microorganisms contaminating
your cultures. (Fig. 1C).
5) Keeping the culture tube at an angle, insert the inoculating loop and remove a loopful
of inoculum (Fig. 1D).
6) Again pass the lip of the culture tube through the flame (Fig. 1E).
7) Replace the cap (Fig. 1F).
b. Removing inoculum from a plate culture (organisms growing on an agar surface in a petri
plate):
1)Sterilizing the inoculating loop in the flame of a gas burner (Fig. 3A).
2) Lift the lid of the petri plate slightly and stab the loop into the agar away from the
growth to cool the loop.
3) Scrape off a small amount of the organisms and close the lid (Fig. 3B).
3. Transfer the Inoculum to the Sterile Medium.
a. Transferring the inoculum into a broth tube:
1) Pick up the sterile broth tube and remove the cap with the little finger of your loop
hand. Do not set the cap down (Fig. 2A).
2) Briefly pass the lip of the broth tube through the flame (Fig. 2B).
3) Place the loopful of inoculum into the broth, and withdraw the loop (Fig. 2C). Do not
lay the loop down!
4) Again pass the lip of the culture tube through the flame (Fig. 2D).
5) Replace the cap (Fig. 2E).
6) Resterilize the loop by placing it in the flame until it is orange (Fig. 2F). Now you may
lay the loop down until it is needed again.
This procedure is summarized in Figures 1A-1F and 2A-2F.
16
LABORATORY 2:
ASEPTIC TECHNIQUE
b. Transferring the inoculum onto a petri plate:

1). If the agar surface of the plate is visibly wet, use a sterile swab to gently remove the
water.
2) Lift the edge of the lid just enough to insert the loop.
3) Streak the loop across the surface of the agar medium using the either the pattern
shown in Fig. 4 or the pattern shown in Fig. 5. These streaking patterns allow you to
obtain single isolated bacterial colonies originating from a single bacterium or
arrangement of bacteria (see Fig. 6).
In order to avoid digging into the agar as you streak the loop over the top of the agar
you must keep the loop parallel to the agar surface. Always start streaking at the
"12:00 position" of the plate (see Fig. 3C) and streak side-to-side as you pull the loop
toward you. As you follow either Fig. 4 or Fig. 5, each time you flame and cool the loop
between sectors, rotate the plate counterclockwise so you are always working in the
"12:00 position" of the plate. This keeps the inoculating loop parallel with the agar
surface and helps prevent the loop from digging into the agar.
4) Remove the loop and close the lid.
5) Resterilize the inoculating loop.
In the future, every procedure in the lab will be done using similar aseptic technique.
B. FORMS OF CULTURE MEDIA

1. Broth tubes are tubes containing a liquid medium. A typical nutrient containing broth medium such as
Trypticase Soy broth contains substrates for microbial growth such as pancreatic digest of casein, papaic
digest of soybean meal, sodium chloride, and water. After incubation, growth (development of many cells
from a few cells) may be observed as one or a combination of three forms (Figure 7):
a. Pellicle: A mass of organisms is floating on top of the broth.
b. Turbidity: The organisms appear as a general cloudiness throughout the broth.
c. Sediment: A mass of organisms appears as a deposit at the bottom of the tube.
2. Slant tubes (Figure 8A) are tubes containing a nutrient medium plus a solidifying agent, agar-agar.
The medium has been allowed to solidify at an angle in order to get a flat inoculating surface (Figure 8B).
Growth on agar slants can be described by means of the terms found in Appendix A.
3. Stab tubes (deeps) are tubes of hardened agar medium that are inoculated by "stabbing" the inoculum
into the agar (Figure 9).
4. Agar plates are sterile petri plates that are aseptically filled with a melted sterile agar medium and
allowed to solidify. Plates are much less confining than slants and stabs and are commonly used in the
culturing, separating, and counting of microorganisms. Single colonies of microorganisms on agar plates
can be described using the terms found in Appendix A.
17
LABORATORY 2:
ASEPTIC TECHNIQUE
FIG. 1:
Aseptic Removal of Microorganisms from a Broth Culture
A. Sterilize the loop.
D. Remove the inoculum.
B. Remove the cap of the broth

culture.
C. Pass the lip of the tube through the

flame.
E. Pass the lip of the tube through

the flame.
18
F. Replace the cap.
LABORATORY 2:
ASEPTIC TECHNIQUE
FIG. 2:
Transferring Microorganisms into a Broth Tube
A. Remove the cap of the broth

tube.
D. Pass the lip of the tube through the

flame.
B. Pass the lip of the tube through the

flame.
E. Replace the cap.
19
C. Inoculate the tube.
F. Re-sterilize the loop.
LABORATORY 2:
ASEPTIC TECHNIQUE
Fig. 3:
Aseptic Removal of Microorganisms from a Plate Culture
B. Scrape off a small amount of the

organisms and close the lid.
A. Sterilize the loop.
C. Keep the inoculating loop parallel with the agar and rotate the plate
so you are always streaking the agar in the "12:00" position.
Fig. 4:
Inoculating a Petri Plate - Method 1
Step 1: Streak area 1.

Sterilize the loop.
Step 2: Rotate counterclockwise.

Spread area 1 over area 2. Sterilize
the loop.
20
Step 3: Rotate Counterclockwise.

Spread area 2 over area 3.
Sterilize the loop.
LABORATORY 2:
ASEPTIC TECHNIQUE
Fig. 5:
Streaking for Isolation, Method 2

Sterilize the loop.

Sterilize the loop.

Sterilize the loop

Sterilize the loop.
Step 5:Draw your loop through area

"4" and spread it down the center of
the plate without touching any of the
areas already streaked.
21
LABORATORY 2:
ASEPTIC TECHNIQUE
Fig. 6:
Single Colonies of a Bacterium on an Agar Plate
Fig. 7:
Bacterial Growth in Broth Tubes
Pellicle
Turbidity
22
Sediment
LABORATORY 2:
ASEPTIC TECHNIQUE
Fig. 8A:
Slant Tube
Fig. 8B:
Slant Culture
Uninoculated slant tube (side view)
Bacterial Growth on a Slant tube
Fig. 9:
Bacterial Growth in a Stab Tube
23
LABORATORY 2:
ASEPTIC TECHNIQUE
C. OXYGEN REQUIREMENTS FOR MICROBIAL GROWTH

Microorganisms show a great deal of variation in their requirements for gaseous oxygen. Most can be placed in
one of the following groups:
1. Obligate aerobes are organisms that grow only in the presence of oxygen. They obtain energy from
aerobic respiration.
2. Microaerophiles are organisms that require a low concentration of oxygen for growth. They obtain
energy from aerobic respiration.
3. Obligate anaerobes are organisms that grow only without oxygen and, in fact, are inhibited or killed
by oxygen. They obtain energy from anaerobic respiration or fermentation.
4. Aerotolerant anaerobes, like obligate anaerobes, cannot use oxygen for growth but they tolerate it
fairly well. They obtain energy from fermentation.
5. Facultative anaerobes are organisms that grow with or without oxygen, but generally better with
oxygen. They obtain energy from aerobic respiration, anaerobic respiration, or fermentation. Most
bacteria are facultative aerobes.
D. TEMPERATURE REQUIREMENTS
Microorganisms have a minimum and maximum temperature at which they can grow, as well as an optimum
temperature where they grow best. Microorganisms can be divided into groups on the basis of their preferred
range of temperature:
1. Psychrophiles are cold-loving organisms. Their optimum growth temperature is between -5C and 15C.
They are usually found in the Arctic and Antarctic regions and in streams fed by glaciers.
2. Mesophiles are organisms that grow best at moderate temperatures. Their optimum growth
temperature is between 25C and 45C. Most bacteria are mesophilic and include common soil bacteria
and bacteria that live in and on the body.
3. Thermophiles are heat-loving organisms. Their optimum growth temperature is between 45C and 70C
and are comonly found in hot springs and in compost heaps.
4. Hyperthermophiles are bacteria that grow at very high temperatures. Their optimum growth
temperature is between 70C and 110C. They are usually members of the Archae and are found growing
near hydrothermal vents at great depths in the ocean.
E. COLONY MORPHOLOGY AND PIGMENTATION

A colony is a visible mass of microorganisms growing on an agar surface and usually originating from a single
organism or arrangement of organisms. Different microorganisms will frequently produce colonies that differ in
their morphological appearance (form, elevation, margin, surface, optical characteristics, and pigmentation).
Single colonies can be described using standard terms, as listed in Appendix A.
Probably the most visual characteristic is pigmentation (color). Some microorganisms produce pigment during
growth and are said to be chromogenic. Often, however, formation of pigment depends on environmental factors
such as temperature, nutrients, pH and moisture. For example, Serratia marcescens produces a deep red
pigment at 25 C, but does not produce pigment at 37 C.
24
LABORATORY 2:
ASEPTIC TECHNIQUE
Pigments can be divided into two basic types: water-insoluble and water-soluble. If the pigment is waterinsoluble (Fig. 10A), as in the case of most chromogenic bacteria, it does not diffuse out of the organism. As a
result, the colonies are pigmented but the agar remains the normal color. If the pigment is water-soluble (Fig.
10B) (as in the case of Pseudomonas aeruginosa) it will diffuse out of the organism into the surrounding medium.
Both the colonies and the agar will appear pigmented.
Below is a list of several common chromogenic bacteria:
Staphylococcus aureus - gold; water-insoluble
Micrococcus luteus - yellow; water-insoluble
Micrococcus roseus - pink; water-insoluble
Mycobacterium phlei - orange; water-insoluble
Serratia marcescens - orange/red; water-insoluble
Pseudomonas aeruginosa - green/blue; water-soluble
Fig. 10:
Water Insoluble and Water-Soluble Pigment
in Chromogenic Bacteria
A. Water-insoluble pigment
B. Water-soluble pigment
MEDIA
Trypticase Soy Broth tubes (4), Trypticase Soy Agar slant tubes (4), Trypticase Soy Agar stab tubes (4), and
Trypticase Soy Agar plates (7).
ORGANISMS
Trypticase Soy Broth cultures of Bacillus subtilis, Escherichia coli and Micrococcus luteus, and Trypticase Soy
Agar plate cultures of Mycobacterium phlei.
25
LABORATORY 2:
ASEPTIC TECHNIQUE
PROCEDURE (to be done in pairs)

1. Aseptically inoculate one Trypticase Soy Broth tube, one Trypticase Soy Agar slant tube, one Trypticase Soy
Agar stab tube, and one Trypticase Soy Agar plate with B. subtilis. (See Fig. 11)
Remember to label all tubes with a wax marker. When streaking the agar plates, use either of the patterns shown
in Figure 2A or 2B. This procedure is termed streaking for isolation and has a diluting effect. The friction of the
loop against the agar causes organisms to fall off the loop. Near the end of the streaking pattern, individual
organisms become separated far enough apart on the agar surface to give rise to isolated single colonies after
incubation. (See Fig. 6)
Agar stab tube, and one Trypticase Soy Agar plate with E. coli. (See Fig. 11)
Agar stab tube, and one Trypticase Soy Agar plate with M. luteus. (See Fig. 11)
Agar stab tube, and one Trypticase Soy Agar plate with M. phlei. (See Fig. 11)
5. Incubate all the tubes and plates inoculated with B. subtilis, E. coli, M. luteus, and M. phlei at 37 C. Place the
tubes in a plastic beaker to keep them upright. Incubate the plates upside down (lid on the bottom) to prevent
condensing water from falling down on the growing colonies and causing them to run together.
6. In order to illustrate that microorganisms are all around us and to demonstrate the necessity for proper aseptic
technique, contaminate three Trypticase Soy Agar plates as follows:
a. Remove the lid from the first agar plate and place the exposed agar portion in or out of the building for
the duration of today's lab. Replace the lid, label, and incubate it at room temperature. Do this plate
first.
b. Using a wax marker, divide a second petri plate in half. You and your partner both moisten a sterile
cotton swab in sterile water. Rub your swab over some surface in the building or on yourself. Use this
swab to inoculate your half of the second agar plate. Label the plate and incubate at room temperature.
c. With a wax marker, divide a third petri plate in half. Rub your fingers over the surface of your half of the
third agar plate. Label and incubate at 37 C. Do this plate last.
26
LABORATORY 2:
ASEPTIC TECHNIQUE
Fig. 11:
Procedure for Lab 2
Inoculate 1 broth tube, 1 stab tube, 1 slant tube, and 1 petri plate with each bacterium.
27
LABORATORY 2:
ASEPTIC TECHNIQUE
RESULTS
1. Draw and describe the growth seen in each of the four broth cultures.
B. subtilis
Type(s) of growth:
E. coli
Type(s) of growth:
M. luteus
Type(s) of growth:
M. phlei
Type(s) of growth:
2. Observe the growth in the slant cultures and stab cultures for pigmentation and purity.
3. Using the terms in the Appendix A, compare a single colony of B. subtilis with a single colony of M. luteus. Use
a hand lens or a dissecting microscope to magnify the colony.
Characteristics
B. subtilis
M. luteus
Form of colony
Elevation
Margin (edge)
surface
Optical characteristics
pPgmentation
4. Observe the results of the three "contamination" plates and note the differences in colony appearances.
28
LABORATORY 2:
ASEPTIC TECHNIQUE
5. Observe the demonstration plates of chromogenic bacteria and state the color and water-solubility of each
pigment.
Organism
Color
Solubility
Micrococcus luteus
Micrococcus roseus
Mycobacterium phlei
Serratia marcescens
Pseudomonas aeruginosa
29
LABORATORY 2:
ASEPTIC TECHNIQUE
LABORATORY 2
DISCUSSION
1. Define the following terms: pure culture, sterile medium, inoculum, aseptic technique, and colony.
2. State and define the three types of growth that may be seen in a broth culture.
3. Define the following terms: obligate aerobe, microaerophile, obligate anaerobe, aerotolerant anaerobe,
and facultative anaerobe.
4. Define the following terms: psychrophile, mesophile, thermophile, and hyperthermophile.
5. Define the following terms: chromogenic, water-soluble pigment, and water-insoluble pigment.
PROCEDURE
1. Using an inoculating loop, demonstrate how to aseptically remove some inoculum from either a broth
tube, slant tube, stab tube, or petri plate, and inoculate a sterile broth tube, slant tube, stab tube, or petri
plate without introducing outside contamination.
2. Label all tubes and plates and place them on the proper shelf in the incubator.
3. Dispose of all materials when the experiment is completed, being sure to remove all markings from the
glassware. Place all tubes and plates in the designated areas.
RESULTS
1. Recognize and identify the following types of growth in a broth culture: pellicle, turbidity, sediment, and
any combination of these.
2. State the color and water-solubility of pigment seen on a plate culture of a chromogenic bacterium.
30
LABORATORY 3:
OBTAINING PURE CULTURES FROM A MIXED POPULATION
LABORATORY 3
OBTAINING PURE CULTURES FROM A MIXED
POPULATION
A. Streak Plate Method of Isolation
B. The Pour Plate and Spin Plate Methods of
C. Use of Specialized Media
DISCUSSION
As stated in Lab 2, microorganisms exist in nature as mixed populations. However, to study microorganisms in
the laboratory we must have them in the form of a pure culture, that is, one in which all organisms are
descendants of the same organism.
Two major steps are involved in obtaining pure cultures from a mixed population:
1. First, the mixture must be diluted until the various individual microorganisms become separated far
enough apart on an agar surface that after incubation they form visible colonies isolated from the
colonies of other microorganisms. This plate is called an isolation plate.
2. Then, an isolated colony can be aseptically "picked off" the isolation plate (see Fig. 1) and
transferred to new sterile medium (see Fig. 3). After incubation, all organisms in the new culture will be
descendants of the same organism, that is, a pure culture.
A. STREAK PLATE METHOD OF ISOLATION

The most common way of separating bacterial cells on the agar surface to obtain isolated colonies is the streak
plate method we used in Lab 2 to inoculate a petri plate. It provides a simple and rapid method of diluting the
sample by mechanical means. As the loop is streaked across the agar surface, more and more bacteria are
rubbed off until individual separated organisms are deposited on the agar. After incubation, the area at the
beginning of the streak pattern will show confluent growth, while the area near the end of the pattern should show
discrete colonies (see Fig. 2).
B. THE POUR PLATE AND SPIN PLATE METHODS OF ISOLATION

Another method of separating bacteria is the pour plate method. With the pour plate method, the bacteria are
mixed with melted agar until evenly distributed and separated throughout the liquid. The melted agar is then
poured into an empty plate and allowed to solidify. After incubation, discrete bacterial colonies can then be found
growing both on the agar and in the agar.
The spin plate method involves diluting the bacterial sample in tubes of sterile water, saline, or broth. Small
samples of the diluted bacteria are then pipetted onto the surface of agar plates. A sterile, bent-glass rod is then
used to spread the bacteria evenly over the entire agar surface. In Lab 4 we will use this technique as part of the
plate count method of enumerating bacteria.
31
LABORATORY 3:
Fig. 1:
Picking off an isolated colony from an isolation plate
Fig. 2:
Isolated colonies of two bacteria seen on an
isolation plate
Fig. 3:
Obtaining Pure Cultures from an Isolation Plate
32
LABORATORY 3:
C. USE OF SPECIALIZED MEDIA

To supplement mechanical techniques of isolation such as the streak plate method, many special-purpose
media are available to the microbiologist to aid in the isolation and identification of specific microorganisms.
These special purpose media fall into four groups: selective media, differential media, enrichment media, and
combination selective and differential media.
1. Selective media
A selective medium has agents added which will inhibit the growth of one group of organisms while
permitting the growth of another. For example, Columbia CNA agar has the antibiotics colistin and
nalidixic acid added which inhibit the growth of gram-negative bacteria but not the growth of
gram-positives. It is, therefore, said to be selective for gram-positive organisms, and would be useful in
separating a mixture of gram-positive and gram-negative bacteria.
2. Differential media
A differential medium contains additives that cause an observable color change in the medium
when a particular chemical reaction occurs. They are useful in differentiating bacteria according to
some biochemical characteristic. In other words, they indicate whether or not a certain organism can
carry out a specific biochemical reaction during its normal metabolism. Many such media will be used
in future labs to aid in the identification of microorganisms.
3. Enrichment media
An enrichment medium contains additives that enhance the growth of certain organisms. This is
useful when the organism you wish to culture is present in relatively small numbers compared to the other
organisms growing in the mixture.
4. Combination selective and differential media
A combination selective and differential medium permits the growth of one group of organisms
while inhibiting the growth of another. In addition, it differentiates those organisms that grow based on
whether they can carry out particular chemical reactions. For example, Eosin Methylene Blue (EMB)
agar is selective for gram-negative bacteria. The dyes eosin Y and methylene blue found in the medium
inhibit the growth of gram-positive bacteria but not the growth of gram-negatives. In addition, it is useful in
differentiating the various gram-negative enteric bacilli belonging to the bacterial family
Enterobacteriaceae (see Labs 12 & 13). The appearance of typical members of this bacterial family on
EMB agar is as follows:
Escherichia coli: large, blue-black colonies with a green metallic sheen
Enterobacter and Klebsiella: large, mucoid, pink to purple colonies with no metallic sheen
Salmonella and Shigella and Proteus: large, colorless colonies
Shigella: colorless to pink colonies
The color changes in the colonies are a result of bacterial fermentation of the sugar lactose while
colorless colonies indicate lactose non-fermenters. Fermentation reactions will be discussed in more
detail in Lab 8.
33
LABORATORY 3:
There are literally hundreds of special-purpose media available to the microbiologist. Today we will
combine both a mechanical isolation technique (the streak plate) with selective and selective-differential
media to obtain pure cultures from a mixture of bacteria. In future labs, such as 12 - 16, which deal with
the isolation and identification of pathogenic bacteria, we will use many additional special-purpose media.
MEDIA
One plate of each of the following media: Trypticase Soy agar, Columbia CNA agar, and EMB agar.
ORGANISMS
A broth culture containing a mixture of one of the following gram-positive bacteria and one of the following gramnegative bacteria:
Possible gram-positive bacteria:
Micrococcus luteus. A gram-positive coccus with a tetrad or a sarcina arrangement; produces
circular, convex colonies with a yellow, water-insoluble pigment on Trypticase Soy agar.
Staphylococcus epidermidis. A gram-positive coccus with a staphylococcus arrangement;
produces circular, convex, non-pigmented colonies on Trypticase Soy agar.
Possible gram-negative bacteria:
Escherichia coli. A gram-negative bacillus; produces irregular, raised, non-pigmented colonies on
Trypticase Soy agar.
Enterobacter aerogenes. A gram-negative bacillus; produces irregular raised, non-pigmented,
possibly mucoid colonies on Trypticase Soy agar.
During the next three labs you will attempt to obtain pure cultures of each organism in your mixture and determine
which two bacteria you have. Today you will try to separate the bacteria in the mixture in order to obtain isolated
colonies; next lab you will identify the two bacteria in your mixture and pick off single isolated colonies of each of
the two bacteria in order to get a pure culture of each. The following lab you will prepare microscopy slides of
each of the two pure cultures to determine if they are indeed pure.

1. First attempt to obtain isolated colonies of the two organisms in your mixture by using mechanical methods on
an all-purpose growth medium, Trypticase Soy agar. Streak the mixture on a plate of Trypticase Soy agar using
one of the two streaking patterns illustrated in Lab 2, Fig. 4 or Fig. 5.
2. Streak the same mixture for isolation on a plate of Columbia CNA agar (selective for gram-positive bacteria).
3. Streak the same mixture for isolation on a plate of EMB agar (selective for gram-negative bacteria and
differential for certain members of the bacterial family Enterobacteriaceae).
4. Incubate the three plates at 37 C until the next lab period.
34
LABORATORY 3:
Lab 2, Fig. 4:

Sterilize the loop.

the loop.

Sterilize the loop.
Lab 2, Fig. 5:

Sterilize the loop.

Sterilize the loop.
Continued on next page.
35

Sterilize the loop.
LABORATORY 3:

Sterilize the loop

RESULTS
1. Observe isolated colonies on the plates of Trypticase Soy agar, Columbia CNA agar, and EMB agar. Record
your observations and conclusions.
Trypticase Soy agar
Observations
Conclusions
Columbia CNA agar
Observations
Conclusions
EMB agar
Observations
Conclusions
36
LABORATORY 3:
2. Using any of the three plates, pick off a single isolated colony of each of the two organisms in your
original mixture and aseptically transfer them to separate plates of Trypticase Soy agar (see Fig. 3). When
picking off single colonies, remove the top portion of the colony without touching the agar surface itself to
avoid picking up any inhibited bacteria from the surface of the agar (Fig. 1). Use your regular petri plate-streaking
pattern to inoculate these plates and incubate at 37 C until the next lab period. These will be your pure cultures
for Lab 5 (Direct and Indirect stains).
37
LABORATORY 3:
LABORATORY 3
After completing this lab, the student will be able to complete the following objectives:
DISCUSSION
1. Given a mixture of a gram-positive and a gram-negative bacterium and plates of of Columbia CNA,
EMB, and Trypticase Soy agar, describe the steps you would take to eventually obtain pure cultures of
each organism.
2. Define the following: selective medium, differential medium, enrichment medium, and combination
selective-differential medium.
3. State the usefulness of Columbia CNA agar and EMB agar.
4. Describe how each of the following would appear when grown on EMB agar:
a. Escherichia coli
b. Enterobacter aerogenes
c. Salmonella
PROCEDURE
1. Using the streak plate method of isolation, obtain isolated colonies from a mixture of microorganisms.
2. Pick off isolated colonies of microorganisms growing on a streak plate and aseptically transfer them to
sterile media to obtain pure cultures.
RESULTS
1. When given a plate of Columbia CNA agar or EMB agar showing discrete colonies, correctly interpret
the results.
38
LABORATORY 4:
ENUMERATION OF MICROORGAMISMS
LABORATORY 4
ENUMERATION OF MICROORGANISMS
A. Plate Count
B. Direct Microscopic Method
C. Turbidity
DISCUSSION
As part of daily routine, the laboratory microbiologist often has to determine the number of bacteria in a given
sample as well as having to compare the amount of bacterial growth under various conditions. Enumeration of
microorganisms is especially important in dairy microbiology, food microbiology, and water microbiology.
Since the enumeration of microorganisms involves the use of extremely small dilutions and extremely large
numbers of cells, scientific notation is routinely used in calculations. A review of exponential numbers, scientific
notation, and dilutions is found in Appendix B.
A. THE PLATE COUNT (VIABLE COUNT)

The number of bacteria in a given sample is usually too great to be counted directly. However, if the sample
is serially diluted (see Fig. 7) and then plated out on an agar surface in such a manner that single isolated
bacteria form visible isolated colonies (see Fig. 1), the number of colonies can be used as a measure of
the number of viable (living) cells in that known dilution. However, keep in mind that if the organism normally
forms multiple cell arrangements, such as chains, the colony-forming unit may consist of a chain of bacteria
rather than a single bacterium. In addition, some of the bacteria may be clumped together. Therefore, when
doing the plate count technique, we generally say we are determining the number of Colony-Forming Units
(CFUs) in that known dilution. By extrapolation, this number can in turn be used to calculate the number of
CFUs in the original sample.
Normally, the bacterial sample is diluted by factors of 10 and plated on agar. After incubation, the number of
colonies on a dilution plate showing between 30 and 300 colonies is determined (see Fig. 1). A plate having
30-300 colonies is chosen because this range is considered statistically significant. If there are less than 30
colonies on the plate, small errors in dilution technique or the presence of a few contaminants will have a
drastic effect on the final count. Likewise, if there are more than 300 colonies on the plate, there will be poor
isolation and colonies will have grown together.
Generally, one wants to determine the number of CFUs per milliliter (ml) of sample. To find this, the
number of colonies (on a plate having 30-300 colonies) is multiplied by the number of times the original ml of
bacteria was diluted (the dilution factor of the plate counted). For example, if a plate containing a
1/1,000,000 dilution of the original ml of sample shows 150 colonies, then 150 represents 1/1,000,000 the
number of CFUs present in the original ml. Therefore the number of CFUs per ml in the original sample is
found by multiplying 150 x 1,000,000 as shown in the formula below:
39
LABORATORY 4:
The number of CFUs per ml of sample =
The number of colonies (30-300 plate)
X
The dilution factor of the plate counted
In the case of the example above, 150 x 1,000,000 = 150,000,000 CFUs per ml.
Fig. 1:
A petri plate showing between 30 and 300 colonies
For a more accurate count it is advisable to plate each dilution in duplicate or triplicate and then find an
average count.
B. DIRECT MICROSCOPIC METHOD (TOTAL CELL COUNT)

In the direct microscopic count, a counting chamber consisting of a ruled slide and a coverslip is employed.
It is constructed in such a manner that the coverslip, slide, and ruled lines delimit a known volume. The
number of bacteria in a small known volume is directly counted microscopically and the number of
bacteria in the larger original sample is determined by extrapolation.
The Petroff-Hausser counting chamber (Fig. 2), for example, has small etched squares 1/20 of a millimeter
(mm) by 1/20 of a mm and is 1/50 of a mm deep. The volume of one small square therefore is 1/20,000 of a
cubic mm or 1/20,000,000 of a cubic centimeter (cc). There are 16 small squares in the large double-lined
squares that are actually counted, making the volume of a large double-lined square 1/1,250,000 cc. The
normal procedure is to count the number of bacteria in five large double-lined squares and divide by five
to get the average number of bacteria per large square. This number is then multiplied by 1,250,000,
since the square holds a volume of 1/1,250,000 cc, to find the total number of organisms per cc in the original
sample.
40
LABORATORY 4:
If the bacteria are diluted, such as by mixing the bacteria with dye before being placed in the
counting chamber, then this dilution must also be considered in the final calculations.
The formula used for the direct microscopic count is:
The number of bacteria per cc =
The average number of bacteria per large double-lined square
X
The dilution factor of the large square (1,250,000)
X
The dilution factor of any dilutions made prior to placing.
the sample in the counting chamber
Fig. 2:
Large double-lined square of a Petroff-Hausser counting chamber
C. TURBIDITY
As seen in Lab 2, when you mix the bacteria growing in a liquid medium, the culture appears turbid. This is
because a bacterial culture acts as a colloidal suspension that blocks and reflects light passing through the
culture. Within limits, the light absorbed by the bacterial suspension will be directly proportional to the
concentration of cells in the culture. By measuring the amount of light absorbed by a bacterial suspension,
one can estimate and compare the number of bacteria present.
The instrument used to measure turbidity is a spectrophotometer. It consists of a light source, a filter that
allows only a single wavelength of light to pass through, the sample tube containing the bacterial suspension,
and a photocell that compares the amount of light coming through the tube with the total light entering the
tube.
The ability of the culture to block the light can be expressed as either percent of light transmitted through
the tube or the amount of light absorbed in the tube (see Fig. 4). The percent of light transmitted is
inversely proportional to the bacterial concentration. (The greater the percent transmittance, the lower the
number of bacteria.) The absorbance (or optical density) is directly proportional to the cell concentration.
(The greater the absorbance, the greater the number of bacteria.)
41
LABORATORY 4:
Turbidimetric measurement is often correlated with some other method of cell count, such as the direct
microscopic method or the plate count. In this way, turbidity can be used as an indirect measurement of the
cell count. For example:
1. Several dilutions can be made of a bacterial stock.
2. A Petroff-Hausser counter can then be used to perform a direct microscopic count on each
dilution.
3. Then a spectrophotometer can be used to measure the absorbance of each dilution tube.
4. A standard curve comparing absorbance to the number of bacteria can be made by plotting
absorbance versus the number of bacteria per cc (see Fig. 5)
5. Once the standard curve is completed, any dilution tube of that organism can be placed in a
spectrophotometer and its absorbance read. Once the absorbance is determined, the standard curve
can be used to determine the corresponding number of bacteria per cc (see Fig. 6)
Fig. 4:
Absorbance and % Light Transmitted
Fig. 5:
A Standard Curve Plotting the Number of
Bacteria per cc versus Absorbance
Fig. 6:
Using a Standard Curve to Determine the Number of
Bacteria per cc in a Sample by Measuring the Sample's
Absorbance
42
LABORATORY 4:
MATERIALS
6 tubes each containing 9.0 ml sterile saline, 3 plates of Trypticase Soy agar, 2 sterile 1.0 ml pipettes, pipette
filler, turntable, bent glass rod, dish of alcohol
ORGANISM
Trypticase Soy broth culture of Escherichia coli
PROCEDURE
A. Plate Count (to be done in pairs)
1. Take 6 dilution tubes, each containing 9.0 ml of sterile saline. Aseptically dilute 1.0 ml of a sample of E. coli
as shown in Fig. 7 and described below.
a. Remove a sterile 1.0 ml pipette from the bag. Do not touch the portion of the pipette that will
go into the tubes and do not lay the pipette down. From the tip of the pipette to the "0" line is 1
ml; each numbered division (0.1, 0.2, etc.) represents 0.1 ml 1.0 ml (see Fig. 8).
b. Insert the cotton-tipped end of the pipette into a blue 2 ml pipette filler.
c. Flame the sample flask, insert the pipette to the bottom of the flask, and withdraw 1.0 ml of the
sample (up to the "0" line; see Fig. 8) by turning the filler knob towards you. Draw the sample up
slowly so that it isn't accidentally drawn into the filler itself (see Fig. 9). Re-flame and cap the
sample.
d. Flame the first dilution tube and dispense the 1.0 ml of sample into the tube by turning the filler
knob away from you. Draw the liquid up and down in the pipette several times to rinse the pipette
and help mix. Re-flame and cap the tube.
e. Mix the tube thoroughly by either holding the tube in one hand while vigorously tapping the
bottom with the other hand, or by using a vortex mixer. This is to assure an even distribution of the
bacteria throughout the liquid.
f. Using the same procedure, aseptically withdraw 1.0 ml of the sample (see Fig. 8). from the first
dilution tube and dispense into the second dilution tube. Continue doing this from tube to tube as
shown in Fig. 7 until the dilution is completed. Discard the pipette in the biowaste disposal containers
at the front of the room and under the hood.
Your instructor will demonstrate these pipetting and mixing techniques.
43
LABORATORY 4:
Fig. 7:
Plate count dilution procedure
2. Using a new 1.0 ml pipette, aseptically transfer 0.1 ml (see Fig. 8) from each of the last three dilution
tubes onto the surface of the corresponding plates of trypticase soy agar as shown in Figure 7 and Figure
10. Note that since only 0.1 ml of the bacterial dilution (rather than the desired 1.0 ml) is placed on the plate,
the bacterial dilution on the plate is 1/10 the dilution of the tube from which it came.
3. Using a turntable and sterile bent glass rod, immediately spread the solution over the surface of the
plates as follows:
a. Place the plate containing the 0.1 ml of dilution on a turntable.
b. Sterilize the glass rod by dipping the bent portion in a dish of alcohol and igniting the alcohol with
the flame from your burner. Let the flame burn out.
c. Place the bent portion of the glass rod on the agar surface and spin the turntable for about 30
seconds to distribute the 0.1 ml of dilution evenly over the entire agar surface (see Figure 12).
d. Replace the lid and re-sterilize the glass rod with alcohol and flaming.
e. Repeat for each plate.
f. Discard the pipette in the biowaste disposal containers at the front of the room and under the hood.
4. Incubate the 3 agar plates upside down at 37 C until the next lab period. Place the used dilution tubes in
the disposal baskets in the hood.
44
LABORATORY 4:
Fig. 8:
A 1.0 ml pipette
Fig. 9:
Removing bacteria from a tube with a pipette.
45
Fig. 10:
Using a pipette to transfer bacteria to an agar plate.
LABORATORY 4:
Fig. 11:
Using a turntable and bent glass rod to spread bacteria
evenly over the surface of an agar plate.
Fig. 12:
Using a vortex mixer to distribute bacteria evenly
throughout the tube.
B. Direct Microscopic Method (demonstration)

1. Pipette 1.0 ml (see Fig. 8) of the sample of E. coli into a tube containing 1.0 ml of the dye
methylene blue. This gives a 1/2 dilution of the sample.
2. Using a Pasteur pipette, fill the chamber of a Petroff-Hausser counting chamber with this 1/2
dilution.
3. Place a coverslip over the chamber and focus on the squares using 400X (40X objective).
4. Count the number of bacteria in 5 large double-lined squares. For those organisms on the lines,
count those on the left and upper lines but not those on the right and lower lines. Divide this total
number by 5 to find the average number of bacteria per large square.
5. Calculate the number of bacteria per cc as follows:
The number of bacteria per cc =

The average number of bacteria per large square
X
The dilution factor of the large square (1, 250,000)
X
The dilution factor of any dilutions made prior to placing
the sample in the counting chamber (2 in this case)
46
LABORATORY 4:
C. Turbidity
Your instructor will set up a spectrophotometer demonstration illustrating that as the number of bacteria in a
broth culture increases, the absorbance increases (or the percent light transmitted decreases).
RESULTS
A. Plate Count
1. Choose a plate that appears to have between 30 and 300 colonies. Count the exact number of
colonies on that plate using the colony counter (as demonstrated by your instructor).
2. Calculate the number of CFUs per ml of original sample as follows:
The number of CFUs per ml of sample =
The number of colonies (30-300 plate)
X
The dilution factor of the plate counted
____________ = The number of colonies

____________ = The dilution factor of plate counted
____________ = The number of CFUs per ml
3. Record your results on the blackboard.
B. Direct Microscopic Method

Observe the demonstration of the Petroff - Hausser counting chamber.
C. Turbidity
Observe your instructor's demonstration of the spectrophotometer.
47
LABORATORY 4:
LABORATORY 4
DISCUSSION
1. State the formula for determining the number of CFUs per ml of sample when using the plate count
technique.
2. When given a diagram of a plate count dilution and the number of colonies on the resulting plates, choose
the correct plate for counting, determine the dilution factor of that plate, and calculate the number of CFUs
per ml in the original sample. (See this objective in the on-line Lab Manual for practice problems.)
3. State the principle behind the direct microscopic method of enumeration.
4. State the formula for determining the number of bacteria per cc of sample when using the direct
microscopic method of enumeration.
5. When given the total number of bacteria counted in a Petroff-Hausser chamber, the total number of large
squares counted, and the dilution of the bacteria placed in the chamber, calculate the total number of bacteria
per cc in the original sample. (See this objective in the on-line Lab Manual for practice problems.)
6. State the function of a spectrophotometer.
7. State the relationship between absorbance (optical density) and the number of bacteria in a broth sample.
8. State the relationship between percent light transmitted and the number of bacteria in a broth sample.
PROCEDURE
1. Perform a serial dilution of a bacterial sample according to instructions in the lab manual and plate out
samples of each dilution using the spin-plate technique.
RESULTS
1. Using a colony counter, count the number of colonies on a plate showing between 30 and 300
colonies and, by knowing the dilution of this plate, calculate the number of CFUs per ml in the original
sample.
48
LABORATORY 5:
DIRECT STAINING AND INDIRECT STAINING
LABORATORY 5
DIRECT STAINING and INDIRECT STAINING
A. Introduction to Staining
B. Direct Staining Using a Basic Dye
C. Indirect Staining Using an Acidic Dye
A. INTRODUCTION TO STAINING
DISCUSSION
In our laboratory, bacterial morphology (form and structure) may be examined in two ways:
- observing living unstained organisms (wet mount), or
- observing killed stained organisms.
Since bacteria are almost colorless and therefore show little contrast with the broth in which they are suspended,
they are difficult to observe when unstained. Staining microorganisms enables one to:
- see greater contrast between the organism and the background,
- differentiate various morphological types (by shape, arrangement, gram reaction, etc.),
- observe certain structures (flagella, capsules, endospores, etc.).
Before staining bacteria, you must first understand how to "fix" the organisms to the glass slide. If the
preparation is not fixed, the organisms will be washed off the slide during staining. A simple method is that of air
drying and heat fixing. The organisms are heat fixed by passing an air-dried smear of the organisms through the
flame of a gas burner. The heat coagulates the organisms' proteins causing the bacteria to stick to the slide.
The procedure for heat fixation is as follows:

1. If the culture is taken from an agar medium:
a. Using the dropper bottle of distilled water found in your staining rack, place 1/2 of typical sized
drop of water on a clean slide by touching the dropper to the slide.
b. Aseptically remove a small amount of the culture from the agar surface and just touch it
several times to the drop of water until it just turns cloudy.
c. Burn the remaining bacteria off of the loop. (If too much culture is added to the water, you will
not see stained individual bacteria.)
d. Using the loop, spread the suspension over the entire slide to form a thin film.
e. Allow this thin suspension to completely air dry.
f. Pass about one inch of the slide (film-side up) through the flame of the bunsen burner
several times until it just becomes uncomfortable to hold in order to heat-fix the bacteria to
49
LABORATORY 5:
the slide. Caution: Too much heat might distort the organism and, in the case of the gram stain,
may cause gram-positive organisms to stain gram-negatively.
2. If the organism is taken from a broth culture:
a. Aseptically place 2 or 3 loops of the culture on a clean slide. Do not use water.
b. Using the loop, spread the suspension over the entire slide to form a thin film.
c. Allow this thin suspension to completely air dry.
d. Pass about one inch of the slide (film-side up) through the flame of the bunsen burner
the slide.
In order to understand how staining works, it will be helpful to know a little about the physical and chemical nature
of stains. Stains are generally salts in which one of the ions is colored. (A salt is a compound composed of a
positively charged ion and a negatively charged ion.) For example, the dye methylene blue is actually the salt
methylene blue chloride that will dissociate in water into a positively charged methylene blue ion that is blue in color
and a negatively charged chloride ion that is colorless.
Dyes or stains may be divided into two groups: basic and acidic. If the color portion of the dye resides in the
positive ion, as in the above case, it is called a basic dye (examples: methylene blue, crystal violet, safranin). If the
color portion is in the negatively charged ion, it is called an acidic dye (examples: nigrosin, congo red).
Because of its chemical nature, the cytoplasm of all bacterial cells has a slight negative charge when growing
in a medium of near neutral pH. Therefore, when using a basic dye, the positively charged color portion of the stain
combines with the negatively charged bacterial cytoplasm (opposite charges attract) and the organism becomes
directly stained (see Fig. 1 and Fig. 2). An acidic dye, due to its chemical nature, reacts differently. Since the color
portion of the dye is on the negative ion, it will not readily combine with the negatively charged bacterial cytoplasm
(like charges repel). Instead, it forms a deposit around the organism, leaving the organism itself colorless (see Fig.
1 and Fig. 3). Since the organism is seen indirectly, this type of staining is called indirect or negative, and is used to
get a more accurate view of bacterial size, shapes, and arrangements.
Fig. 1:
Direct Staining and Indirect Staining
50
LABORATORY 5:
Fig. 2:
Direct stain of Escherichia coli
Fig. 3:
Indirect stain of Micrococcus luteus
In today's lab, we will make both direct and indirect stains of several microorganisms.
B. DIRECT STAIN USING A BASIC DYE

In direct staining the positively charged color portion of the basic dye combines with the negatively charged
bacterium and the organism becomes directly stained (Fig. 1 and Fig. 2).
ORGANISMS
Your pure cultures of Staphylococcus epidermidis (coccus with staphylococcus arrangement) or
Micrococcus luteus (coccus with sarcina arrangement) and Escherichia coli (small bacillus) or Enterobacter
aerogenes (small bacillus) from Lab 3.
PROCEDURE (to be done individually)

1. Heat-fix a smear of either Escherichia coli or Enterobacter aerogenes as follows:
a. Using the dropper bottle of distilled water found in your staining rack, place 1/2 of a
typical sized drop of water on a clean slide by touching the dropper to the slide.
b. Aseptically remove a small amount of the culture from the agar surface and touch it
c. Burn the remaining bacteria off of the loop. (If too much culture is added to the water,
you will not see stained individual bacteria.)
51
LABORATORY 5:
f. Pass about one inch of the slide (film-side up) through the flame of the bunsen
burner several times until it just becomes uncomfortable to hold in order to heat-fix
the bacteria to the slide.
2. Place the slide on a staining tray and cover the entire film with safranin. Stain for one minute.
3. Pick up the slide by one end and hold it at an angle over the staining tray. Using the wash bottle
on the bench top, gently wash off the excess safranin from the slide. Also wash off any stain that
got on the bottom of the slide as well.
4. Use a book of blotting paper to blot the slide dry. Observe using oil immersion microscopy.
(Review the focusing steps from Lab 1, section D before you start.)
5. Heat-fix a smear of either Micrococcus luteus or Staphylococcus epidermidis as follows:
a. Using the dropper bottle of distilled water found in your staining rack, place 1/2 of a
typical sized drop of water on a clean slide by touching the dropper to the slide.
b. Aseptically remove a small amount of the culture from the agar surface and touch it
c. Burn the remaining bacteria off of the loop. (If too much culture is added to the water,
you will not see stained individual bacteria.)
f. Pass about one inch of the slide (film-side up) through the flame of the bunsen
burner several times until it just becomes uncomfortable to hold in order to heat-fix
the bacteria to the slide.
6. Stain with methylene blue for one minute.
7. Wash off the excess methylene blue with water.
8. Blot dry and observe using oil immersion microscopy.
9. Prepare a third slide of the normal flora and cells of your mouth.
a. Use a sterile cotton swab to vigorously scrape the inside of your mouth and gums.
b. Rub the swab over the slide (do not use water), air dry, and heat-fix.
c. Stain with crystal violet for 30 seconds.
d. Wash off the excess crystal violet with water.
e. Blot dry and observe. Find epithelial cells using your 10X objective, center them in the
field, and switch to oil immersion to observe your normal flora bacteria on and around your
epithelial cells.
52
LABORATORY 5:
C. INDIRECT STAIN USING AN ACIDIC DYE

In negative staining, the negatively charged color portion of the acidic dye is repelled by the negatively
charged bacterial cell. Therefore the background will be stained and the cell will remain colorless (Fig. 1 and
Fig. 3).
ORGANISM
Use your pure culture of Staphylococcus epidermidis or Micrococcus luteus from lab 3.

1. Place a small drop of nigrosin towards one end of a clean microscope slide.
2. Aseptically add a small amount of Staphylococcus epidermidis or Micrococcus luteus to the dye
and mix gently with the loop.
3. Using the edge of another slide, spread the mixture with varying pressure across the slide so that
there are alternating light and dark areas. Make sure the dye is not to thick or you will not see
the bacteria!
4. Let the film of dyed bacteria air dry completely on the slide. Do not heat fix and do not wash
off the dye.
5. Observe using oil immersion microscopy. Find an area that has neither too much nor too little dye
(an area that appears light purple where the light comes through the slide). If the dye is too thick,
not enough light will pass through; if the dye is too thin, the background will be too light for sufficient
contrast.
53
LABORATORY 5:
RESULTS
Make drawings of your three direct stain preparations and your indirect stain preparation.
Direct stain of
Escherichia coli
or Enterobacter aerogenes
Shape =
Direct stain of
Staphylococcus epidermidis
or Micrococcus luteus
Shape =
Arrangement =
Indirect stain of
Micrococcus luteus
Direct stain of
epithelial cells from
your mouth
Shape =
Arrangement =
54
LABORATORY 5:
LABORATORY 5
INTRODUCTION TO STAINING
DISCUSSION
1. Describe the procedure for heat fixation.
2. Define the following: acidic dye, basic dye, direct stain, and indirect stain.
3. State in chemical and physical terms the principle behind direct staining and the principle behind indirect
staining.
DIRECT STAINING
PROCEDURE
1. Transfer a small number of bacteria from an agar surface or a broth culture to a glass slide and heat-fix
the preparation.
2. Prepare a direct stain when given all the necessary materials.
RESULTS
1. Recognize a direct stain preparation when it is observed through a microscope and state the shape and
arrangement of the organism.
INDIRECT STAINING
PROCEDURE
1. Perform an indirect stain when given all the necessary materials.
2. State why the dye is not washed off during an indirect stain.
RESULTS
1. Recognize an indirect stain preparation when it is observed through a microscope and state the shape
and arrangement of the organism.
55
LABORATORY 6:
GRAM STAIN AND CAPSULE STAIN
56
LABORATORY 6:
LABORATORY 6
A. The Gram Stain
B. The Capsule Stain
A. THE GRAM STAIN

DISCUSSION
The gram stain is the most widely used staining procedure in bacteriology. It is called a differential stain
since it differentiates between gram-positive and gram-negative bacteria. Bacteria that stain purple with the
gram staining procedure are termed gram-positive; those that stain pink are said to be gram-negative. The
terms positive and negative have nothing to do with electrical charge, but simply designate two distinct
morphological groups of bacteria.
Gram-positive and gram-negative bacteria stain differently because of fundamental differences in the
structure of their cell walls. The bacterial cell wall serves to give the organism its size and shape as well as to
prevent osmotic lysis.
In electron micrographs, the gram-positive cell wall appears as a broad, dense wall 20-80 nm thick and
consisting of numerous interconnecting layers of peptidoglycan (see Figs. 1A and 1B). Chemically, 60 to 90%
of the gram-positive cell wall is peptidoglycan. Interwoven in the cell wall of gram-positive are teichoic acids.
Teichoic acids, which extend through and beyond the rest of the cell wall, are composed of polymers of
glycerol, phosphates, and the sugar alcohol ribitol. Some have a lipid attached (lipoteichoic acid). The outer
surface of the peptidoglycan is studded with proteins that differ with the strain and species of the bacterium.
The gram-negative cell wall, on the other hand, contains only 2-3 layers of peptidoglycan and is surrounded
by an outer membrane composed of phospholipids, lipopolysaccharide, lipoprotein, and proteins (see Figs.
2A and 2B). Only 10% - 20% of the gram-negative cell wall is peptidoglycan. The phospholipids are located
mainly in the inner layer of the outer membrane, as are the lipoproteins that connect the outer membrane to
the peptidoglycan. The lipopolysaccharides, located in the outer layer of the outer membrane, consist of a
lipid portion called lipid A embedded in the membrane and a polysaccharide portion extending outward from
the bacterial surface. The outer membrane also contains a number of proteins that differ with the strain and
species of the bacterium.
57
LABORATORY 6:
Fig. 1A:
Electron Micrograph of a Gram-Positive Cell Wall
Fig. 2A:
Electron Micrograph of a Gram-Negative Cell Wall
Fig. 1B:
Illustration of a Gram-Positive
Cell Wall
Fig. 2B:
Illustration of a Gram-Negative
Cell Wall
The gram staining procedure involves four basic steps:

1. The bacteria are first stained with the basic dye crystal violet. Both gram-positive and
gram-negative bacteria become directly stained and appear purple after this step.
2. The bacteria are then treated with gram's iodine solution. This allows the stain to be retained
better by forming an insoluble crystal violet-iodine complex. Both gram-positive and gram-negative
bacteria remain purple after this step.
3. Gram's decolorizer, a mixture of ethyl alcohol and acetone, is then added. This is the
differential step. Gram-positive bacteria retain the crystal violet-iodine complex while gram-negative
are decolorized.
4. Finally, the counterstain safranin (also a basic dye) is applied. Since the gram-positive bacteria
are already stained purple, they are not affected by the counterstain. Gram-negative bacteria, which
are now colorless, become directly stained by the safranin. Thus, gram-positive appear purple, and
gram-negative appear pink.
58
LABORATORY 6:
With the current theory behind gram staining, it is thought that in gram-positive bacteria, the crystal violet
and iodine combine to form a larger molecule that precipitates out within the cell. The alcohol/acetone mixture
then causes dehydration of the multilayered peptidoglycan, thus decreasing the space between the
molecules and causing the cell wall to trap the crystal violet-iodine complex within the cell. In the case of
gram-negative bacteria, the alcohol/acetone mixture, being a lipid solvent, dissolves the outer membrane of
the cell wall and may also damage the cytoplasmic membrane to which the peptidoglycan is attached. The
single thin layer of peptidoglycan is unable to retain the crystal violet-iodine complex and the cell is
decolorized.
It is important to note that gram-positivity (the ability to retain the purple crystal violet-iodine complex) is not
an all-or-nothing phenomenon but a matter of degree. There are several factors that could result in a
gram-positive organism staining gram-negatively:
1. The method and techniques used. Overheating during heat fixation, over decolorization with
alcohol, and even too much washing with water between steps may result in gram-positive bacteria
losing the crystal violet-iodine complex.
2. The age of the culture. Cultures more than 24 hours old may lose their ability to retain the crystal
violet-iodine complex.
3. The organism itself. Some gram-positive bacteria are more able to retain the crystal violet-iodine
complex than others.
Therefore, one must use very precise techniques in gram staining and interpret the results with discretion.
ORGANISMS
Trypticase Soy agar plate cultures of Escherichia coli (a small, gram-negative bacillus) and Staphylococcus
epidermidis (a gram-positive coccus with a staphylococcus arrangement).

1. Heat-fix a smear of Escherichia coli as follows:
a. Using the dropper bottle of distilled water found in your staining rack, place 1/2 a drop of water on
a clean slide by touching the dropper to the slide.
b. Aseptically remove a small amount of the Escherichia coli from the agar surface and just
touch it several times to the drop of water until it just turns cloudy. Flame the loop and let it
cool.
c. Using the loop, spread the bacteria/water mixture over the entire slide to form a thin film.
d. Allow this thin suspension to completely air dry.
e. Pass about one inch of the slide (film-side up) through the flame of the bunsen burner several
times until it just becomes uncomfortable to hold in order to heat-fix the bacteria to the slide.
2. Stain with Hucker's crystal violet for one minute. Gently wash with water. Shake off the excess water
but do not blot dry between steps.
3. Stain with gram's iodine solution for one minute and gently wash with water.
59
LABORATORY 6:
4. Decolorize by adding gram's decolorizer drop by drop until the purple stops flowing. Wash
immediately with water.
4. Stain with safranin for one minute and wash with water.
5. Blot dry and observe using oil immersion microscopy.
(First review the focusing steps from Lab 1, section D.)
6. Make a second gram stain using a plate culture of Staphylococcus epidermidis and repeating steps
1-6.
B. THE CAPSULE STAIN

DISCUSSION
Many bacteria secrete a slimy, viscous covering called a capsule or glycocalyx (see Fig. 3). This is
usually composed of polysaccharide, polypeptide, or both.
The ability to produce a capsule is an inherited property of the organism, but the capsule is not an
absolutely essential cellular component. Capsules are often produced only under specific growth
conditions.
Even though not essential for life, capsules probably help bacteria to survive in nature. Capsules help many
pathogenic and normal flora bacteria to initially resist phagocytosis by the host's phagocytic cells. In soil
and water, capsules help prevent bacteria from being engulfed by protozoans. Capsules also help many
bacteria to adhere to surfaces and thus resist flushing.
Fig.3:
Capsule stain of Enterobacter aerogenes
60
LABORATORY 6:
ORGANISM
Skim Milk broth culture of Enterobacter aerogenes. The skim milk supplies essential nutrients for capsule
production and also provides a slightly stainable background.

1. Stir up the Skim Milk broth culture with your loop and place 2-3 loops of Enterobacter aerogenes on a
slide.
2. Using your loop, spread it out over the entire slide to form a thin film.
3. Let it completely air dry. Do not heat fix. Capsules stick well to glass, and heat may destroy the capsule.
4. Stain with crystal violet for one minute.
5. Wash off the excess stain with copper sulfate solution. Do not use water!
6. Blot dry and observe using oil immersion microscopy. The organism and the milk dried on the slide will
pick up the purple dye while the capsule will remain colorless. (Fig. 3)
7. Observe the demonstration capsule stain of Streptococcus lactis, an encapsulated bacterium that is
normal flora in milk.
61
LABORATORY 6:
RESULTS
A. The Gram Stain
Make drawings of each bacterium on your gram stain preparation.
Gram stain of
Escherichia coli
Gram stain of
Color =
Color =
Gram reaction =
Gram reaction =
Shape =
Arrangement =
B. The Capsule Stain

Make a drawing of your capsule stain preparation of Enterobacter aerogenes and the demonstration capsule
stain of Streptococcus lactis.
Capsule stain of
Enterobacter aerogenes
Capsule stain of
Streptococcus lactis
62
LABORATORY 6:
LABORATORY 6
THE GRAM STAIN

DISCUSSION
1. State why the gram stain is said to be a differential stain.
2. Describe the differences between a gram-positive and a gram-negative cell wall.
3. Describe a theory as to why gram-positive bacteria retain the crystal violet-iodine complex while
gram-negatives become decolorized.
4. Describe three conditions that may result in a gram-positive organism staining gram-negatively.
PROCEDURE
1. State the procedure for the gram stain.
2. Perform a gram stain when given all the necessary materials.
RESULTS
1. Determine if a bacterium is gram-positive or gram-negative when microscopically viewing a gram stain
preparation and state the shape and arrangement of the organism.
THE CAPSULE STAIN

DISCUSSION
1. State the chemical nature and major functions of bacterial capsules.
RESULTS
1. Recognize capsules as the structures observed when microscopically viewing a capsule stain preparation.
63
64
LABORATORY 7:
ENDOSPORE STAIN AND MOTILITY TESTING
LABORATORY 7
ENDOSPORE STAIN AND BACTERIAL MOTILITY
A. Endospore Stain
B. Bacterial Motility
A. ENDOSPORE STAIN
DISCUSSION
A few genera of bacteria, such as Bacillus and Clostridium have the ability to produce resistant survival
forms termed endospores. Unlike the reproductive spores of fungi or plants, these endospores are resistant
to heat, drying, radiation, and various chemical disinfectants (see Labs 19 & 20).
Endospore-producing bacteria need an environment that is physiologically favorable for biosynthesis in
order to produce endospores. Once produced, however, these endospores can survive various adverse
conditions. Endospore formation (sporulation) occurs through a complex series of events. One endospore is
produced within each vegetative bacterium. Once the endospore is formed, the vegetative portion of the
bacterium is degraded and the dormant endospore is released.
First the DNA replicates and a cytoplasmic membrane septum forms at one end of the cell. A second layer
of cytoplasmic membrane then forms around one of the DNA molecules (the one that will become part of the
endospore) to form a forespore. Both of these membrane layers then synthesize peptidoglycan in the space
between them to form the first protective coat, the cortex. Calcium dipocolinate is also incorporated into the
forming endospore. A spore coat composed of a keratin-like protein then forms around the cortex.
Sometimes an outer membrane composed of lipid and protein and called an exosporium is also seen (see
Fig. 1).
Finally, the remainder of the bacterium is degraded and the endospore is released. endospore is released.
Sporulation generally takes around 15 hours.
The endospore is able to survive for long periods of time until environmental conditions again become
favorable for growth. The endospore then germinates, producing a single vegetative bacterium.
Bacterial endospores are resistant to antibiotics, most disinfectants, and physical agents such as radiation,
boiling, and drying. The impermeability of the spore coat is thought to be responsible for the endospore's
resistance to chemicals. The heat resistance of endospores is due to a variety of factors:
o
o
o
o
Calcium-dipicolinate, abundant within the endospore, may stabilize and protect the endospore's
DNA.
Specialized DNA-binding proteins saturate the endospore's DNA and protect it from heat, drying,
chemicals, and radiation.
The cortex may osmotically remove water from the interior of the endospore and the dehydration that
results is thought to be very important in the endospore's resistance to heat and radiation.
Finally, DNA repair enzymes contained within the endospore are able to repair damaged DNA during
germination.
Due to the resistant nature of the endospore coats, endospores are difficult to stain. Strong dyes and
vigorous staining conditions such as heat are needed. Once stained, however, endospores are equally hard
65
LABORATORY 7:
to decolorize. Since few bacterial genera produce endospores, the endospore stain is a good diagnostic test
for species of Bacillus and Clostridium.
Fig. 1:
Endospore formation within a vegetative bacterium
ORGANISMS
Trypticase Soy agar plate cultures of Bacillus megaterium.

1. Heat-fix a smear of Bacillus megaterium as follows:
a. Using the dropper bottle of distilled water found in your staining rack, place a small drop of water
on a clean slide by touching the dropper to the slide.
b. Aseptically remove a small amount of the culture from the edge of the growth on the agar
surface and generously mix it with the drop of water until the water turns cloudy.
c. Burn the remaining bacteria off of the loop.
f. Pass about one inch of the slide (film-side up) through the flame of the bunsen burner
the slide.
2. Place a piece of blotting paper over the smear and saturate with malachite green.
3. Let the malachite green sit on the slide for one minute and proceed to the next step.
4. Holding the slide with forceps, carefully heat the slide in the flame of a bunsen burner until the stain just
begins to steam. Remove the slide from the heat until steaming stops; then gently reheat. Continue
steaming the smear in this manner for five minutes. As the malachite green evaporates, continually add
more. Do not let the paper dry out.
66
LABORATORY 7:
5. After five minutes of steaming, wash the excess stain and blotting paper off the slide with water. Don't
forget to wash of any dye that got onto the bottom of the slide.
6. Blot the slide dry.
7. Now flood the smear with safranin and stain for one minute.
8. Wash off the excess safranin with water, blot dry, and observe using oil immersion microscopy. With this
endospore staining procedure, endospores will stain green while vegetative bacteria will stain red (see Fig.
2).
9. Observe the demonstration slide of Bacillus anthracis. With this staining procedure, the vegetative bacteria
stain blue and the endospores are colorless. Note the long chains of rod-shaped, endospore-containing
bacteria (Fig. 3).
10. Observe the demonstration slide of Clostridium tetani. With this staining procedure, the vegetative
bacteria stain blue and the endospores are colorless. Note the "tennis racquet" appearance of the
endospore-containing Clostridium (Fig. 4).
Fig. 2:
Endospores of Bacillus megaterium
Fig. 3:
Endospores of Bacillus anthracis
67
LABORATORY 7:
Fig. 4:
Endospores of Clostridium tetani
B. BACTERIAL MOTILITY
DISCUSSION
Many bacteria are capable of motility (the ability to move under their own power). Most motile bacteria
propel themselves by special organelles termed flagella (Fig. 5). The bacterial flagellum is a noncontractile,
semi-rigid, helical tube composed of protein and anchors to the bacterial cytoplasmic membrane and cell well
by means of disk-like structures. The rotation of the inner disk causes the flagellum to act much like a
propeller.
Bacterial motility constitutes unicellular behavior. In other words, motile bacteria are capable of a behavior
called taxis. Taxis is a motile response to an environmental stimulus and functions to keep bacteria in an
optimum environment.
The arrangement of the flagella about the bacterium is of use in classification and identification. The
following flagellar arrangements may be found:
1. monotrichous - a single flagellum at one pole (see Fig. 7).
2. amphitrichous - single flagella at both poles.
3. lophotrichous - two or more flagella at one or both poles of the cell (Fig. 8).
4. peritrichous - completely surrounded by flagella (Fig. 9).
These arrangements are shown in Figure 6.
68
LABORATORY 7:
Fig. 5:
Insertion of a bacterial flagellum
Fig. 6:
Arrangements of bacterial flagella
One group of bacteria, the spirochetes, has internally-located axial filaments or endoflagella. Axial
filaments wrap around the spirochete towards the middle from both ends. They are located above the
peptidoglycan cell wall but underneath the outer membrane or sheath (Fig. 10).
Fig. 7:
Monotrichous arrangement of flagella
69
LABORATORY 7:
Fig. 8:
Lophotrichous arrangement of flagella
Fig. 9:
Peritrichous arrangement of flagella
Fig. 10
Axial filaments of a spirochete
Fig. 11
Leptospira seen under dark-field microscopy
To detect bacterial motility, we can use any of the following three methods: 1) direct observation by means
of special-purpose microscopes (phase-contrast and dark-field), 2) motility media, and, indirectly, 3) flagella
staining.
1. Direct observation of motility using special-purpose microscopes.
a. Phase-contrast microscopy
A phase-contrast microscope uses special phase-contrast objectives and a condenser
assembly to control illumination and give an optical effect of direct staining. The special
optics convert slight variations in specimen thickness into corresponding visible variation in
brightness. Thus, the bacterium and its structures appear darker than the background.
b. Dark-field microscopy
A dark-field microscope uses a special condenser to direct light away from the objective
lens. However, bacteria (or other objects) lying in the transparent medium will scatter light so
that it enters the objective. This gives the optical effect of an indirect stain. The organism will
70
LABORATORY 7:
appear bright against the dark background. Dark field microscopy is especially valuable
in observing the very thin spirochetes (see Fig. 11).
2. Motility Test medium
Semi-solid Motility Test medium may also be used to detect motility. The agar concentration (0.3%)
is sufficient to form a soft gel without hindering motility. When a non-motile organism is stabbed
into Motility Test medium, growth occurs only along the line of inoculation. Growth along the stab
line is very sharp and defined. When motile organisms are stabbed into the soft agar, they swim
away from the stab line. Growth occurs throughout the tube rather than being concentrated along
the line of inoculation (Fig. 12). Growth along the stab line appears much more cloud-like as it
moves away from the stab. A dye incorporated in the medium turns the growth red as a result of
bacterial metabolism. The more bacteria present at any location, the darker red the growth
appears.
3. Flagella staining
If we assume that bacterial flagella confer motility, flagella staining can then be used indirectly to
denote bacterial motility. Since flagella are very thin (20-28 nm in diameter), they are below the
resolution limits of a normal light microscope. They cannot be seen unless one first treats them with
special dyes and mordants that build up as layers of precipitate along the length of the flagella,
making them microscopically visible. This is a delicate staining procedure and will not be attempted
here. We will, however look at several demonstration flagella stains.
Fig. 12:
Motility Test Medium
Non-motile
Motile
71
LABORATORY 7:
ORGANISMS
Trypticase Soy broth cultures of Pseudomonas aeruginosa and Staphylococcus aureus.
these organisms as pathogens.
Caution: handle
MEDIUM
Motility Test medium (2 tubes)
PROCEDURE (to be done individually and in pairs)

1. Observe the phase-contrast microscopy demonstration of motile Pseudomonas aeruginosa.
2. Observe the dark-field microscopy demonstration of motile Pseudomonas aeruginosa.
3. Take 2 tubes of Motility Test medium per pair. Stab one with Pseudomonas aeruginosa and the other with
Staphylococcus aureus. When you stab the tubes, take care not to tilt or twist the loop so that the loop
comes up through the same cut as it went down. Incubate at 37 C until the next lab period.
4. Observe the flagella stain demonstrations of a Vibrio species (monotrichous), Proteus vulgaris
(peritrichous) and Spirillum undula (lophotrichous) as well as the dark-field photomicrograph of the spirochete
Leptospira. When observing flagella stain slides, keep in mind that flagella often break off during the
staining procedure so you have to look carefully to observe the true flagellar arrangement.
RESULTS
A. Endospore Stain
Make drawings of the various endospore stain preparations.
Endospore stain of
Bacillus megaterium
Endospore stain of
Bacillus anthracis
72
LABORATORY 7:
Endospore stain of
Clostridium tetani
B. Bacterial Motility
1. Observe the phase contrast and dark-field microscopy demonstrations of bacterial motility.
2. Observe the two tubes of Motility Test medium.
Conclusion:
Conclusion:
73
LABORATORY 7:
3. Make drawings of the flagella stain demonstrations.
Vibrio
Proteus
Arrangement:
Arrangement:
Spirillum
Arrangement:
74
LABORATORY 7:
LABORATORY 7
ENDOSPORE STAIN
DISCUSSION
1. Name two endospore-producing genera of bacteria.
2. State the function of bacterial endospores.
RESULTS
1. Recognize endospores as the structures observed in an endospore stain preparation.
2. Identify a bacterium as an endospore-containing Clostridium by its "tennis racquet" appearance.
BACTERIAL MOTILITY
DISCUSSION
1. Define the following flagellar arrangements: monotrichous, lophotrichous, amphitrichous, peritrichous, and
axial filaments.
2. State the chemical nature and function of bacterial flagella.
3. Describe three methods of testing for bacterial motility and indicate how to interpret the results.
RESULTS
1. Recognize bacterial motility when using phase-contrast or dark-field microscopy.
2. Interpret the results of Motility Test Medium.
3. Recognize monotrichous, lophotrichous, amphitrichous, and peritrichous flagellar arrangements.
75
LABORATORY 8:
IDENTIFYING BACTERIA THROUGH BIOCHEMICAL TESTING
76
LABORATORY 8:
LABORATORY 8
IDENTIFICATION OF BACTERIA
THROUGH BIOCHEMICAL TESTING
A. Introduction
B. Starch Hydrolysis
C. Protein Hydrolysis
D. Fermentation of Carbohydrates
E. Indole and Hydrogen Sulfide Production
F. Catalase Activity
A. INTRODUCTION
In the three previous labs we examined bacteria microscopically. Staining provides valuable information as to
bacterial morphology, gram reaction, and presence of such structures as capsules and endospores. Beyond that,
however, microscopic observation gives little additional information as to the genus and species of a particular
bacterium.
To identify bacteria, we must rely heavily on biochemical testing. The types of biochemical reactions each organism
undergoes act as a "thumbprint" for its identification. This is based on the following chain of logic:
Each different species of bacterium has a different molecule of DNA (i.e., DNA with a unique series of
nucleotide bases).
Since DNA codes for protein synthesis, then different species of bacteria must, by way of their unique DNA,
be able to synthesize different protein enzymes.
Enzymes catalyze all the various chemical reactions of which the organism is capable. This in turn means
that different species of bacteria must carry out different and unique sets of biochemical reactions.
When identifying a suspected organism, you inoculate a series of differential media (see Lab 3). After incubation,
you then observe each medium to see if specific end products of metabolism are present. This can be done by
adding indicators to the medium which react specifically with the end product being tested, giving some form of
visible reaction such as a color change. The results of these tests on the suspected microorganism are then
compared to known results for that organism to confirm its identification.
Lab 7 will demonstrate that different bacteria, because of their unique enzymes, are capable of different biochemical
reactions. It will also show the results of the activity of those enzymes. In later labs we will use a wide variety of
special purpose differential media frequently used in the clinical laboratory to identify specific pathogenic and
opportunistic bacteria.
In general, we can classify enzymes as being either exoenzymes or endoenzymes. Exoenzymes are secreted by
bacteria into the surrounding environment in order to break down larger nutrient molecules so they may enter the
bacterium (see Fig. 1). Once inside the organism, some of the nutrients are further broken down to yield energy for
driving various cellular functions, while others are used to form building blocks for the synthesis of cellular
components. These later reactions are catalyzed by endoenzymes located within the bacterium.
77
LABORATORY 8:
Fig. 1: B. subtilis producing an exoenzyme to hydrolize the milk
protein casein.
B. STARCH HYDROLYSIS
DISCUSSION
Starch is a polysaccharide that appears as a branched polymer of the simple sugar glucose. This means
that starch is really a series of glucose molecules hooked together to form a long chain. Additional glucose
molecules then branch off of this chain as shown below.
GLU
|
( ---GLU-GLU-GLU-GLU-GLU-GLU-GLU--- )n
Some bacteria are capable of using starch as a source of carbohydrate but in order to do this they must first
hydrolyze or break down the starch so it may enter the cell. The bacterium secretes an exoenzyme that
hydrolyzes the starch by breaking the bonds between the glucose molecules. This enzyme is called a
diastase.
( ---GLU
GLU
GLU
GLU
GLU
GLU
The glucose can then enter the bacterium and be used for metabolism.
78
GLU--- )n
LABORATORY 8:
MEDIUM
Starch agar (one plate)
ORGANISMS
Trypticase Soy broth cultures of Bacillus subtilis and Escherichia coli.

1. Using a wax marker, draw a line on the bottom of a Starch agar plate so as to divide the plate in half.
Label one half B. subtilis and the other half E. coli.
2. Make a single streak line with the appropriate organism on the corresponding half of the plate as shown
below.
3. Incubate at 37 C until the next lab period.

4. Next period, iodine will be added to see if the starch remains in the agar or has been hydrolyzed by the
exoenzyme diastase. Iodine reacts with starch to produce a dark brown or blue/black color. If starch has
been hydrolyzed there will be a clear zone around the bacterial growth because the starch is no longer
in the agar to react with the iodine. If starch has not been hydrolyzed, the agar will be a dark brown or
blue/black color.
C. PROTEIN HYDROLYSIS
DISCUSSION
Proteins are made up of various amino acids linked together in long chains by means of peptide bonds.
Many bacteria can hydrolyze a variety of proteins into peptides (short chains of amino acids) and eventually
into individual amino acids. They can then use these amino acids to synthesize their own proteins and other
cellular molecules or to obtain energy. The hydrolysis of protein is termed proteolysis and the enzyme
involved is called a protease. In this exercise we will test for bacterial hydrolysis of the protein casein, the
protein that gives milk its white, opaque appearance (see Fig. 1).
79
LABORATORY 8:
MEDIUM
Skim Milk agar (one plate)
ORGANISMS
Trypticase Soy broth cultures of Bacillus subtilis and Escherichia coli.

1. Divide the Skim Milk agar plate in half and inoculate one half with Bacillus subtilis and the other half with
Escherichia coli as done above with the above starch agar plate.
2. Incubate at 37 C until the next lab period. If casein is hydrolyzed, there will be a clear zone around the
bacterial growth (see Fig. 1). If casein is not hydrolyzed, the agar will remain white and opaque.
D. FERMENTATION OF CARBOHYDRATES
DISCUSSION
Carbohydrates are complex chemical substrates that serve as energy sources when broken down by
bacteria and other cells. They are composed of carbon, hydrogen, and oxygen (with hydrogen and oxygen
being in the same ratio as water; [CH2O]) and are usually classed as either sugars or starches.
Facultative anaerobic and anaerobic bacteria are capable of fermentation, an anaerobic process during
which carbohydrates are broken down for energy production. A wide variety of carbohydrates can be
fermented by different bacteria in order to obtain energy and the types of carbohydrates which are fermented
by a specific organism can serve as a diagnostic tool for the identification of that organism.
We can detect whether a specific carbohydrate has been fermented by looking for common end
products of fermentation. When carbohydrates are fermented as a result of bacterial enzymes, the
following fermentation end products may be produced:
1. acid end products, or
2. acid and gas end products.
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LABORATORY 8:
In order to test for these fermentation products, you inoculate and incubate tubes of media containing a
single carbohydrate (such as lactose or maltose), a pH indicator (such as phenol red) and a Durham tube
(a small inverted tube to detect gas production). If the particular carbohydrate is fermented by the
bacterium, acid end products will be produced which lowers the pH, causing the pH indicator to
change color (phenol red turns yellow). If gas is produced along with the acid, it collects in the
Durham tube as a gas bubble (Fig. 2). If the carbohydrate is not fermented, no acid or gas will be
produced and the phenol red will remain red.
Fig. 2:
Gas bubble (arrow) seen in a Durham tube.
MEDIA
3 tubes of Phenol Red Lactose broth and 3 tubes of Phenol Red Maltose broth.
ORGANISMS
Trypticase Soy agar cultures of Bacillus subtilis, Escherichia coli, and Staphylococcus aureus.

1. Label each tube with the name of the sugar in the tube and the name of the bacterium you are
growing.
2. Inoculate one Phenol Red Lactose broth tube and one Phenol Red Maltose broth tube with Bacillus
subtilis.
3. Inoculate a second Phenol Red Lactose broth tube and a second Phenol Red Maltose broth tube with
Escherichia coli.
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LABORATORY 8:
4. Inoculate a third Phenol Red Lactose broth tube and a third Phenol Red Maltose broth tube with
Staphylococcus aureus.
5. Incubate all tubes at 37 C until next lab period.
E. INDOLE AND HYDROGEN SULFIDE PRODUCTION

DISCUSSION
Sometimes we look for the production of products produced by only a few bacteria. As an example, Indole
is a compound formed by the breakdown of the amino acid tryptophan by the enzyme tryptophanase. Since
only a few bacteria contain this enzyme, the formation of indole from a tryptophan substrate can be another
useful diagnostic tool for the identification of an organism. Indole production is a key test for the identification
of Escherichia coli. The pathway for the production of indole is shown below:
tryptophanase
tryptophan ------------------> indole + pyruvic acid + ammonia
By adding Kovac's reagent to the medium after incubation we can determine if indole was produced.
Kovac's reagent will react with the indole and turn red.
Likewise, some bacteria are capable of breaking down sulfur containing amino acids (cystine, methionine)
or reducing inorganic sulfur-containing compounds (such as sulfite, sulfate, or thiosulfate) to produce
hydrogen sulfide (H2S). This reduced sulfur may then be incorporated into other cellular amino acids, or
perhaps into coenzymes. The ability of an organism to reduce sulfur-containing compounds to hydrogen
sulfide can be another test for identifying unknown organisms such as certain Proteus and Salmonella. To
test for hydrogen sulfide production, a medium with a sulfur-containing compound and iron salts is inoculated
and incubated. If the sulfur is reduced and hydrogen sulfide is produced, it will combine with the iron salt to
form a visible black ferric sulfide (FeS) in the tube. The pathway for hydrogen sulfide production from sulfur
reduction is shown below:
+
2+
2H
Fe
S -------> H2S -------> FeS (black)
2-
MEDIUM
Three tubes of SIM (Sulfide, Indole, Motility) medium. This medium contains a sulfur source, an iron salt, the
amino acid tryptophan, and is semi-solid in agar content (0.3%). It can be used to detect hydrogen sulfide
production, indole production, and motility.
ORGANISMS
Trypticase Soy agar cultures of Proteus mirabilis, Escherichia coli, and Enterobacter cloacae.
PROCEDURE
1. Stab one SIM medium tube with Proteus mirabilis.
2. Stab a second SIM medium tube with Escherichia coli.
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LABORATORY 8:
3. Stab a third SIM medium tube with Enterobacter cloacae.

4. Incubate at 37 C until the next lab period.
5. Next lab period add Kovac's reagent to each tube to detect indole production.
F. CATALASE ACTIVITY (Demonstration)

DISCUSSION
Catalase is the name of an enzyme found in most bacteria which initiates the breakdown of hydrogen
peroxide (H2O2) into water and free oxygen:
catalase
2H2O2 ---------------> 2H2O + O2
+
During the normal process of aerobic respiration, hydrogen ions (H )are given off and must be removed by
the cell. The electron transport chain takes these hydrogen ions and combines them with half a molecule of
oxygen (an oxygen atom) to form water (H2O). During the process, energy is given off and is trapped and
stored in ATP. Water is then a harmless end product. Some cytochromes in the electron transport system,
however, form toxic hydrogen peroxide (H2O2) instead of water and this must be removed. This is done by
the enzyme catalase breaking the hydrogen peroxide into water and oxygen as shown above. Most bacteria
are catalase-positive; however, certain genera that don't carry out aerobic respiration, such as Streptococcus,
Lactobacillus, and Clostridium, are catalase-negative.
MATERIALS
Trypticase Soy agar cultures of Staphylococcus aureus and Streptococcus lactis, 3% hydrogen peroxide.
PROCEDURE (demonstration)
Add a few drops of 3% hydrogen peroxide to each culture and look for the release of oxygen as a result of
hydrogen peroxide breakdown. This appears as foaming.
RESULTS
A. Starch Hydrolysis
When iodine is added to starch, the iodine-starch complex that forms gives a characteristic dark
brown or deep purple color reaction. If the starch has been hydrolyzed into glucose molecules by the
diastase exoenzyme, it no longer gives this reaction.
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LABORATORY 8:
Flood the surface of the Starch agar plate with gram's iodine.
If the bacterium produced an exoenzyme that hydrolized the starch in the agar, a
clear zone will surround the bacterial growth because the starch is no longer there to
react with the iodine.
If the bacterium lacks the exoenzyme to hydrolize the starch, the agar around the
growth should turn dark brown or deep purple due to the iodine-starch complex.
Record your results and indicate which organism was capable of hydrolyzing the starch
(+ = hydrolysis; - = no hydrolysis).
Escherichia coli
Bacillus subtilis
Starch hydrolysis =
Starch hydrolysis =
B. Protein Hydrolysis
The protein casein exists as a colloidal suspension in milk and gives milk its characteristic white,
opaque appearance. If the casein in the agar is hydrolyzed into peptides and amino acids it will lose its
opaqueness.
If the bacterium produced an exoenzyme capable of hydrolyzing the casein, there will
be a clear zone around the bacterial growth (Fig. 1).
If the bacterium lacks the exoenzyme to break down casein, the Skim Milk agar will
remain white and opaque (Fig. 1).
Record your results and indicate which organism was capable of hydrolyzing casein
(+ = hydrolysis; - = no hydrolysis).
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LABORATORY 8:
Escherichia coli
Bacillus subtilis
Casein hydrolysis =
Casein hydrolysis =
C. Fermentation of Carbohydrates
As mentioned above, we can detect whether a specific carbohydrate is fermented by looking for common end
products of fermentation. When carbohydrates are fermented as a result of bacterial enzymes, the following
fermentation end products may be produced:
1. acid end products, or

2. acid and gas end products.
The results of fermentation may be acid alone or acid plus gas, but never gas alone.
Phenol red pH indicator appears red or orange at neutral pH but appears yellow or clear at an acidic pH.
A change in color in the tube from red or orange to yellow or clear indicates that the organism
has fermented that particular carbohydrate, producing acid end products.
A substantial gas bubble at the top of the Durham tube, the inverted test tube within the broth,
indicates gas was also produced from the fermentation of the carbohydrate.
If the phenol red remains red, no acid was produced and the carbohydrate was not fermented.
Possible results are as follows:
Carbohydrate fermentation producing acid but no gas: acidic (yellow or clear); no substantial gas
bubble in the Durham tube.
Carbohydrate fermentation producing acid and gas: acidic (yellow or clear); a substantial gas
No carbohydrate fermentation. No acid or gas (neutral pH (red or orange); no substantial gas
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LABORATORY 8:
Carbohydrate Fermentation
Record your results below (+ = positive; - = negative).
Organism
Phenol Red Maltose
Phenol Red Lactose
Bacillus subtilis
Acid
Gas
Fermentation
Escherichia coli
Acid
Gas
Fermentation
Acid
Gas
Fermentation
D. Production of Indole and Hydrogen Sulfide

Carefully add about inch of Kovac's reagent to each of the 3 SIM agar tubes and observe.
1. Production of hydrogen sulfide (H2S)
If the bacterium produces the enzyme to reduce sulfur to hydrogen sulfide (H2S),
the agar will turn black indicating that the organism has produced hydrogen sulfide.
If the bacterium lacks the enzyme, the agar does not turn black, indicating that
hydrogen sulfide was not produced.
2. Production of indole
If the bacterium produces the enzyme to break down tryptophan into molecules of
indole, pyruvic acid, and ammonia, the Kovac's reagent will turn red, indicating the
organism is indole-positive.
If the Kovac's reagent remains yellow, no indole was produced and the organism is
indole-negative.
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LABORATORY 8:
SIM Medium
Record your results below (+ = positive; - = negative).
Organism
Indole
Hydrogen sulfide
Escherichia coli
Enterobacter cloacae
Proteus mirabilis
E. Catalase Activity
Catalase is the name of an enzyme found in most bacteria which initiates the breakdown of hydrogen
peroxide (H2O2) into water and free oxygen.
If the bacterium produces the enzyme catalase, then the hydrogen peroxide added to
the culture will be broken down into water and free oxygen. The oxygen will bubble
through the water causing a surface froth to form. This is a catalase-positive bacterium.
A catalase-negative bacterium will not produce catalase to break down the hydrogen
peroxide, and no frothing will occur.
Catalase Test
Record your results below (foaming = positive; no foaming = negative).
Organism
Catalase reaction
Streptococcus lactis
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LABORATORY 8:
LABORATORY 8
After the completion of this lab, the student will be able to complete the following objectives:
A. INTRODUCTION
DISCUSSION
1. State the chemical nature and function of enzymes.
2. Define endoenzyme and exoenzyme.
B. STARCH HYDROLYSIS
DISCUSSION
1. Describe a method of testing for starch hydrolysis and state how to interpret the results.
RESULTS
1. Interpret the results of starch hydrolysis on a Starch agar plate that has been inoculated, incubated,
and flooded with iodine.
C. PROTEIN HYDROLYSIS
DISCUSSION
1. Describe a method of testing for casein hydrolysis and state how to interpret the results.
RESULTS
1. Interpret the results of casein hydrolysis on a Skim Milk agar plate after it has been inoculated and
incubated.
D. FERMENTATION OF CARBOHYDRATES
DISCUSSION
1. Name the general end products which may be formed as a result of the bacterial fermentation of
sugars and describe how these end products change the appearance of a broth tube containing a sugar,
the pH indicator phenol red, and a Durham tube.
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LABORATORY 8:
RESULTS
1. Interpret the carbohydrate fermentation results in tubes of Phenol Red Carbohydrate broth containing a
Durham tube after it has been inoculated and incubated.
E. INDOLE AND HYDROGEN SULFIDE PRODUCTION

DISCUSSION
1. State the pathway for the breakdown of tryptophan to indole.
2. State the pathway for the detection of sulfur reduction in SIM medium.
3. State three reactions that may be tested for in SIM medium and describe how to interpret the results.
RESULTS
1. Interpret the hydrogen sulfide and indole results in a SIM medium tube after inoculation, incubation,
and addition of Kovac's reagent.
F. CATALASE ACTIVITY
DISCUSSION
1. State the function of the enzyme catalase and describe a method of testing for catalase activity.
RESULTS
1. Interpret the results of a catalase test after adding hydrogen peroxide to a plate culture of bacteria.
89
90
LABORATORY 9:
YEASTS
LABORATORY 9
FUNGI PART 1: THE YEASTS
INTRODUCTION
Fungi are eukaryotic organisms (see Fig. 3) and include the yeasts, molds, and fleshy fungi. Yeasts are
microscopic, unicellular fungi; molds are multinucleated, filamentous fungi (such as mildews, rusts, and common
household molds); the fleshy fungi include mushrooms and puffballs.
All fungi are chemoheterotrophs, requiring organic compounds for both an energy and carbon source, which
obtain nutrients by absorbing them from their environment. Most live off of decaying organic material and are termed
saprophytes. Some are parasitic, getting their nutrients from living plants or animals.
The study of fungi is termed mycology and the diseases caused by fungi are called mycotic infections or mycoses.
In general, fungi are beneficial to humans. They are involved in the decay of dead plants and animals (resulting in
the recycling of nutrients in nature), the manufacturing of various industrial and food products, the production of many
common antibiotics, and may be eaten themselves for food. Some fungi, however, damage wood and fabrics, spoil
foods, and cause a variety of plant and animal diseases, including human infections.
YEASTS
DISCUSSION
Yeasts are unicellular, oval or spherical fungi which increase in number asexually by a process termed
budding (see Fig. 1). A bud forms on the outer surface of a parent cell, the nucleus divides with one nucleus
entering the forming bud, and cell wall material is laid down between the parent cell and the bud. Usually the
bud breaks away to become a new daughter cell but sometimes, as in the case of the yeast Candida, the
buds remain attached forming fragile branching filaments called hyphae (see Fig. 2). Because of their
unicellular and microscopic nature, yeast colonies appear similar to bacterial colonies on solid media. It
should be noted that certain dimorphic fungi (see Lab 10) are able to grow as a yeast or as a mold,
depending on growth conditions.
Yeasts are facultative anaerobes and can therefore obtain energy by both aerobic respiration and
anaerobic fermentation. The vast majority of yeasts are nonpathogenic and some are of great value in
industrial fermentations. For example, Saccharomyces species are used for both baking and brewing.
The yeast Candida is normal flora of the gastrointestinal tract and is also frequently found on the skin and
on the mucous membranes of the mouth and vagina. Candida is normally held in check in the body by:
1) normal immune defenses, and
2) normal flora bacteria.
However, Candida may become an opportunistic pathogen and overgrow an area of colonization if the host
becomes immunosuppressed or is given broad-spectrum antibiotics that destroy the normal bacterial flora.
(Since Candida is eukaryotic, antibiotics used against prokaryotic bacteria do not affect it.)
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LABORATORY 9:
YEASTS
Fig. 1:
A typical budding yeast.
Fig. 2:
Candida albicans on Rice Extract agar. Note hyphae, blastoconidia
(blastospores), and chlamydoconidia (chlamydospores).
Fig. 3:
Candida albicans (Eukaryotic Cell)
Fig. 4:
India ink preparation of Cryptococcus
neoformans in spinal fluid.
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LABORATORY 9:
YEASTS
Any infection caused by the yeast Candida is termed candidiasis. The most common forms of
candidiases are oral mucocutaneous candidiasis (thrush), vaginitis, onychomycosis (infection of the nails),
and dermatitis (diaper rash and other infections of moist skin). However, antibiotic therapy, cytotoxic and
immunosuppressive drugs, and immunosuppressive diseases such as diabetes, leukemias, and AIDS can
enable Candida to cause severe opportunistic systemic infections involving the skin, lungs, heart, and other
organs. In fact, Candida now accounts for 10% of the cases of septicemia. Candidiasis of the esophagus,
trachea, bronchi, or lungs, in conjunction with a positive HIV antibody test, is one of the indicator diseases for
AIDS.
The most common Candida species causing human infections is C. albicans. Candida is said to be
dimorphic in that it can grow as an oval, budding yeast, but under certain culture conditions, the budding
yeast may elongate and remain attached producing filament-like structures called pseudohyphae. C.
albicans may also produce true hyphae similar to molds. In this case long, branching filaments lacking
complete septa form. The hyphae help the yeast to invade deeper tissues after it colonizes the epithelium.
Asexual spores called blastoconidia (blastospores) develop in clusters along the hyphae, often at the points
of branching. Under certain growth conditions, thick-walled survival spores called chlamydoconidia
(chlamydospores) may also form at the tips or as a part of the hyphae (see Fig. 2).
A lesser known but often more serious pathogenic yeast is Cryptococcus neoformans. Like many fungi, this
yeast can also reproduce sexually and the name given to the sexual form of the yeast is Filobasidiella
neoformans. It appears as an oval yeast 5-6 m in diameter, forms buds with a thin neck, and is surrounded
by a thick capsule (see Fig. 4). It does not produce pseudohyphae and chlamydospores. The capsule
enables the yeast to resist phagocytic engulfment.
Cryptococcus infections are usually mild or subclinical but, when symptomatic, usually begin in the lungs
after inhalation of the yeast in dried bird feces. It is typically associated with pigeon and chicken droppings
and soil contaminated with these droppings. Cryptococcus, found in soil, actively grows in the bird feces but
does not grow in the bird itself. Usually the infection does not proceed beyond this pulmonary stage.
However, in an immunosuppressed host it may spread through the blood to the meninges and other body
areas, often causing cryptococcal meningoencephalitis. Any disease by this yeast is usually called
cryptococcosis.
Dissemination of the pulmonary infection can result in severe and often fatal cryptococcal meningitis.
Cutaneous and visceral infections are also found. Although exposure to the organism is probably common,
large outbreaks are rare, indicating that an immunosuppressed host is usually required for the development
of severe disease. Extrapulmonary cryptococcosis, in conjunction with a positive HIV antibody test, is another
indicator disease for AIDS
Cryptococcus can be identified by preparing an India ink or nigrosin negative stain of suspected sputum or
cerebral spinal fluid in which the encapsulated, budding, oval yeast cells may be seen (Fig. 4). It can be
isolated on Saboraud Dextrose agar and identified by biochemical testing. Direct and indirect serological tests
(discussed in Labs 17 & 18) may also be used in diagnosis.
Pneumocystis jiroveci (formerly called Pneumocystis carinii) causes an often-lethal disease called
Pneumocystis pneumonia (PCP). It is seen almost exclusively in highly immunosuppressed
individuals such as those with AIDS, late stage malignancies, or leukemias. PCP and a positive HIVantibody test is one of the more common indicators of AIDS.
In biopsies from lung tissue or in tracheobronchial aspirates, both a unicellular organism about 1-3 m in
diameter with a distinct nucleus and a cyst (see Fig. 5) form between 4-7m in diameter with 6-8 intracystic
bodies, often in rosette formation, can be seen.
Cysts of Pneumocystis jiroveci in lung tissue, Gomori methenamine silver stain method. The walls of the
cysts are stained black and often appear crescent shaped or like crushed ping-pong balls. The intracystic
bodies are not visible with this stain.
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LABORATORY 9:
YEASTS
Today we will use three agars to grow our yeast: Saboraud Dextrose agar (SDA), Mycosel agar, and
Rice Extract agar. Saboraud Dextrose agar (SDA) is an agar similar to trypticase soy agar but with a
higher sugar concentration and a lower pH, both of which inhibit bacterial growth but promote fungal
growth. SDA, therefore, is said to be selective for fungi. Another medium, Mycosel agar, contains
chloramphenicol to inhibit bacteria and cycloheximide to inhibit most saprophytic fungi. Mycosel agar,
therefore, is said to be selective for pathogenic fungi. Rice Extract agar with polysorbate 80
stimulates the formation of hyphae, blastoconidia (blastospores), and chlamydoconidia
(chlamydospores), structures unique to C. albicans, and may be used in its identification. The speciation
of Candida is based on sugar fermentation patterns.
Fig. 5:
Cysts of Pneumocystis jiroveci in Smear from Bronchoalveolar Lavage
Cysts of Pneumocystis carinii in lung tissue, Gomori methenamine silver stain method. The
walls of the cysts are stained black and often appear crescent shaped or like crushed pingpong balls. The intracystic bodies are not visible with this stain. (Courtesy of the Centers for
Disease Control and Prevention.)
MATERIALS
Coverslips, alcohol, forceps, and one plate each of Saboraud Dextrose agar, Mycosel agar, and Rice Extract
agar.
ORGANISMS
Trypticase Soy broth cultures of Candida albicans and Saccharomyces cerevisiae.

1. With a wax marker, divide a Saboraud Dextrose agar and a Mycosel agar plate in half. Using a sterile
swab, inoculate one half of each plate with C. albicans and the other half with S. cerevisiae as shown
below. Incubate the two plates at 37 C until the next lab period.
94
LABORATORY 9:
YEASTS
Inoculation of SDA and Mycosel Agars
2. Using a sterile swab, streak two straight lines of C. albicans into a plate of Rice Extract agar plate. Pick
up a glass coverslip with forceps, dip the coverslip in alcohol, and ignite with the flame of your gas burner.
Let the coverslip cool for a few seconds and place it over a portion of the streak line as shown below so that
the plate can be observed directly under the microscope after incubation. Repeat for the second steak line
and incubate the plate at room temperature until the next lab period.
Inoculation of Rice Extract Agar
95
LABORATORY 9:
YEASTS
3. Observe the following demonstrations:

a. direct stain of Saccharomyces cerevisiae
b. direct stain of Candida albicans
c. oral smear from a person with thrush
d. lung tissue infected with Candida albicans
e. India ink preparation of Cryptococcus neoformans
f. cyst form of Pneumocystis jiroveci from lung tissue.
RESULTS
1. Describe the appearance of Candida albicans and Saccharomyces cerevisiae on Saboraud Dextrose agar
and on Mycosel agar.
Yeast
SDA
Mycosel agar
Candida albicans
Description:
Description:
2. Remove the lid of the Rice Extract agar plate and put the plate on the stage of the microscope. Using your
yellow-striped 10X objective, observe an area under the coverslip that appears "fuzzy" to the naked eye.
Reduce the light by moving the iris diaphragm lever almost all the way to the right. Raise the stage all the
way up using the coarse focus (large knob) and then lower the stage using the coarse focus until the yeast
comes into focus. Draw the hyphae, blastoconidia (blastospores), and chlamydoconidia (chlamydospores.)
Candida albicans producing

hyphae,blastoconidia, and
chlamydoconidia on Rice Extract agar
96
LABORATORY 9:
YEASTS
3. Observe and make drawings of the demonstration yeast slides.
Direct stain of
Direct stain of
Candida albicans
Mouth smear showing thrush

(Candida albicans)
Mouse lung infected with

Candida albicans
India ink preparation of

Cryptococcus neoformans
Lung tissue showing cysts of

Pneumocystis jiroveci
97
LABORATORY 9:
YEASTS
LABORATORY 9
INTRODUCTION
1. Define mycology and mycosis.
2. State three ways fungi may be beneficial to humans and three ways they may be harmful.
THE YEAST
DISCUSSION
1. Describe the typical appearance of a yeast cell and its usual mode of reproduction.
2. Describe yeasts in terms of their oxygen requirements.
3. State two ways the yeast Saccharomyces is beneficial to humans.
4. Name two yeasts that commonly infect humans.
5. Name four common forms of candidiasis.
6. Describe two conditions that may enable Candida to cause severe opportunistic systemic infections.
7. Describe pseudohyphae, hyphae, blastoconidia (blastospores), and chlamydoconidia (chlamydospores).
8. State the usefulness of Saboraud Dextrose agar, Mycosel agar, and Rice Extract agar.
9. State how Cryptococcus neoformans is transmitted to humans, where in the body it normally infects, and
possible complications.
10. State the primary method of identifying Cryptococcus neoformans.
11. State what disease is caused by Pneumocystis jiroveci and indicate several predisposing conditions a
person is normally seen to have before they contract the disease.
RESULTS
1. Describe the appearance of Saccharomyces cerevisiae and Candida albicans on Saboraud Dextrose agar
and on Mycosel agar.
2. When given a plate of Mycosel agar showing yeast-like growth and a plate of Rice Extract agar showing
hyphae, (blastospores), and chlamydoconidia (chlamydospores), identify the organism as Candida albicans.
3. Recognize the following observed microscopically:
a. Saccharomyces cerevisiae and Candida albicans as yeasts in a gram stain preparation
b. A positive specimen for thrush by the presence of budding Candida albicans
c. Cryptococcus neoformans in an India ink preparation
d. a cyst of Pneumocystis jiroveci in lung tissue
98
LABORATORY 10:
MOLDS
LABORATORY 10
FUNGI PART 2: THE MOLDS
A. Non-pathogenic Molds
B. Dermatophytes
C. Dimorphic Fungi
DISCUSSION
Molds are multinucleated, filamentous fungi composed of hyphae. A hypha is a branching, tubular structure from 210 m in diameter and is usually divided into eukaryotic cell-like units by crosswalls called septa. The total mass of
hyphae is termed a mycelium. The portion of the mycelium that anchors the mold and absorbs nutrients is called the
vegetative mycelium; the portion that produces asexual reproductive spores is termed the aerial mycelium (see
Fig. 1).
Fig. 1:
Asexual reproduction in molds.
Molds possess a rigid polysaccharide cell wall composed mostly of chitin and, like all fungi, are eukaryotic (see Fig.
2). Molds reproduce primarily by means of asexual reproductive spores such as conidiospores, sporangiospores,
and arthrospores. These spores are disseminated by air, water, animals or objects and upon landing on a suitable
environment, germinate and produce new hyphae (see Fig. 1). Molds may also reproduce by means of sexual spores
such as ascospores and zygospores, but this is not common. The form and manner in which the spores are
produced, along with the appearance of the hyphae and mycelium, provide the main criteria for identifying and
classifying molds.
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LABORATORY 10:
MOLDS
Fig. 2:
Segment of a Mold Hypha Showing Eukaryotic Nature
A. NON-PATHOGENIC MOLDS
To illustrate how morphological characteristics such as the type and form of asexual reproductive spores
and the appearance of the mycelium may be used in identification, we will look at three common nonpathogenic molds.
The two most common types of asexual reproductive spores produced by molds are conidiospores and
sporangiospores. Conidiospores are borne externally in chains on an aerial hypha called a conidiophore
(see Fig. 3); sporangiospores are produced within a sac or sporangium on an aerial hypha called a
sporangiophore (see Fig. 4).
Penicillium and Aspergillus are examples of molds that produce conidiospores. Penicillium is one of the
most common household molds and is a frequent food contaminant. The conidiospores usually appear
grey, green, or blue and are produced in chains on finger-like projections called phialides coming off the
conidiophore (see Fig. 5). Aspergillus is another common contaminant. Although usually nonpathogenic, it
may become opportunistic in the respiratory tract of a compromised host and, in certain foods, can produce
mycotoxins. The conidiophore terminates in a ball-like structure called a vesicle. Its conidiospores, which
typically appear brown to black, are produced in chains on phialides coming off of the vesicle (see Fig 6).
Rhizopus is an example of a mold that produces sporangiospores. Although usually nonpathogenic, it
sometimes causes opportunistic wound and respiratory infections in the compromised host. At the end of its
sporangiophore is dome-shaped end called a columella that extends into a sac-like structure called a
sporangium. Its sporangiospores, typically brown or black, are produced within the sporangium (see Fig
7). Anchoring structures called rhizoids are also produced on the vegetative hyphae.
Rhizopus can also reproduce sexually. During sexual reproduction (see Fig 8), hyphal tips of (+) and (-)
mating type join together and their nuclei fuse to form a sexual spore called a zygospore (see Fig. 8). This
gives rise to a new sporangium producing sporangiospores having DNA that is a recombination of the two
parent strain's DNA.
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LABORATORY 10:
MOLDS
Non-pathogenic molds are commonly cultured on fungal-selective or enriched media such as Saboraud
Dextrose agar (SDA), Corn Meal agar, and Potato Dextrose agar.
Fig. 3:
Fungal Conidiospores
Fig. 4
Fungal Sporangiospores within a Sporangium
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LABORATORY 10:
MOLDS
Fig. 5:
Penicillium
Note chains of conidiospores on phialides.
Fig. 7:
Rhizopus:
Note sporangium filled with sporangiospores.
Fig. 6:
Aspergillus
Note chains of conidiospores on a
vesicle.
Fig. 8:
Sexual reproduction of Rhizopus
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LABORATORY 10:
MOLDS
B. DERMATOPHYTES
The dermatophytes are a group of molds that cause superficial mycoses of the hair, skin, and nails
and utilize the protein keratin, found in hair, skin, and nails, as a nitrogen and energy source. Infections
are commonly referred to as ringworm or tinea infections and include tinea capitis (head), tinea barbae (face
and neck), tinea corporis (body), tinea cruris (groin), tinea unguium (nails), and tinea pedis (athlete's foot).
The three common dermatophytes are Microsporum, Trichophyton, and Epidermophyton. These
organisms grow well at 25 C. They may produce large leaf or club-shaped asexual spores called
macroconidia as well as small spherical asexual spores called microconidia, both from vegetative hyphae
(see Fig. 10A and Fig. 10B).
Microsporum commonly infects the skin and hair, Epidermophyton, the skin and nails, and Trichophyton,
the hair, skin, and nails. Dermatophytic infections are acquired by contact with fungal spores from infected
humans, animals, or objects. On the skin, the dermatophytes typically cause reddening, itching, edema, and
necrosis of tissue. This is a result of fungal growth and a hypersensitivity of the host to the fungus and its
products. Frequently there is secondary bacterial or Candida invasion of the traumatized tissue.
To diagnose dermatophytic infections, tissue scrapings can be digested with 10% potassium hydroxide
(which causes lysis of the human cells but not the fungus) and examined microscopically for the presence of
fungal hyphae and spores. To establish the specific cause of the infection, fungi from the affected tissue
can be cultured on Dermatophyte Test Medium (DTM) and Saboraud Dextrose agar (SDA).
Dermatophyte Test Medium (DTM) has phenol red as a pH indicator with the medium yellow (acid) prior
to inoculation. As the dermatophytes utilize the keratin in the medium, they produce alkaline end products
that raise the pH, thus turning the phenol red in the medium from yellow (acid) to red (alkaline).
The types of macroconidia and microconidia can be observed by growing the mold on SDA and observing
under a microscope (see Fig. 10B). Many dermatophyte species produce yellow to red-pigmented colonies
on SDA and the most common species of Microsporum fluoresce under ultraviolet light.
Fig. 10A:
Macroconidia and macroconidia of
dermatophytes
Fig. 10B:
Macroconidia of the dermatophyte Microsporum (arrows)
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LABORATORY 10:
MOLDS
C. DIMORPHIC FUNGI
Dimorphic fungi may exhibit two different growth forms. Outside the body they grow as a mold,
producing hyphae and asexual reproductive spores, but inside the body they grow as a yeast-like form.
Dimorphic fungi may cause systemic mycoses that usually begin by inhaling spores from the mold form.
After germination in the lungs, the fungus grows as a yeast. Factors such as body temperature, osmotic
stress, oxidative stress, and certain human hormones activate a dimorphism-regulating histidine kinase
enzyme in dimorphic molds, causing them to switch from their avirulent mold form to their more virulent yeast
form.
The infection usually remains localized in the lungs and characteristic lesions called granuloma may be
formed in order to wall-off and localize the organism. In rare cases, usually in an immunosuppressed host,
the organism may disseminate to other areas of the body and be life threatening. Examples of dimorphic
fungi include Coccidioides immitis, Histoplasma capsulatum, and Blastomyces dermatitidis.
Coccidioides immitis (See Fig. 11) is a dimorphic fungus that causes coccidioidomycosis, a disease
endemic to the southwestern United States. The mold form of the fungus grows in arid soil and produces
thick-walled, barrel-shaped asexual spores called arthrospores by a fragmentation of its vegetative hyphae.
After inhalation, the arthrospores germinate and develop into endosporulating spherules in the lungs.
Coccidioidomycosis can be diagnosed by culture, by a coccidioidin skin test, and by indirect serologic tests
(discussed in Lab 18).
Histoplasma capsulatum (see Fig. 12) is a dimorphic fungus that causes histoplasmosis, a disease
commonly found in the Great Lakes region and the Mississippi and Ohio River valleys. The mold form of the
fungus often grows in bird or bat droppings or soil contaminated with these droppings and produces large
tuberculate macroconidia and small microconidia. After inhalation of these spores and their germination in
the lungs, the fungus grows as a budding, encapsulated yeast. Histoplasmosis can be diagnosed by
culture, by a histoplasmin skin test, and by indirect serologic tests (discussed in Lab 18).
Symptomatic and disseminated histoplasmosis and coccidioidomycosis are seen primarily in individuals
who are immunosuppressed. Along with a positive HIV antibody test, both are indicator diseases for the
diagnosis of AIDS.
Blastomycosis, caused by Blastomyces dermatitidis produces a mycelium with small conidiospores
and grows actively in bird droppings and contaminated soil. When spores are inhaled or enter breaks in the
skin, they germinate and the fungus grows as a yeast having a characteristic thick cell wall.
Blastomycosis is common around the Great Lakes region and the Mississippi and Ohio River valleys. It is
diagnosed by culture and by biopsy examination.
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LABORATORY 10:
MOLDS
Fig. 11:
Dimorphic cycle of Coccidioides immitis.
Fig. 12:
Dimorphic cycle of Histoplasma capsulatum.
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LABORATORY 10:
MOLDS

1. Using a dissecting microscope, observe the SDA plate cultures of Penicillium, Aspergillus, and
Rhizopus. Note the colony appearance and color and the type and form of the asexual spores
produced.
2. Observe the prepared slides of Penicillium, Aspergillus, and Rhizopus under high magnification.
Note the type and form of the asexual spores produced.
3. Observe the prepared slide showing the zygospore of Rhizopus produced during sexual
reproduction.
B. DERMATOPHYTES
1. Observe the dermatophyte Microsporum growing on DTM. Note the red color (from alkaline end
products) characteristic of a dermatophyte.
2. Microscopically observe the SDA culture of Microsporum. Note the macroconidia and
microconidia.
3. Observe the photographs of dermatophytic infections.
C. DIMORPHIC FUNGI
1. Observe the prepared slide of Coccidioides immitis arthrospores.
2. Observe the 35mm slides showing the mold form and yeast form of Histoplasma capsulatum.
3. Observe the photographs of systemic fungal infections.
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LABORATORY 10:
MOLDS
RESULTS
Make drawings of the molds as they appear microscopically under high magnification and indicate the type of
asexual spore they produce. Also note their color and appearance on SDA.
Penicillium
Aspergillus
Type of asexual spore:
Color on SDA:
Color on SDA:
Rhizopus
zygospores of Rhizopus
Color on SDA:
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LABORATORY 10:
MOLDS
B. DERMATOPHYTES
1. Describe the results of Microsporum growing on Dermatophyte Test Medium (DTM):
Original color of DTM =
Color following growth of Microsporum =
Reason for Color Change =
2. Draw the macroconidia and microconidia seen on the SDA culture of Microsporum.
Macroconidia and
microconidia of Microsporum
C. DIMORPHIC FUNGI
1. Draw the two forms of Coccidioides immitis.
Mold form of Coccidioides

showing arthrospores.
Endosporulating spherules
of Coccidioides in the lungs.
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LABORATORY 10:
MOLDS
2. Draw the mold form and yeast form of Histoplasma capsulatum.
Mold form of Histoplasma

showing tuberculate
macroconidia.
Yeast form of Histoplasma in

the lungs.
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LABORATORY 10:
MOLDS
LABORATORY 10
DISCUSSION
1. Define the following: hypha, mycelium, vegetative mycelium, and aerial mycelium.
2. Describe the principle way molds reproduce asexually.
3. State the main criteria used in identifying molds.
NON-PATHOGENIC MOLDS
1. Describe conidiospores and sporangiospores and name a mold that produces each of these.
2. Recognize the following genera of molds when given an SDA plate culture and a dissecting microscope
and state the type of asexual spore seen:
a. Penicillium
b. Aspergillus
c. Rhizopus
3. Recognize the following genera of molds when observing a prepared slide under high magnification and
state the type of asexual spore seen:
a. Penicillium
b. Aspergillus
c. Rhizopus
4. Recognize Rhizopus zygospores.
DERMATOPHYTES
1. Define dermatophyte and list three common genera of dermatophytes.
2. Name four dermatophytic infections and state how they are contracted by humans.
3. Describe macroconidia and microconidia.
4. Describe how the following may be used to identify dermatophytes: potassium hydroxide preparations of
tissue scrapings, DTM, and SDA.
5. Recognize a mold as a dermatophyte and state how you can tell when given the following:
a. A flask of DTM showing alkaline products
b. An SDA culture (under a microscope) or picture showing macroconidia.
6. Recognize macroconidia and microconidia.
DIMORPHIC FUNGI
1. Define dimorphic fungi and state how humans usually contract them.
2. Name three common dimorphic fungal infections found in the United States, state how they are transmitted
to humans, and indicate where they are found geographically.
3. Describe the mold form and the nonmycelial form of the following:
a. Coccidioides immitis
b. Histoplasma capsulatum
c. Blastomyces dermatitidis
4. Recognize Coccidioides immitis and its arthrospores when given a prepared slide and a microscope.
110
LABORATORY 11:
VIRUSES: THE BACTERIOPHAGES
LABORATORY 11
VIRUSES: THE BACTERIOPHAGE
DISCUSSION
Viruses are infectious agents with both living and non-living characteristics.
1. Living characteristics of viruses
a. They reproduce at a fantastic rate, but only in living host cells.
b. They can mutate.
2. Non-living characteristics of viruses
a. They are acellular, that is, they contain no cytoplasm or cellular organelles.
b. They carry out no metabolism on their own and must replicate using the host cell's metabolic
machinery. In other words, viruses don't grow and divide. Instead, new viral components are
synthesized and assembled within the infected host cell.
c. With few exceptions, they possess DNA or RNA but never both.
Viruses are usually much smaller than bacteria. Most are submicroscopic, ranging in size from 10-250 nanometers.
Structurally, viruses are much more simple than bacteria. Every virus contains a genome of single-stranded or
double-stranded DNA or RNA that functions as its genetic material. This is surrounded by a protein shell, called a
capsid or core, composed of protein subunits called capsomeres. Many viruses consist of no more than nucleic acid
and a capsid, in which case they are referred to as nucleocapsid or naked viruses.
Most animal viruses have an envelope surrounding the nucleocapsid and are called enveloped viruses. The
envelope usually comes from the host cell's membranes by a process called budding, although the virus does
incorporate glycoprotein of its own into the envelope.
Bacteriophages are viruses that infect only bacteria. In addition to the nucleocapsid or head, some have a rather
complex tail structure used in adsorption to the cell wall of the host bacterium (Fig. 1).
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LABORATORY 11:
Fig. 1:
Structure of Coliphage T4, a bacteriophage that infects E. coli
Since viruses lack organelles and are totally dependent on the host cell's metabolic machinery for replication,
they cannot be grown in synthetic media. In the laboratory, animal viruses are grown in animals, in embryonated
eggs, or in cell culture. (In cell culture, the host animal cells are grown in synthetic medium and then infected with
viruses.) Plant viruses are grown in plants or in plant cell culture. Bacteriophages are grown in susceptible
bacteria.
Today we will be working with bacteriophages since they are the easiest viruses to study in the lab. Most
bacteriophages, such as Coliphage T4 that we are using today, replicate by the lytic life cycle and are called lytic
bacteriophages.
The lytic life cycle of Coliphage T4 (see Figs. 2-7) consists of the following steps:
1. Adsorption
Attachment sites on the bacteriophage tail adsorb to receptor sites on the cell wall of a susceptible
host bacterium (Fig. 2).
2. Penetration
A bacteriophage enzyme "drills" a hole in the bacterial cell wall and the bacteriophage injects its
genome into the bacterium (Fig. 3). This begins the eclipse period, the period in which no intact
bacteriophages are seen within the bacterium.
3. Replication
Enzymes coded by the bacteriophage genome shut down the bacterium's macromolecular (protein,
RNA, DNA) synthesis. The bacteriophage genome replicates and the bacterium's metabolic
machinery is used to synthesize bacteriophage enzymes and bacteriophage structural components
(Fig. 4 and 5).
4. Maturation
The bacteriophage parts assemble around the genome (Fig. 6).
5. Release
A bacteriophage-coded lysozyme breaks down the bacterial peptidoglycan causing osmotic lysis of
the bacterium and release of the intact bacteriophages (Fig. 7).
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LABORATORY 11:
6. Reinfection
From 50-200 bacteriophages may be produced per infected bacterium and they now infect
surrounding bacteria.
Some bacteriophages replicate by the lysogenic life cycle and are called temperate bacteriophages. When a
temperate bacteriophage infects a bacterium, it can either 1) replicate by the lytic life cycle and cause lysis of the host
bacterium, or it can 2) incorporate its DNA into the bacterium's DNA and assume a noninfectious state. In the latter
case, the cycle begins by the bacteriophage adsorbing to the host bacterium and injecting its genome, as in the lytic
cycle. However, the bacteriophage does not shut down the host bacterium. Instead, the bacteriophage DNA inserts or
integrates into the host bacterium's DNA. At this stage, the virus is called a prophage. Expression of the
bacteriophage genes controlling bacteriophage replication is repressed by a repressor protein and the bacteriophage
DNA replicates as a part of the bacterial nucleoid. However, in approximately one in every million to one in every
billion bacteria containing a prophage, spontaneous induction occurs. The bacteriophage genes are activated and
bacteriophages are produced as in the lytic life cycle.
Figs. 2-7
The Lytic Life Cycle of Coliphage T4.
Fig. 2: Adsorption
Tail fibers of Coliphage T4 adsorb to receptors on
the cell wall of E. coli B.
Fig. 3: Penetration
The bacteriophage injects its DNA genome into the
cytoplasm of the bacterium.
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LABORATORY 11:
Fig. 4: Early Replication
The genome of the bacteriophage replicates and
begins to direct the metabolic machinery of the
bacterium to produce phage structural components
and enzymes.
Fig. 6: Maturation
The phage parts assemble producing intact
bacteriophages.
Fig. 5: Late Replication, Early Maturation

Bacteriophage parts continue to be produced and
begin to assemble.
Fig. 7: Release
Phage-coded lysozyme breaks down the bacteriums cell
wall causing lysis. The bacteriophages are released.
Today you will infect the bacterium Escherichia coli B with its specific bacteriophage, Coliphage T4.
In the first part of the lab you will perform a plaque count. A plaque is a small, clear area on an agar plate where the
host bacteria have been lysed as a result of the lytic life cycle of the infecting bacteriophages (see Fig. 14). As the
bacteria replicate on the plate they form a "lawn" of confluent growth. Meanwhile, each bacteriophage that adsorbs to
a bacterium will reproduce and cause lysis of that bacterium. The released bacteriophages then infect neighboring
bacteria, causing their lysis. Eventually a visible self-limiting area of lysis, a plaque, is observed on the plate.
114
LABORATORY 11:
Fig. 14:
Plaques
The second part of the lab will demonstrate viral specificity. Viral specificity means that a specific strain of
bacteriophage will only adsorb to a specific strain of susceptible host bacterium. In fact, viral specificity is just as
specific as an enzyme-substrate reaction or an antigen-antibody reaction. Therefore, viral specificity can be used
sometimes as a tool for identifying unknown bacteria. Known bacteriophages are used to identify unknown bacteria
by observing whether or not the bacteria are lysed (see Fig. 15). This is called phage typing.
Fig. 15:
Lysis of an unknown bacterium by a known bacteriphage.
Phage typing is useful in identifying strains of such bacteria as Staphylococcus aureus, Pseudomonas aeruginosa
and Salmonella species. For example, by using a series of known staphylococcal bacteriophages against the
Staphylococcus aureus isolated from a given environment, one can determine if it is identical to or different from the
strain of Staphylococcus aureus isolated from a lesion or from a food. This can be useful in tracing the route of
transmission.
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LABORATORY 11:
A. PLAQUE COUNT
MATERIALS
1 tube containing 9.9 ml of sterile saline; 3 tubes containing 9.0 ml of sterile saline; 3 sterile empty dilution
tubes; 3 Trypticase Soy agar plates; 3 sterile 1.0 ml pipettes; 1 sterile 10.0 ml pipette; bottle of melted
Motility Test medium from a water bath held at 47C.
CULTURES
Trypticase Soy broth culture of Escherichia coli B, suspension of Coliphage T4.
PROCEDURE (to be done in groups of three)

1. Take 1 tube containing 9.9 ml of sterile saline, 3 tubes containing 9.0 ml of sterile saline, and 2 sterile
empty dilution tubes and label the tubes as shown in Fig. 8.
2. Dilute the Coliphage T4 stock as described below and shown in Fig. 8.
a. Remove a sterile 1.0 ml pipette from the bag. Do not touch the portion of the pipette that will
go into the tubes and do not lay the pipette down. From the tip of the pipette to the "0" line is 1
ml; each numbered division (0.1, 0.2, etc.) represents 0.1 ml (see Fig. 11).
b. Insert the cotton-tipped end of the pipette into a blue 2 ml pipette filler.
c. Uncap the sample of Coliphage T4, insert the pipette to the bottom of the tube, and withdraw 0.1
ml (see Fig. 11) of the sample by turning the filler knob towards you. Re cap the tube.
-2
d. Flame the 10 dilution tube and dispense the 0.1 ml of sample into the tube by turning the filler
knob away from you. Draw the liquid up and down in the pipette several times to rinse the pipette
-2
and help mix. Flame and cap the tube. This will give a 1/100 or 10 dilution of the bacteriophage.
e. Using a vortex mixer, mix the tube thoroughly. This is to assure an even distribution of the
bacteriophage throughout the liquid.
-2
f. Using the same pipette and procedure, aseptically withdraw 1.0 ml (see Fig. 11H) from the 10
-3
-3
dilution tube and dispense into the 10 dilution tube and mix. This will give a 1/1000 or 10 dilution
of the bacteriophage. Using a vortex mixer, mix the tube thoroughly.
g. Using the same pipette and procedure, aseptically withdraw 1.0 ml (up to the "0" line; see Fig.
-3
-4
11H) from the 10 dilution tube and dispense into the 10 dilution tube. This will give a 1/10,000 or
-4
10 dilution of the bacteriophage. Using a vortex mixer, mix the tube thoroughly.
-4
h. Using the same pipette and procedure, aseptically withdraw 1.0 ml (see Fig. 11H) from 10
-5
-5
dilution tube and dispense into the 10 dilution tube. This will give a 1/100,000 or 10 dilution of the
bacteriophage. Using a vortex mixer, mix the tube thoroughly. Discard the pipette in the
biowaste container.
3. Take 3 empty, sterile tubes and treat as described below and shown in Fig. 8.
a. Using a new sterile 1.0 ml pipette and the procedure described above, aseptically remove 0.1 ml
-5
-6
(see Fig. 11H) of the 10 bacteriophage dilution and dispense into the 10 empty tube (Fig. 8).
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LABORATORY 11:
-4
b. Using the same pipette and procedure, aseptically remove 0.1 ml of the 10 bacteriophage
-5
dilution and dispense into the 10 empty tube (Fig. 8).
-3
c. Using the same pipette and procedure, aseptically remove 0.1 ml of the 10 bacteriophage
-4
dilution and dispense into the 10 empty tube (Fig. 8). Discard the pipette in the biowaste container.
4. Using a new sterile 1.0 ml pipette, add 0.5 ml (see Fig. 11H) of E. coli B to the 0.1 ml of diluted
bacteriophage in each of the 3 tubes from step 3 and mix (Fig. 9). Discard the pipette in the biowaste
container.
5. Using a sterile 10.0 ml pipette, add 2.5 ml (see Fig. 11I) of sterile, melted Motility Test medium to the
bacteria-bacteriophage mixture in each of the 3 tubes from step 4 and mix (Fig. 10). Discard the pipette in the
biowaste container.
6. Quickly pour the motility medium-bacteria-bacteriophage mixtures onto separate plates of Trypticase Soy
agar and swirl to distribute the contents over the entire agar surface.
7. Incubate the 3 TSA plates right-side-up at 37 C until the next lab period.
Fig. 8:
Diluting Coliphage T4 for the plaque count experiment.
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LABORATORY 11:
Fig. 9:
Adding the E. coli to the diluted bacteriophages
Fig. 10:
Adding the melted motility medium to the E. coli and bacteriophages
118
LABORATORY 11:
Fig. 11:
A 1.0 ml pipette. Use the blue filler.
Fig. 12:
A 10.0 ml pipette. Use the green filler.
119
LABORATORY 11:
B. VIRAL SPECIFICITY
MATERIALS
Trypticase Soy agar plates (2)
CULTURES
Trypticase Soy broth cultures of 4 unknown bacteria labelled #1, #2, #3, and #4; suspension of Coliphage T4.
PROCEDURE (to be done in groups of three)

1. Using a wax marker, draw a line on the bottom of both Trypticase Soy agar plates dividing them in half.
Number the 4 sectors 1, 2, 3, and 4, to correspond to the 4 unknown bacteria.
2. Draw a circle about the size of a dime in the center of each of the 4 sectors.
3. Using a sterile inoculating loop, streak unknown bacterium #1 on sector 1 of the first Trypticase Soy agar
plate by streaking the loop through the circle you drew. Be careful not to streak into the other half of the
plate.
4.Streak unknown bacterium #2 on sector 2 of the first Trypticase Soy agar plate.
5. Streak unknown bacterium #3 on sector 3 of the second Trypticase Soy agar plate.
6. Streak unknown bacterium #4 on sector 4 of the second Trypticase Soy agar plate.
7. Using a sterile Pasteur pipette and rubber bulb, add 1 drop of Coliphage T4 to each sector in the area
outlined by the circle.
8. Incubate the 2 TSA plates right side up at 37 C until the next lab period.
120
LABORATORY 11:
RESULTS
A. Plaque Count
Observe the 3 plates for plaque formation and make a drawing.
10-4 dilution
10-5 dilution
10-6 dilution
121
LABORATORY 11:
B. Viral Specificity
Make a drawing of your results and state which of the unknowns (#1, #2, #3, or #4) was E. coli.
Which unknown bacterium is E. coli?
_____
How can you tell?
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LABORATORY 11:
LABORATORY
DISCUSSION
1. Define the following: bacteriophage, plaque, and phage typing.
2. Describe the structure of the bacteriophage coliphage T4.
3. Describe the lytic life cycle of bacteriophages.
4. Define viral specificity.
RESULTS
1. Recognize plaques and state their cause.
2. Interpret the results of a viral specificity test using Coliphage T4.
123
124
LABORATORY 12:
ENTEROBACTERIACEAE AND PSEUDOMONAS: PART 1
LABORATORY 12
ISOLATION AND IDENTIFICATION OF
ENTEROBACTERIACEAE AND PSEUDOMONAS:
PART 1
A. Enterobacteriaceae: Fermentative, Gram-Negative, Enteric Bacilli
B. Pseudomonas and Other Non-fermentative, Gram-Negative Bacilli
C. Isolation of Enterobacteriaceae and Pseudomonas
D. Differentiating Between the Enterobacteriaceae and Pseudomonas
E. Identifying the Enterobacteriaceae Using the EnterotubeII
DISCUSSION
A. ENTEROBACTERIACEAE: THE FERMENTATIVE, GRAM-NEGATIVE,
ENTERIC BACILLI
Bacteria belonging to the family Enterobacteriaceae are the most commonly encountered organisms
isolated from clinical specimens. The Enterobacteriaceae is a large diverse family of bacteria belonging to the
order Enterobacteriales in the class Gammaproteobacter of the phylum Proteobacter. Medically important
members of this family are commonly referred to as fermentative, gram-negative, enteric bacilli,
because they are gram-negative rods that can ferment sugars. Many are normal flora of the intestinal tract
of humans and animals while others infect the intestinal tract. Members of this family have the following five
characteristics in common:
1. They are gram-negative rods
2. If motile, they possess a peritrichous arrangement of flagella
3. They are facultative anaerobes
4. They are oxidase negative
5. All species ferment the sugar glucose but otherwise vary widely in their biochemical characteristics.
Forty-four genera and well over 100 species of Enterobacteriaceae have been recognized. Some of the more
common clinically important genera of the family Enterobacteriaceae include:
Salmonella
Shigella
Proteus
Escherichia
Citrobacter
Enterobacter
Serratia
Klebsiella
125
Morganella
Yersinia
Edwardsiella
Providencia
LABORATORY 12:
Several genera of Enterobacteriaceae are associated with gastroenteritis and food-borne disease.
These include:
Salmonella,
Shigella,
certain strains of Escherichia coli, and
certain species of Yersinia.
All intestinal tract infections are transmitted by the fecal-oral route.
Any infection caused by Salmonella is called a salmonellosis. An estimated 2,000,000 3,000,000
people a year in the U.S. become infected with Salmonella and at least 500 die. Since many different animals
carry Salmonella in their intestinal tract, people usually become infected from ingesting improperly
refrigerated, uncooked or undercooked poultry, eggs, meat, or dairy products contaminated with animal
feces.
Enteritis is the most common form of salmonellosis. Symptoms generally appear 6-48 hours after
ingestion of the bacteria and include vomiting, nausea, non-bloody diarrhea, fever, abdominal
cramps, myalgias, and headache. Symptoms generally last from 2 days to 1 week followed by
spontaneous recovery. All species of Salmonella can cause bacteremia but S. typhi, S. paratyphi, and S.
choleraesuis are the most common species to cause bacteremia. S. typhi, frequently disseminates into
the blood causing a severe form of salmonellosis called typhoid fever.
Any Shigella infection is called a shigellosis. Unlike Salmonella, which can infect many different animals,
Shigella only infects humans and other higher primates. Over 23,600 cases of shigellosis were reported in
the U.S. in 1998 but most cases are not reported. An estimated 450,000 are thought to occur each year in the
U.S.
Symptoms of shigellosis include diarrhea, bloody stool, abdominal cramps, and fever. The
incubation period is 1-3 days. Initial profuse watery diarrhea typically appears first as a result of
enterotoxin. Within 1-2 days this progresses to abdominal cramps, with or without bloody stool. Classic
shigellosis presents itself as lower abdominal cramps and stool abundant with blood and pus develops as
the Shigella invade the mucosa of the colon.
While Escherichia coli is one of the dominant normal flora in the intestinal tract of humans and
animals, some strains can cause infections of the intestines.
Enterotoxigenc E. coli (ETEC) produce enterotoxins that cause the loss of sodium ions and water
from the small intestines resulting in a watery diarrhea. Over half of all travelers' diarrhea is due to
ETEC; almost 80,000 cases a year in the U.S.
Enteropathogenic E. coli (EPEC) causes n endemic diarrhea in areas of the developing world,
especially in infants younger than 6 months. The bacterium disrupts the normal microvilli (def) on the
epithelial cells of the small intestines resulting in maladsorbtion and diarrhea.
Enteroaggregative E. coli (EAEC) is a cause of persistant diarrhea in developing countries. It
probably causes diarrhea by adhering to mucosal epithelial cells of the small intestines and
interfering with their function.
Enteroinvasive E. coli (EIEC) invade and kill epithelial cells of the large intestines causing a
dysentery-type syndrome similar to Shigella common in underdeveloped countries.
Enterohemorrhagic E. coli (EHEC), such as E. coli 0157:H7, produce a shiga-like toxin that kills
epithelial cells of the large intestines causing hemorrhagic colitis, a bloody diarrhea. In rare cases,
the shiga-toxin enters the blood and is carried to the kidneys where, usually in children, it damages
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LABORATORY 12:
vascular cells and causes hemolytic uremic syndrome. E. coli 0157:H7 is thought to cause more than
20,000 infections and up to 250 deaths per year in the U.S.
Diffuse aggregative E. coli (DAEC) causes watery diarrhea in infants 1-5 years of age. They
stimulate elongation of the microvilli on the epithelial cells lining the small intestines.
Several species of Yersinia, such as Y. enterocolitica and Y. pseudotuberculosis are also causes of
diarrheal disease.
Many other genera of the family Enterobacteriaceae are normal flora of the intestinal tract and are
considered opportunistic pathogens. The most common genera of Enterobacteriaceae causing
opportunistic infections in humans are:
Escherichia coli,
Proteus,
Enterobacter,
Klebsiella,
Citrobacter, and
Serratia.
They act as opportunistic pathogens when they are introduced into body locations where they are not
normally found, especially if the host is debilitated or immunosuppressed. They all cause the same types of
opportunistic infections, namely:
urinary tract infections,
wound infections,
pneumonia, and
septicemia.
These normal flora gram-negative bacilli, along with gram-positive bacteria such as Enterococcus species
(see Lab 14) and Staphylococcus species (see Lab 15), are the leading cause of hospital-acquired or
nosocomial infections. The four most common gram-negative bacteria causing nosocomial infections are
Escherichia coli , Pseudomonas aeruginosa (discussed below), Enterobacter species, and Klebsiella
pneumoniae. Collectively, these four bacteria accounted for 32 percent of all nosocomial infections in the
U.S. between 1990 and 1996. There are over two million nosocomial infections per year in the U.S.
The most common infection caused by these opportunistic Enterobacteriaceae is a urinary tract
infection (UTI). UTIs account for more than 7,000,000 physician office visits per year in the U.S. Among
the non-hospitalized and non-debilitated population, UTIs are more common in females because of their
shorter urethra and the closer proximity between their anus and the urethral opening. (Over 20 percent of
women have recurrent UTIs.) However, anyone can become susceptible to urinary infections in the
presence of predisposing factors that cause functional and structural abnormalities of the urinary tract.
These abnormalities increase the volume of residual urine and interfere with the normal clearance of
bacteria by urination. Such factors include prostate enlargement, sagging uterus, expansion of the uterus
during pregnancy, paraplegia, spina bifida, scar tissue formation, and catheterization. Between 35 and 40
percent of all nosocomial infections, about 900,000 per year in the U.S., are UTIs and are usually
associated with catheterization.
E. coli causes around 80 percent of all uncomplicated urinary tract infections (UTIs) and more than
50 percent of nosocomial UTIs. Staphylococcus saprophyticus (see Lab 15) causes 10 - 20 percent of
uncomplicated UTIs and approximately 5 percent of UTIs are caused by other gram-negative enterics such
as species of Proteus and Klebsiella or by Enterococcus species (see Lab 14
The traditional laboratory culture standard for a UTI has been the presence of more than 100,000 CFUs
(colony-forming units; see Lab 4) per milliliter (ml) of midstream urine, or any CFUs from a catheter-obtained
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LABORATORY 12:
urine sample. More recently, this has been modified and counts of as few as 1000 colonies of a single type
per ml or as little as 100 coliforms per ml are now considered as indicating a UTI.
Wound infections are due to fecal contamination of external wounds or a result of wounds that cause
trauma to the intestinal tract (surgical wounds, gunshot wounds, etc.).
Although they sometimes cause pneumonia, the Enterobacteriaceae account for less than 5% of the
bacterial pneumonias requiring hospitalization.
Gram-negative septicemia is a result of these opportunistic bacteria getting into the blood. They are
usually introduced into the blood from some other infection site, such as an infected kidney, wound, or lung.
There are approximately 750,000 cases of septicemia per year in the U.S. and the mortality rate is between
20 and 50 percent. Over 210,000 people a year in the U.S. die from septic shock. Approximately 45 percent
of the cases of septicemia are due to gram-negative bacteria. Klebsiella, Proteus, Enterobacter, Serratia, and
E. coli, are all common Enterobacteriaceae causing septicemia. (Another 45 percent are a result of grampositive bacteria (see Labs 14 and 15) and 10 percent are due to fungi, mainly the yeast Candida.
In the outer membrane of the gram-negative cell wall, the lipid A moiety of the lipopolysaccharide
functions as an endotoxin (see Fig 4). Endotoxin indirectly harms the body when massive amounts are
released during severe gram-negative infections. This, in turn, causes an excessive cytokine response.
1. The LPS released from the outer membrane of the gram-negative cell wall first binds to a LPSbinding protein circulating in the blood and this complex, in turn, binds to a receptor molecule
(CD14) found on the surface of body defense cells called macrophages (see Fig. 1) located in
most tissues and organs of the body.
2. This is thought to promote the ability of the toll-like receptor TLR-4 to respond to the LPS,
triggering the macrophages to release various defense regulatory chemicals called cytokines,
including tumor necrosis factor-alpha (TNF-alpha), interleukin-1 (IL-1), interleukin-6 (IL-6), and
interleukin-8 (IL-8), and platelet-activating factor (PAF) (see Fig. 1). The cytokines then bind to
cytokine receptors on target cells and initiate inflammation and activate both the complement
pathways and the coagulation pathway (see Fig. 1).
3. The complex of LPS and LPS binding protein can also attach to molecules called CD14 on the
surfaces of phagocytic white blood cells called neutrophils causing them to release proteases and
toxic oxygen radicals for extracellular killing. Chemokines such as interleukin-8 (IL-8) also
stimulate extracellular killing. In addition, LPS and cytokines stimulate the synthesis of a
vasodilator called nitric oxide.
During minor local infections with few bacteria present, low levels of LPS are released leading to
moderate cytokine production by the monocytes and macrophages and in general, promoting body
defense by stimulating inflammation and moderate fever, breaking down energy reserves to supply
energy for defense, activating the complement pathway and the coagulation pathway, and generally
stimulating immune responses (see Fig. 1). Also as a result of these cytokines, circulating phagocytic
white blood cells such as neutrophils and monocytes stick to the walls of capillaries, squeeze out and
enter the tissue, a process termed diapedesis. The phagocytic white blood cells such as neutrophils then
kill the invading microbes with their proteases and toxic oxygen radicals.
However, during severe systemic infections with large numbers of bacteria present, high levels of LPS
are released resulting in excessive cytokine production by the monocytes and macrophages and this can
harm the body (see Fig. 2). In addition, neutrophils start releasing their proteases and toxic oxygen
radicals that kill not only the bacteria, but the surrounding tissue as well. Harmful effects include high
fever, hypotension, tissue destruction, wasting, acute respiratory distress syndrome (ARDS),
disseminated intravascular coagulation (DIC), and damage to the vascular endothelium resulting in
shock, multiple system organ failure (MOSF), and often death.
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LABORATORY 12:
This excessive inflammatory response is referred to as Systemic Inflammatory Response Syndrome or

SIRS. Death is a result of what is called the shock cascade. The sequence of events is as follows:
Systemic Inflammatory Response Syndrome (SIRS): the Shock Cascade.
During a severe systemic infection, an excessive inflammatory response triggered by
overproduction of cytokines such as TNF-alpha, IL-1, IL-6, IL-8, and PAF often occurs. This leads to
the following sequence of cytokine-induced events:
Blood vessels dilate and phagocytic WBCs called neutrophils adhere to capillary walls in massive
amounts. Chemokines such as IL-8 activate neutrophils causing them to release proteases and
toxic oxygen radicals while still in the blood vessels. These are the same toxic chemicals
neutrophils use to kill microbes, but now they are dumped onto the vascular endothelial cells to
which the neutrophils have adhered. These events result in damage to the capillary walls and
leakage of blood.
Prolonged vasodilation and increased capillary permeability causes plasma to leave the
bloodstream and enter the tissue. Prolonged vasodilation also leads to decreased vascular
resistance that, in turn, results in a drop in blood pressure (hypotension) and reduced perfusion of
blood through tissues and organs.
At high levels of TNF, vascular smooth muscle tone and myocardial contractility are inhibited.
This results in a marked drop in blood pressure. Cytokine-induced overproduction of nitric oxide
(NO) by cardiac muscle cells and vascular smooth muscle cells can also lead to heart failure.
Damage to the capillaries and prolonged vasodilation result in blood and plasma leaving the
bloodstream and entering the tissue. This can lead to a decreased volume of circulating blood
(hypovolemia).
Activation of the blood coagulation pathway and concurrent down-regulation of anticoagulation
mechanisms cause clots to form within the blood vessels throughout the body. This is called
disseminated intravascular coagulation (DIC). Activation of neutrophils also leads to their
accumulation and plugging of the vasculature. This further limits the perfusion of blood and
oxygen through tissues and organs.
The increased capillary permeability and injury to capillaries in the alveoli of the lungs results in
acute inflammation, pulmonary edema , and loss of gas exchange. This is called acute respiratory
distress syndrome (ARDS).
Reduced perfusion and capillary damage in the liver results in impaired liver function and a failure
to maintain normal blood glucose levels. Overuse of glucose by muscle and a failure of the liver
to replace glucose can lead to a drop in blood glucose level below what is needed to sustain life.
Reduced perfusion also leads to kidney and bowel injury.
The combination of hypotension, hypovolemia, DIC, ARDS, and loss of perfusion leads to
acidosis. A blood pH range between 6.8 and 7.8 is needed for normal cellular metabolic activities
in humans. Changes in the pH of arterial blood extracellular fluid outside this range lead to
irreversible cell damage.
Collectively, this cascade of hypotension, hypovolemia, DIC, ARDS, loss of perfusion, drop in blood
glucose level, acidosis, and cardiac failure leads to irreversible septic shock, multiple system organ
failure (MSOF), and death.
The gram-negative cell wall also contains surface proteins that function as adhesins, allowing the
bacterium to adhere intimately to host cells and other surfaces in order to colonize and resist flushing.
Some gram-negative bacteria also produce invasins, allowing some bacteria to penetrate host cells. Pili,
flagella, capsules, and exotoxins also play a role in the virulence of some Enterobacteriaceae
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LABORATORY 12:
Many of the Enterobacteriaceae also carry R (resistance) plasmids (see Lab 21). These plasmids are
small pieces of circular non-chromosomal DNA that may code for multiple antibiotic resistance. In
addition, the plasmid may code for a sex pilus, enabling the bacterium to pass R plasmids to other
bacteria by conjugation. As mentioned earlier, there are over 2,000,000 nosocomial infections per year
in the U.S. Between 50 and 60 percent of the bacteria causing these infections are antibiotic resistant.
B. PSEUDOMONAS AND OTHER NON-FERMENTATIVE GRAMNEGATIVE BACILLI

Non-fermentative gram-negative bacilli refer to gram-negative rods or coccobacilli that cannot ferment
sugars. The non-fermentative gram-negative bacilli are often normal inhabitants of soil and water. They may
cause human infections when they colonize immunosuppressed individuals or gain access to the body
through trauma. However, less than one-fifth of the gram-negative bacilli isolated from clinical specimens are
non-fermentative bacilli. By far, the most common gram-negative, non-fermentative rod that causes human
infections is Pseudomonas aeruginosa. Pseudomonas belongs to the family Pseudomonadaceae in the order
Pseudomonadales in the class Gammaproteobacter of the phylum Proteobacter.
Pseudomonas aeruginosa is also an opportunistic pathogen. It is a common cause of nosocomial
infections and can be found growing in a large variety of environmental locations. In the hospital environment,
for example, it has been isolated from drains, sinks, faucets, water from cut flowers, cleaning solutions,
medicines, and even disinfectant soap solutions. It is especially dangerous to the debilitated or
immunocompromised patient.
Like the opportunistic Enterobacteriaceae, Pseudomonas is a gram-negative rod, it is frequently found in
small amounts in the feces, and it causes similar opportunistic infections: urinary tract infections, wound
infections, pneumonia, and septicemia. P. aeruginosa is responsible for 12 percent of hospital-acquired
pneumonia cases, 10 percent of the cases of septicemia, and 16 percent of nosocomial pneumonia cases. In
addition, P. aeruginosa is a significant cause of burn infections with a 60 percent mortality rate. It also
colonizes and chronically infects the lungs of people with cystic fibrosis. Like other opportunistic gramnegative bacilli, Pseudomonas aeruginosa also releases endotoxin and frequently possesses R-plasmids. A
number of other species of Pseudomonas have also been found to cause human infections.
Other non-fermentative gram-negative bacilli that are sometimes opportunistic pathogens in humans
include Acinetobacter, Aeromonas, Alcaligenes, Eikenella, Flavobacterium, and Moraxella.
C. ISOLATION OF ENTEROBACTERIACEAE AND PSEUDOMONAS

To isolate Enterobacteriaceae and Pseudomonas, specimens from the infected site are plated out on any
one of a large number of selective and differential media such as EMB agar (used in Lab 3), Endo agar,
Deoxycholate agar, MacConkey agar, Hektoen Enteric agar, and XLD agar.
XLD agar is selective for gram-negative bacteria. In addition, different gram-negative bacilli, due to their
biochemical reactions, produce different appearing colonies. Typical reactions for some of the
Enterobacteriaceae and Pseudomonas are shown below:
1. Escherichia coli: flat yellow colonies; some strains may be inhibited.
2. Enterobacter and Klebsiella: mucoid yellow colonies.
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LABORATORY 12:
3. Proteus: red to yellow colonies; may have black centers.
4. Salmonella: usually red colonies with black centers
5. Shigella and Pseudomonas: red colonies without black centers
The biochemical reasons for these color reactions will be discussed in Lab 13. Some species and
subspecies, however, may not show typical reactions.
Pseudosel agar is selective for Pseudomonas aeruginosa and also stimulates P. aeruginosa to
produce its characteristic pigment as well as fluorescent products. Pseudomonas aeruginosa will typically
produce a green to blue water-soluble pigment on this agar and will also fluoresce when the plate is placed
under a short wavelength ultraviolet light.
D. DIFFERENTIATING BETWEEN THE ENTEROBACTERIACEAE

AND PSEUDOMONAS
Once the gram-negative rod is isolated, a number of tests can be performed to determine if it is one of the
Enterobacteriaceae or if it is Pseudomonas. Several of these tests are listed below:
1. Production of the enzyme oxidase. The oxidase test is based on the bacterial production of an
oxidase enzyme. Cytochrome oxidase, in the presence of oxygen, oxidizes the para-amino
dimetheylanaline oxidase test reagent in a Taxo-N disc to form a rose-colored compound
indophenol. The Enterobacteriaceae are oxidase-negative; Pseudomonas aeruginosa and most
other non-fermentative gram-negative rods are oxidase-positive. The procedure for the oxidase test
is described later in this lab.
2. Fermentation of glucose. All of the Enterobacteriaceae ferment the sugar glucose;
Pseudomonas aeruginosa and other non-fermentative gram-negative rods will not.
3. Pigment production. None of the Enterobacteriaceae produces pigment at 37 C; Pseudomonas
aeruginosa produces a green to blue, water-soluble pigment called pyocyanin. It also produces a
product called fluorescein that will fluoresce under short wavelength (254nm) ultraviolet light.
Pseudosel agar can be used to stimulate the production of pigment and fluorescent products.
4. Odor. Most of the Enterobacteriaceae have a rather foul smell; Pseudomonas aeruginosa
produces a characteristic fruity or grape juice-like aroma due to production of an aromatic compound
called aminoacetophenone.
Some common biotypes of Pseudomonas as well as all members of the Enterobacteriaceae can also be
identified by means of biochemical tests found in commercially produced systems such as the API-20E
System or the EnterotubeII (discussed below).
E. IDENTIFYING THE ENTEROBACTERIACEAE USING THE

ENTEROTUBEII SYSTEM
A number of techniques can be used for the identification of specific species and subspecies of
Enterobacteriaceae. Speciation is important because it provides data regarding patterns of susceptibility to
antimicrobial agents and changes that occur over a period of time. It is also essential for epidemiological
studies such as determination of nosocomial infections and their spread.
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LABORATORY 12:
In an effort to simplify the speciation of the Enterobacteriaceae and reduce the amount of prepared media
and incubation space needed by the clinical lab, a number of self-contained multi-test systems have been
commercially marketed. Some of these multi-test systems have been combined with a computer-prepared
manual to provide identification based on the overall probability of occurrence for each of the biochemical
reactions. In this way, a large number of biochemical tests can economically be performed in a short period of
time, and the results can be accurately interpreted with relative ease and assurance.
The EnterotubeII is a self-contained, compartmented plastic tube containing 12 different agars
(enabling the performance of a total of 15 standard biochemical tests) and an enclosed inoculating
wire (Fig. 1). After inoculation and incubation, the resulting combination of reactions, together with a
Computer Coding and Identification System (CCIS), allows for easy identification. The various biochemical
reactions of the EnterotubeII and their correct interpretation are discussed in Lab 13. Although it is designed
to identify members of the bacterial family Enterobacteriaceae, it will sometimes also identify common
biotypes of Pseudomonas and other non-fermentative gram-negative bacilli.
Fig. 1:
An Enterotube II
ORGANISMS (Trypticase Soy agar plate cultures)

Possible unknowns include:
Escherichia coli
Enterobacter aerogenes
Enterobacter cloacae
Proteus mirabilis
Proteus vulgaris
Salmonella enteritidis
Klebsiella pneumoniae
Citrobacter freundii
CAUTION: TREAT EACH UNKNOWN AS A PATHOGEN! Inform your instructor of any spills or
accidents. WASH AND SANATIZE YOUR HANDS WELL before you leave the lab.
MATERIALS
Taxo N disk, alcohol, dropper bottle of distilled water, platinum inoculating loop, and either a plate of XLD
agar and an EnterotubeII or a plate of Pseudosel agar and an EnterotubeII
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LABORATORY 12:

Each pair will be given one of the above unknowns. You will determine its identity doing the tests below.
1. Using the Trypticase Soy agar culture of your unknown, first perform an oxidase test as follows:
a. Using alcohol-flamed forceps, remove a Taxo-N disc and moisten it with a drop of sterile distilled water.
b. Place the moistened disc on the colonies of the Trypticase Soy agar plate culture of your unknown.
c. Using a sterile swab, scrape off some of the colonies and spread them on the Taxo-N disc.
In the immediate test, oxidase-positive reactions will turn a rose color within 30 seconds. This reaction only lasts
a couple of minutes. In the delayed test, oxidase-positive colonies within 10 mm of the Taxo-N disc will turn black
within 20 minutes and will remain black.
Pseudomonas aeruginosa and most other non-fermentative, gram-negative bacilli are oxidase-positive; all
of the Enterobacteriaceae are oxidase-negative.
Record your oxidase test results in the Results section of Lab 13.
2. Perform a gram stain on your unknown (see Lab 6). All of the Enterobacteriaceae as well as Pseudomonas are
gram-negative bacilli. Record the results of your gram stain in the Results section of Lab 13.
3. If your unknown is oxidase-negative, do the following inoculations:
a. Streak your unknown for isolation on a plate of XLD agar (see Fig. 2). Incubate at 37 C.
b. Inoculate an EnterotubeII as follows:
1. Remove both caps of the EnterotubeII and with the straight end of the inoculating wire, pick
off the equivalent of a colony from your unknown plate. A visible inoculum should be seen on the
tip and side of the wire.
2. Inoculate the EnterotubeII by grasping the bent-end of the inoculating wire, twisting it, and
withdrawing the wire through all 12 compartments using a turning motion.
3. Reinsert the wire into the tube (use a turning motion) through all 12 compartments until the
notch on the wire is aligned with the opening of the tube. (The tip of the wire should be seen in the
citrate compartment.) Break the wire at the notch by bending. Do not discard the wire yet.
4. Using the broken off part of the wire, punch holes through the cellophane which covers the air
inlets located on the rounded side of the last 8 compartments. Your instructor will show you
their correct location. Discard the broken off wire in the disinfectant container.
5. Replace both caps and incubate the EnterotubeII on its flat surface at 37 C.
4. If your unknown is oxidase-positive, do the following inoculations:

a. Streak your unknown for isolation on a plate of Pseudosel agar (see Lab 2, Fig 4). Incubate at 37 C.
b. Inoculate an EnterotubeII as described above in step 3b.
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LABORATORY 12:
Lab 2, Fig. 4:

Sterilize the loop.

the loop.

Sterilize the loop.
Lab 2, Fig. 5:

Sterilize the loop.

Sterilize the loop.
Continued on next page.
134

Sterilize the loop.
LABORATORY 12:

Sterilize the loop

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LABORATORY 12:
LABORATORY 12
A.ENTEROBACTERIACEAE: FERMENTATIVE, GRAM-NEGATIVE, ENTERIC BACILLI

1. Name the bacterial family to which the most commonly encountered organisms isolated from clinical
specimens belong.
2. List five characteristics used to place bacteria into the family Enterobacteriaceae.
3. State what infections are caused by Salmonella and by Shigella and how they are transmitted to humans.
4. Name four strains of Escherichia coli that may infect the gastrointestinal tract.
5. Name five genera of Enterobacteriaceae considered as common opportunistic pathogens, state their
normal habitat, and list four common types opportunistic infections that they all may cause.
6. Name several predisposing factors that make one more susceptible to urinary tract infections.
7. In terms of CFUs, state the laboratory culture standard for a urinary tract infection.
8. Define nosocomial infection.
9. State the significance of endotoxins in infections caused by many of the Enterobacteriaceae.
10. Discuss the significance of R-plasmids in our attempts to treat infections caused by the
Enterobacteriaceae.
B. PSEUDOMONAS AND OTHER NON-FERMENTATIVE, GRAM-NEGATIVE BACILLI

1. Name the most common non-fermentative gram-negative rod that infect humans and list five types of
opportunistic infections it may cause.
C. ISOLATION OF ENTEROBACTERIACEAE AND PSEUDOMONAS

1. State the usefulness of XLD agar and Pseudosel agar for the isolation of Enterobacteriaceae and
Pseudomonas.
D. DIFFERENTIATING BETWEEN THE ENTEROBACTERIACEAE AND PSEUDOMONAS

1. State how to differentiate Pseudomonas aeruginosa from the Enterobacteriaceae using the following tests:
a. oxidase test
b. fermentation of glucose
c. production of pigment and fluorescent products
d. odor
E. IDENTIFYING THE ENTEROBACTERIACEAE USING THE ENTEROTUBEII

1. Briefly describe the EnterotubeII.
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LABORATORY 13:
LABORATORY 13
ENTEROBACTERIACEAE AND PSEUDOMONAS
PART 2: RESULTS OF LAB 12
A. The Oxidase Test
B. The Gram Stain
C. Isolation of Enterobacteriaceae on XLD Agar
D. Isolation and Identification of Pseudomonas on Pseudosel Agar
E. Identifying Members of the Enterobacteriaceae with the Enterotube II
F. Bacteriological Examination of Water: Coliform Counts
In Lab 12, you learned how to isolate members of the Enterobacteriaceae, differentiate them from Pseudomonas,
and identify them by biochemical testing. Today, you will learn how to interpret the results of the various media
you inoculated in Lab 12.
HANDLE ALL BACTERIA AS PATHOGENS ! WASH AND SANATIZE

YOUR HANDS WELL WHEN FINISHED!
A. THE OXIDASE TEST
In Lab 12 you performed on your unknown, an oxidase test using a Taxo N disc. The oxidase test is based on
the bacterial production of an oxidase enzyme. Cytochrome oxidase, in the presence of oxygen, oxidizes the
para-amino dimetheylanaline oxidase test reagent in a Taxo-N disc.
In the immediate test, oxidase-positive reactions will turn a rose color within 30 seconds. Oxidasenegative will not turn a rose color. This reaction only lasts a couple of minutes.
In the delayed test, oxidase-positive colonies within 10 mm of the Taxo-N disc will turn black within 20
minutes and will remain black. If the bacterium is oxidase-negative, the growth around the disc will not turn
black.
Pseudomonas aeruginosa and most other non-fermentative, gram-negative bacilli are oxidase-positive; all of
the Enterobacteriaceae are oxidase-negative. Record the results of your oxidase test in the Results section of
today's lab if you did not do so last time.
B. THE GRAM STAIN

In Lab 12 you also did a gram stain on your unknown. Record your gram stain results in the Results section of
today's lab if you did not do so last time.
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LABORATORY 13:
C. ISOLATION OF ENTEROBACTERIACEAE ON XLD AGAR

In LAB 12, if the oxidase test done on your unknown was negative, you inoculated a plate of XLD agar. Xylose
Lysine Desoxycholate (XLD) agar contains sodium desoxycholate, which inhibits the growth of gram-positive
bacteria but permits the growth of gram-negatives. It also contains the sugars lactose and sucrose, the amino
acid L-lysine, sodium thiosulfate, and the pH indicator phenol red.
If the gram-negative bacterium ferments lactose and/or sucrose, acid end products will be produced and cause
the colonies and the phenol red in the agar around the colonies to turn yellow. If lactose and sucrose are not
fermented but the amino acid lysine is broken down, alkaline end products will cause the phenol red in the agar
around the colonies to turn a deeper red. If hydrogen sulfide is produced from thiosulfate reduction, part or all of the
colony will appear black. Well-isolated colonies are usually needed for good results. Typical colony morphology on
XLD agar is as follows:
1. Escherichia coli: flat yellow colonies; some strains may be inhibited.
2. Enterobacter and Klebsiella: mucoid yellow colonies.
3. Proteus: red to yellow colonies; may have black centers.
4. Salmonella: usually red colonies with black centers
5. Shigella and Pseudomonas: red colonies without black centers
Keep in mind, however, that some species and subspecies do not show typical reactions.
Record the results of your XLD agar in the Results section of today's lab.
D. ISOLATION AND IDENTIFICATION OF PSEUDOMONAS

ON PSEUDOSEL AGAR
As was mentioned in Lab 12, a number of tests can be performed to determine if your unknown is Pseudomonas.
These tests include:
1. Production of the enzyme oxidase. The oxidase test is based on the bacterial production of an oxidase
enzyme. Cytochrome oxidase, in the presence of oxygen, oxidizes the para-amino dimetheylanaline oxidase
test reagent in a Taxo-N disc to form a rose-colored compound indophenol. None of the
Enterobacteriaceae produce oxidase; Pseudomonas aeruginosa and most other non-fermentative gramnegative rods are oxidase-positive.
2. Fermentation of glucose. All of the Enterobacteriaceae ferment the sugar glucose; Pseudomonas
aeruginosa and other non-fermentative gram-negative rods will not.
3. Pigment production. None of the Enterobacteriaceae produces pigment at 37 C; Pseudomonas
aeruginosa produces a green to blue, water-soluble pigment called pyocyanin.
4. Fluoresces under ultraviolet light. Pseudomonas aeruginosa produces a product called fluorescein that
will fluoresce under short wavelength (254nm) ultraviolet light.
5. Odor. Most of the Enterobacteriaceae have a rather foul smell; Pseudomonas aeruginosa produces a
characteristic fruity or grape juice-like aroma due to production of an aromatic compound called
aminoacetophenone.
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LABORATORY 13:
(Some common biotypes of Pseudomonas as well as all members of the Enterobacteriaceae can also be identified
by means of biochemical tests found in commercially produced systems such as the EnterotubeII, as will be
discussed below.)
We will now identify one of the unknowns as Pseudomonas aeruginosa by means of the above-mentioned
tests.
In Lab 12, if your oxidase test was positive, you inoculated a plate of Pseudosel agar with your unknown. Record
your results under Results, part A.
1. Growth on Pseudosel agar (PSA). Pseudosel agar (PSA) contains cetrimide that inhibits most bacteria
other than Pseudomonas aeruginosa.
2. Oxidase positive. Pseudomonas aeruginosa will show a positive immediate oxidase test and a positive
delayed oxidase test with the Taxo-N).
3. Production of a green to blue, water-soluble pigment on the Pseudosel agar plate. Pseudomonas
aeruginosa produces a green to blue, water-soluble pigment called.
4. Production of fluorescent products on the Pseudosel agar plate. Pseudomonas aeruginosa produces a
product called fluorescein that will fluoresce under short wavelength (254nm) ultraviolet light.
5. Fruity odor. Pseudomonas aeruginosa produces a characteristic fruity or grape juice-like aroma due to
production of an aromatic compound called aminoacetophenone. Lift the lid of the PSA and, using your hand,
fan towards your nose.
6. Glucose fermentation. Unlike the Enterobacteriaceae, Pseudomonas does not ferment glucose.
Observe the first agar well in the Enterotube, the one labelled "glucose." If the phenol red remains red or
orange then acid was not produced indicating no glucose fermentation.
7. Since some common biotypes of Pseudomonas can be identified with the EnterotubeII, we will also see
how those results come out. Keep in mind, however, that the EnterotubeII is designed for identifying
members of the bacterial family Enterobacteriaceae and not necessarily non-fermentative gram-negative
bacilli such as Pseudomonas.
E. IDENTIFYING MEMBERS OF THE ENTEROBACTERIACEAE

WITH THE ENTEROTUBE II
The Enterotube II contains 12 different agars that can be used to carry out 15 standard biochemical tests. Interpret
the results of your Enterotube II using the instructions below. For more detail on the 15 biochemical tests in the
Enterotube II, see Table 12-A.
1. Interpret the results of glucose fermentation in compartment 1.
any yellow = +; red or orange = If positive, circle the number 2 under glucose on your Results page.
2. Interpret the results of gas production also in compartment 1.
wax lifted from agar = +; wax not lifted from agar = If positive, circle the number 1 under gas on your Results page.
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LABORATORY 13:
3. Interpret the results of lysine decarboxylase in compartment 2.
any purple = +; yellow = If positive, circle the number 4 under lysine on your Results page.
4. Interpret the results of ornithine decarboxylase in compartment 3.
any purple = +; yellow = If positive, circle the number 2 under ornithine on your Results page.
5. Interpret the results of H2S production in compartment 4.
true black = +; beige = If positive, circle the number 1 under H2S on your Results page.
6. Indole production also in compartment 4. Do not interpret the indole test at this time. Add Kovac's reagent
only after all other tests have been read (see step 16 below).
7. Interpret the results of adonitol fermentation in compartment 5.
any yellow = +; red or orange = If positive, circle the number 2 under adonitol on your Results page.
8. Interpret the results of lactose fermentation in compartment 6.
any yellow = +; red or orange = If positive, circle the number 1 under lactose on your Results page.
9. Interpret the results of arabinose fermentation in compartment 7.
any yellow = +; red or orange = If positive, circle the number 4 under arabinose on your Results page.
10. Interpret the results of sorbitol fermentation in compartment 8.
any yellow = +; red or orange = If positive, circle the number 2 under sorbitol on your Results page.
11. Voges-Praskauer test in compartment 9. This test is not used unless a final VP confirming test is later
called for. Skip this compartment.
12. Interpret the results of dulcitol fermentation in compartment 10.
yellow = +; any other color = If positive, circle the number 1 under dulcitol on your Results page.
13. Interpret the results of PA deaminase also in compartment 10.
black or smoky gray = +; any other color = If positive, circle the number 4 under PA on your Results page.
14. Interpret the results of urea hydrolysis in compartment 11.
Pink, red or purple = +; beige = If positive, circle the number 2 under urea on your Results page.
15. Interpret the results of citrate utilization in compartment 12.
any blue = +; green = If positive, circle the number 1 under citrate on your Results page.
16. Using a hot inoculating loop, burn a small hole in the top of compartment 4 (H2S/Indole). Using a sterile
Pasteur pipette, add 2-3 drops of Kovac's reagent to the indole test by dropping it through the hole.
pink or red = +; yellow = If positive, circle the number 4 under indole on your Results page.
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LABORATORY 13:
17. Add all the circled numbers in each bracketed section and enter each sum in its box provided below
the arrows on the Enterotube II drawing on your Results page.
18. Locate the 5-digit number in the Computer Coding and Identification System (CCIS) booklet and find
the best identification in the column entitled "ID Value." (Should more than one organism be listed, the
confirmatory tests indicated in the CCIS would normally then have to be performed. In addition, an
identification of Salmonella or Shigella would usually be confirmed by direct serologic testing as will be
described in Lab 17.)
If there are any problems, consult your instructor.
19. Every student should do a complete set of results for three different unknowns today:
Pseudomonas aeruginosa and 2 different Enterobacteriaceae.
F. BACTERIOLOGICAL EXAMINATION OF WATER: COLIFORM COUNTS

The identification of lactose-fermenting gram-negative rods belonging to the bacterial family Enterobacteriaceae
(bacteria commonly referred to as coliforms) in water is often used to determine if water has been fecally
contaminated and, therefore, may contain disease-causing pathogens transmitted by the fecal-oral route. The
procedure for this is given in Appendix D.
TABLE 12-A
Interpretation of the Enterotube II
Compartment
Reaction
Negative
Positive
glucose
fermentation
red/orange
yellow
gas
production
wax not
lifted
wax
lifted
Remarks: Glucose - Any degree of yellow is positive. Acid end products from glucose
fermentation turn the pH indicator from red (alkaline) to yellow (acid).
Remarks: Gas - Positive is a definite and complete separation of the white wax overlay from
the surface of the glucose medium. Detects gas from glucose fermentation.
Compartment
Reaction
Negative
Positive
lysine
decarboxylase
activity
yellow
purple
Remarks: Any degree of purple is positive. Alkaline end products from the decarboxylation
of lysine changes the pH indicator from pale yellow (acid) to purple (alkaline).
141
LABORATORY 13:
TABLE 12-A, continued
Compartment
Reaction
Negative
Positive
ornithine
decarboxylase
activity
yellow
purple
Remarks: Any degree of purple is positive. Alkaline end products from the decarboxylation
of ornithine changes the pH indicator from pale yellow (acid) to purple (alkaline).
Compartment
Reaction
Negative
Positive
H2S
production
beige
black
indole
production
(done last)
colorless
red
Remarks: H2S - Only a true black is positive. Reduction of thiosulfate produces H2S which
reacts with iron salts to produce black FeS.
Remarks: Indole - This test is not interpreted until all other compartments have been read.
Kovac's Reagent must be added before reading. Indole, produced from the breakdown of
tryptophan, reacts with Kovac's reagent turning it red.
Compartment
Reaction
Negative
Positive
adonitol
fermentation
red/orange
yellow
Remarks: Any degree of yellow is positive. Acid end products from adonitol fermentation turn
the pH indicator from red (alkaline) to yellow (acid).
Compartment
Reaction
Negative
Positive
lactose
fermentation
red/orange
yellow
Remarks: Any degree of yellow is positive. Acid end products from lactose fermentation turn
142
LABORATORY 13:

Compartment
Reaction
Negative
Positive
arabinose
fermentation
red/orange
yellow
Remarks: Any degree of yellow is positive. Acid end products from arabinose fermentation turn
Compartment
Reaction
Negative
Positive
sorbitol
fermentation
red/orange
yellow
Remarks: Any degree of yellow is positive. Acid end products from sorbitol fermentation turn
Compartment
Reaction
Negative
Positive
9
not normally
used
VogesProskauer
colorless
red
Remarks: This test is not used unless required later as a confirmatory test. Acetoin produced
during the production of butylene glycol from glucose fermentation reacts with the added
reagents KOH and alphanaphthol and turns red.
Compartment
Reaction
Negative
Ppositive
10
dulcitol
fermentation
not
yellow
yellow
10
phenylalanine
deaminase
activity
not
black/
smoky gray
black/
smoky gray
Remarks: Dulcitol - Yellow or pale yellow is positive. Any other color is negative. Acid from
dulcitol fermentation turns the pH indicator from green (alkaline) to yellow (acid).
Remarks: PA - Pyruvic acid produced from deamination of phenylalanine reacts with ferric
salts in the medium turning it black.
143
LABORATORY 13:
Compartment
Reaction
Negative
Positive
11
urea
hydrolysis
beige
red/
purple
Remarks: Hydrolysis of urea forms ammonia which causes the pH indicator to turn from
yellow (acid) to pink/red/purple (alkaline).
Compartment
Reaction
Negative
Positive
12
citrate
utilization
green
blue
Remarks: Any degree of blue is positive. Utilization of citrate produces alkaline products
turning the pH indicator from green (acid) to blue (alkaline).
144
LABORATORY 13:
RESULTS
A. If the oxidase test performed on the unknown on Lab 12 was positive, record the results here.
1. Oxidase test (Taxo Ndisc)
Results (+ or -)
Description of
immediate test
Description of delayed
test
2. Gram stain
Gram reaction
(purple = +; red = -)
Shape
4. Growth on Pseudosel agar

Growth (+ or -)
Conclusion
145
LABORATORY 13:
5. Pigment on Pseudosel
Pigment (+ or -)
Color and solubility of
pigment
6. Fluorescence on Pseudosel agar under ultraviolet light

Fluorescence
(+ or -)
7. Odor on Pseudosel agar

Description of
odor
8. Enterotube II
IDENTITY OF ORGANISM
_________________________________________
146
LABORATORY 13:
B. If the oxidase test performed on the unknown on Lab 12 was negative, record the results here.
Results (+ or -)
Description of immediate
test
Description of delayed test
2. Gram stain
Gram reaction
(purple =+; red =-)
Shape
2. XLD agar
Growth (+ or -)
Conclusion (G+ or G-)
Description of colonies
Probable organism(s)
147
LABORATORY 13:
4. Enterotube II
_________________________________________
148
LABORATORY 13:
C. If the oxidase test performed on the unknown on Lab 12 was negative, record the results here.

Results (+ or -)
Description of immediate
test
Description of delayed test
2. Gram stain
Gram reaction
(purple =+; red =-)
Shape
2. XLD agar
Growth (+ or -)
Conclusion (G+ or G-)
Description of colonies
Probable organism(s)
149
LABORATORY 13:
3. Enterotube II
_________________________________________
150
LABORATORY 13:
LABORATORY 13
ISOLATION OF ENTEROBACTERIACEAE AND PSEUDOMONAS

1. Interpret the results of XLD agar and Pseudosel agar.
IDENTIFICATION OF PSEUDOMONAS
1. Interpret the results of the following tests:
a. oxidase test (Taxo N disc)
b. pigment production on Pseudosel agar
c. fluorescence under ultraviolet light on Pseudosel agar
d. odor
2. Recognize an organism as Pseudomonas aeruginosa and state the reasons why based on the results of
the above 4 tests.
IDENTIFICATION OF ENTEROBACTERIACEAE USING AN ENTEROTUBE II

1. Interpret the results of an Enterotube II.
151
LABORATORY 13:
152
LABORATORY 14:
STREPTOCOCCUS AND ENTEROCOCCUS
LABORATORY 14
STREPTOCOCCI AND ENTEROCOCCI
A. The Genus Streptococcus
1. The Beta Streptococci
2. The Pneumococcus (Streptococcus pneumoniae)
3. The Viridans Streptococci
B. The Enterococci

The streptococci are gram-positive cocci 0.5-1.0m in diameter, typically occurring in pairs and chains of varying
length. They are usually classified clinically based on their hemolytic properties on blood agar and according to
their serologic groups.
The streptococci are usually isolated on Blood agar. Blood agar is one of the most commonly used media in a
clinical lab. It consists of an enriched agar base (Tryptic Soy agar) to which 5% sheep red blood cells have been
added. Blood agar is commonly used to isolate not only streptococci, but also staphylococci and many other
pathogens. Besides providing enrichments for the growth of fastidious pathogens, Blood agar can be used to detect
hemolytic properties.
Hemolysis refers to is the lysis of the red blood cells in the agar surrounding bacterial colonies and is a result of
bacterial enzymes called hemolysins. Although hemolysis can often be observed with the naked eye, ideally it
should be examined microscopically using low power magnification, especially in cases of doubtful hemolysis.
Reactions on blood agar are said to be beta, alpha, gamma, or double-zone:
1. Beta hemolysis (see Fig. 1) refers to a clear, red blood cell-free zone surrounding the colony, where a
complete lysis of the red blood cells by the bacterial hemolysins has occurred. This is best seen in
subsurface colonies where the agar has been stabbed since some bacterial hemolysins, like streptolysin
O, are inactivated by oxygen.
2. Alpha hemolysis appears as a zone of partial hemolysis surrounding the colony, often accompanied by
a greenish discoloration of the agar. This is also best seen in subsurface colonies where the agar has
been stabbed.
3. Gamma reaction refers to no hemolysis or discoloration of the agar surrounding the colony.
4. Double-zone hemolysis refers to both a beta and an alpha zone of hemolysis surrounding the colony.
Many of the streptococci can also be classified under the Lancefield system. In this case, they are divided into 19
different serologic groups on the basis of carbohydrate antigens in their cell wall. These antigenic groups are
designated by the letters A to H, K to M, and O to V. Lancefield serologic groups A, B, C, D, F, and G are the ones
that normally infect humans, however, not all pathogenic streptococci can be identified by Lancefield typing (e.g.,
Streptococcus pneumoniae). Serologic typing to identify microorganisms will be discussed in more detail later in Lab
17. Single-stranded DNA probes complementary to species-specific r-RNA sequences of streptococci and
enterococci are also being used now to identify these organisms.
153
LABORATORY 14:
1. The Beta Streptococci

a. Discussion
Lancefield serologic groups A, B, C, D, F, and G are all streptococci that may show beta hemolysis
on Blood agar. However, some group B streptococci are non-hemolytic and group D streptococci
(discussed below) usually show alpha hemolysis or are non-hemolytic.
Streptococcus pyogenes, often referred to as group A beta streptococci because they belong
to Lancefield serologic group A and show beta hemolysis on blood agar, are responsible for most
acute human streptococcal infections. S. pyogenes isolates are gram-positive cocci 0.5-1.0m in
diameter that typically form short chains in clinical specimens and longer chains in laboratory media.
Between 5% and 20% of children are asymptomatic carriers. The most common infection is
pharyngitis (streptococcal sore throat) with the organism usually being limited to the mucous
membranes and lymphatic tissue of the upper respiratory tract. Pharyngitis is pread person to person
primarily by respiratory droplets; skin infections are spread by direct contact with an infected person
or through fomites.
From the pharynx, however, the streptococci sometimes spread to other areas of the respiratory
tract resulting in laryngitis, bronchitis, pneumonia, and otitis media (ear infection).
Occasionally, it may enter the lymphatic vessels or the blood and disseminate to other areas of
the body, causing septicemia, osteomyelitis, endocarditis, septic arthritis, and meningitis. It
may also infect the skin, causing erysipelas, impetigo, or cellulitis.
Group A beta streptococcus infections can result in two autoimmune diseases, rheumatic fever
and acute glomerulonephritis, where antibodies made against streptococcal antigens cross react
with joint membranes and heart valve tissue in the case of rheumatic fever, or glomerular cells and
basement membranes of the kidneys in the case of acute glomerulonephritis.
Finally certain strains of S. pyogenes cause invasive group A beta streptococcal infections.
Each year in the U.S. there are between 750 and 1500 cases of necrotizing fasciitis where a
streptococcal-coded protease called Exotoxin B destroys the muscle (myositis) or the muscle
covering (necrotizing fasciitis). There are another 750 - 1500 cases of toxic shock-like syndrome
(TSLS) due to group A beta streptococci producing Streptococcal pyrogenic exotoxin (Spe).
Virulence factors include an adhesin called protein F that allows adherence to target host cells; Mprotein, that resists phagocytic engulfment; leukocidin, a toxin that kills leukocytes; Streptococcal
pyrogenic exotoxin (Spe), which functions as a superantigen and causes excess cytokine production
by the body and can lead to blood vessel damage and possible shock; and exotoxin B, a protease
that destroys muscle tissue protein leading to myositis or necrotizing fasciitis.
The group B streptococci (GBS) (Streptococcus agalactiae) usually show a small zone of beta
hemolysis on Blood agar, although some strains are non-hemolytic. S. agalactiae isolates are grampositive cocci 0.6-1.2 m in diameter that typically form short chains in clinical specimens and longer
chains in laboratory media. They often colonize the gastrointestinal tract and genitourinary tract
of healthy adults with from 5% to 40%, depending on the population, carrying the bacteria. This
reservoir, along with nosocomial transmission, provides the inoculum by which many infants are
colonized at birth. Most colonized infants (and adults) remain asymptomatic, however, an estimated
0.5-1.0% of neonates colonized will develop pneumonia, septicemia, and/or meningitis from
this organism. Other infections associated with group B streptococci include urinary tract
infections, skin and soft tissue infections, osteomyelitis, endometritis, and infected ulcers
(decubitus ulcers and ulcers associated with diabetes). In the immunocompromised patient it
sometimes causes pneumonia and meningitis.
154
LABORATORY 14:
The group C streptococci (mainly S.equi, S. equisimilis and S. zooepidemicus) are beta
hemolytic. They sometimes cause pharyngitis and, occasionally, bacteremia, endocarditis,
meningitis, pneumonia, septic arthritis, and cellulitis. Group C streptococci are a common cause of
infections in animals.
The group F streptococci (mainly S. anginosus) have been isolated from abscesses of the brain,
mouth, and jaw. They also sometimes cause endocarditis.
The group G streptococci also show beta hemolysis. They sometimes cause pharyngitis and can
also cause serious infections of the skin and soft tissues (mainly in the compromised host) as well as
endocarditis, bacteremia, and peritonitis.
All of these beta hemolytic streptococci can be identified by biochemical testing and/or by serologic
testing. Today you will look at the isolation and identification of group A beta streptococci
(Streptococcus pyogenes) by biochemical testing. Serological identification will be performed in Lab
17.
b. Isolation and Identification of Group A Beta Streptococci (Streptococcus

pyogenes)
Group A beta streptococci are usually isolated on Blood agar. Streptococcus pyogenes produces:
1. Very small, white to grey colonies approximately 1mm in diameter.
2. A zone of beta hemolysis around 2-3mm in diameter surrounding each colony.
There are two streptococcal hemolysins, streptolysin S and streptolysin O. Streptolysin O
can be inactivated by oxygen so more distinct hemolysis can be seen by stabbing the
agar several times. In this way, some of the organisms form subsurface colonies growing
away from oxygen. Since both streptolysin S and streptolysin O are active in the stabbed
area, a clearer zone of beta hemolysis can be seen.
3. Sensitivity to the antibiotic bacitracin.
Only the group A beta streptococci (Streptococcus pyogenes) are sensitive to bacitracin, as
shown by a zone of inhibition around a Taxo A disc, a paper disc containing low levels
of bacitracin (Fig 1). Other serologic groups of streptococci are resistant to bacitracin and
show no inhibition around the disc. (The Lancefield group of a group A beta streptococcus
can also be determined by direct serologic testing as will be demonstrated in Lab 17.)
155
LABORATORY 14:
Fig. 1:
Blood agar plate with a Taxo A disc inoculated with Streptococcus
pyogenes.
c. Materials (per pair)

Blood agar plates (2), 1 Taxo A (bacitracin) disc, loop, swab, tongue depressor
d. Organism
Trypticase Soy broth culture of Streptococcus pyogenes, a group A beta streptococcus.
HANDLE ALL BACTERIA AS PATHOGENS! WASH AND SANATIZE

YOUR HANDS WELL WHEN FINISHED!
e. Prodedure (to be done in pairs)

1. Take a Blood agar plate and divide it in half with your wax marker. After washing your hands,
do a throat culture on your lab partner as follows:
a. Depress the tongue with a sterile tongue depressor. Do not lay the tongue depressor
down once you pick it up! Using a sterile swab, scrape the sides of the pharynx.
b. Streak about one-third of your half of the plate with the swab (Fig. 2, step 1). Discard the
swab and the tongue depressor in the biowaste container.
156
LABORATORY 14:
c. Using a sterile inoculating loop, spread the portion of the plate that you streaked with
the swab over the remaining portions of the blood agar plate to get isolated colonies (Fig. 2,
step 2).
d. Stab the agar 2-3 times in each of the streaked areas with your loop (Fig. 2, step3).
e. Incubate the plate upside-down at 37 C until the next lab period.
Fig. 2:
Throat culture on Blood agar.
Fig. 2, step 1
Streak the throat swab on 1/3 of
your half of the Blood agar plate.
Fig. 2, step 2
Using a sterile loop, spread this over
the remaining half of the plate.
Fig. 2, step 3
Stab the agar several times.
2. Streak a second plate of Blood agar with Streptococcus pyogenes for isolation as follows:
a. Dip a sterile swab in your culture of S. pyogenes. Squeeze the swab against the side of
the tube to remove the excess inoculum.
b. Streak about one-third of the plate with the swab as shown in Fig. 3, step 1. Immediately
dispose of the swab in the biowaste container.
c. Using a sterile inoculating loop, spread the swabbed area over the remainder of the
plate to get isolated colonies as shown in Fig. 3, step 2.
d. Stab the agar several times in each of the 3 growth areas with your inoculating loop as
shown in Fig. 3, step 3. This detects oxygen sensitive hemolysins.
e. Place a Taxo A disc containing bacitracin in the center of the portion of the plate that
you streaked with the swab as shown in Fig. 3, step 4.
3. Incubate the plate upside-down at 37 C until the next lab period.
4. Do a gram stain of the S. pyogenes (see Lab 6).
157
LABORATORY 14:
Fig. 3:
Inoculation of a Blood agar plate with Streptococcus pyogenes
Fig. 3, step 1
Using a sterile swab, streak about 1/3 of the
blood agar plate with Streptococcus pyogenes.
Fig. 3, step 2
Using a sterile loop, spread the bacteria over the
remaining 2/3 of the plate.
Fig. 3, step 3
Stab the agar several times in each of the 3
growth areas.
Fig. 3, step 4
Place a Taxo A (bacitracin) disc in the center of the
area streaked with the swab.
158
LABORATORY 14:
2. The Pneumococcus (Streptococcus pneumoniae)

a. Discussion
Streptococcus pneumoniae, or the pneumococcus, is a gram-positive lancet-shaped (pointed like a
lance) coccus 0.5-1.2 m in diameter. They typically appear as a diplococcus, but occasionally
appear singularly or in short chains. Pneumococci are frequently found as normal flora of the
nasopharynx of healthy carriers. Pharyngeal colonization occurs in 5-10% of healthy adults and
20-40% of healthy children.
In the U.S., pneumococci are the most common cause of community-acquired pneumonia
requiring hospitalization, causing around 500,000 cases per year and usually occuring as a
secondary infection in the debilitated or immunocompromised host. The pneumococci also cause
over 7,000,000 cases of otitis media per year, are the leading cause of sinusitis in people of all
ages, are responsible for 55,000 cases of bacteremia, and 3000 cases of meningitis, being the
most common cause of meningitis in adults and children over 4 years of age.
The capsule serves as the major virulence factor, enabling the pneumococcus to resist phagocytic
engulfment, and glycopeptides from its gram-positive cell wall can lead to excessive cytokine
production and a massive inflammatory response.
Pneumococci show alpha hemolysis on Blood agar.
b. Isolation and Identification Pneumococci (Streptococcus pneumoniae)

1. Isolation on Blood agar
Pneumococci frequently require enriched media and increased CO2 tension for initial
isolation. They are usually isolated on Blood agar and incubated in a candle jar (a closed
container in which a lit candle is placed to remove O2 and increase CO2 ) at 37 C. On Blood
agar, colonies appear small, shiny, and translucent. They are surrounded by a zone of
alpha hemolysis. Due to autolysis with age, the colonies may show a depressed center
with an elevated rim.
2. Optochin sensitivity
Pneumococci are the only streptococci that are sensitive to the drug optochin
(ethylhydrocupreine hydrochloride). This can be detected by a zone of inhibition around a
Taxo P disc, a paper disc containing the drug optochin, which is placed on the Blood agar
plate prior to incubation (Fig. 4).
3. Bile solubility test
Most colonies of S. pneumoniae will dissolve within a few minutes when a drop of bile is
placed upon them. (This test will not be done in lab today.)
159
LABORATORY 14:
Fig. 4:
A blood agar plate with a Taxo P disc inoculated with Streptococcus
pneumoniae.
4. Gram stain of sputum

Streptococcus pneumoniae will usually appear as encapsulated, gram-positive, lancetshaped diplococci.
c. Procedure (demonstration)
Observe the demonstration of Streptococcus pneumoniae growing on a Blood agar plate with a Taxo
P disc containing optochin.
3. The Viridans Streptococci

a. Discussion
Ten species of streptococci are known as the viridans streptococci. They are the dominant
normal flora in the upper respiratory tract. Species include S. mutans, S. sanguis, S. mitis, and S.
salivarius. S. mutans is the primary cause of dental caries. Viridans streptococci are responsible for
between 50% and 70% of the cases of bacterial endocarditis, especially in people with previously
damaged heart valves. They are also frequently associated with bacteremia, deep wound
infections, dental abscesses, and abscesses of internal organs. The viridans streptococci show
alpha hemolysis or no hemolysis on Blood agar, do not possess Lancefield group antigens, and
can be differentiated from other alpha streptococci by biochemical testing.
Most of the colonies you will see on your throat culture you do today will be alpha and gamma
viridans streptococci.
160
LABORATORY 14:
B. The Genus Enterococcus

a. Discussion
Enterococci are gram-positive streptococci, typically occurring in pairs and short chains, that are
normal flora of the intestinal tract. Enterococci responsible for a variety of opportunistic infections in
humans, and serologically belong to Lancefield group D streptococci.
Enterococcus faecalis (formally Streptococcus faecalis) is the most common enterococcus that infects
humans. E. faecalis is normal flora of the intestinal tract in humans and is regularly isolated from
infections within the peritoneal cavity (especially following penetrating trauma), urinary tract infections,
kidney infections, prostate infections, and infections of damaged or compromised skin such as
diabetic or decubitus ulcers, burns, and surgical wounds. Other opportunistic enterococcal species include E.
faecium and E. durans. The enterococci have become the second most common bacterium isolated
from nosocomial urinary and wound infections, and the third most common cause of nosocomial
bacteremia. Each year in the U.S enterococci account for approximately 110,000 urinary tract infections,
40,000 wound infections, 25,000 cases of nosocomial bacteremia, and 1100 cases of endocarditis.
Furthermore, the enterococci are among the most antibiotic resistant of all bacteria, with some isolates
resistant to all known antibiotics.
b. Isolation and Identification of Enterococci

The enterococci may be isolated and identified using various selective and differential media. Two such
media are:
1. SF broth
SF broth contains sodium azide, which inhibits most bacteria other than enterococci. The
enterococci will grow in SF broth and ferment the dextrose, turning the pH indicator from violet to
a yellow-brown color.
2. Bile Esculin agar
Unlike most bacteria, the enterococci will grow in the presence of the bile salts in the medium. They
hydrolyze the esculin, producing esculetin which reacts with the iron salts in the medium turning
the agar black.
Enterococci are also being identified using chemiluminescent labelled DNA probes complementary to
species-specific bacterial ribosomal RNA (rRNA) sequences.
c. Materials (per pair)

1 tube of SF broth, 1 Bile Esculin agar slant, sterile swab.
d. Organism
Trypticase Soy broth culture of Enterococcus faecalis
161
LABORATORY 14:
e. Procedure (to be done in pairs)

1. Using a sterile swab, inoculate first the Bile Esculin agar slant and then the SF broth tube with
Enterococcus faecalis. Dispose of the swab in the biowaste container.
2. Incubate both tubes at 37 C until the next lab period.
3. Do a gram stain of the E. faecalis (see Lab 6).
RESULTS
1. Group A Beta Streptococci (Streptococcus pyogenes)
a. Blood agar with Taxo A (bacitracin) disc
Description of colony
Type of hemolysis
(alpha, beta, or gamma)
Taxo Adisc (bacitracin) results
(inhibition or no inhibition)
b. Gram stain
Gram stain of Streptococcus

Gram reaction
Shape and
arrangement
162
LABORATORY 14:
2. Pneumococci (Streptococcus pneumoniae)
a. Blood agar with Taxo P (optochin) disc
Description of colony
Type of hemolysis
(alpha, beta, or gamma)
Taxo Pdisc (optochin) results
(inhibition or no inhibition)
3. Viridans streptococci
Observe the results of your throat culture and note the type(s) of hemolysis seen.
B. The Genus Enterococcus (Enterococcus faecalis)

1. SF broth
Growth
(+ or -)
Color of broth
(violet or yellow brown)
Fermentation of dextrose
(+ or -)
2. Bile Esculin agar
Growth
(+ or -)
Color of agar
(black or beige)
Hydrolysis of esculin
(+ or -)
163
LABORATORY 14:
3. Gram stain
Gram stain of Enterococcus

Gram reaction
(purple = +; red =-)
Shape and
arrangement
164
LABORATORY 14:
LABORATORY 14
A THE GENUS STREPTOCOCCUS

1. State the gram reaction and morphology of the streptococci.
2. State two ways the streptococci are classified.
3. Describe alpha hemolysis, beta hemolysis, and gamma reaction on Blood agar plates.
4. State what is meant by the Lancefield system.
5. State the Lancefield group of streptococcus that is the most common cause of acute streptococcal
infections in humans and name five other Lancefield groups that frequently cause human infections.
1. THE BETA STREPTOCOCCI

DISCUSSION
1. State what the term "group A beta" means when referring to streptococci.
2. State the genus and species of the group A beta streptococci.
3. State the most common infection caused by Streptococcus pyogenes and name six other
infections it may cause.
4. Name two autoimmune diseases associated with the group A beta streptococci.
5. State the genus and species of the group B streptococci.
6. State the normal habitat of the group B streptococci, name three infections they may
cause in newborns, and describe how the infants become colonized.
7. Name three infections the group B streptococci may cause in adults.
ISOLATION AND IDENTIFICATION OF GROUP A BETA STREPTOCOCCI

1. Describe the appearance of group A beta streptococci on Blood agar.
2. State why Blood agar is usually stabbed during streaking when isolating beta streptococci.
3. Describe the reaction of group A beta streptococci to a Taxo A disc containing
bacitracin.
RESULTS OF GROUP A BETA STREPTOCOCCI

1. Identify an organism as a group A beta streptococcus (or Streptococcus pyogenes) and
state the reasons why when it is seen growing on a Blood agar plate with a Taxo A disc
containing bacitracin.
2. Recognize beta hemolysis on Blood agar.
165
LABORATORY 14:
2. THE PNEUMOCOCCUS
DISCUSSION
1. State the genus and species of the pneumococcus.
2. State the gram reaction and morphology of Streptococcus pneumoniae.
3. State the natural habitat of Streptococcus pneumoniae and name four infections it may
cause in humans.
ISOLATION AND IDENTIFICATION OF PNEUMOCOCCI

1. Describe the appearance of Streptococcus pneumoniae on Blood agar with a Taxo P
disc containing the drug optochin.
RESULTS OF PNEUMOCOCCI
1. Identify an organism as Streptococcus pneumoniae and state the reasons why when it is
seen growing on a Blood agar plate with a Taxo P disc containing optochin.
2. Recognize alpha hemolysis on Blood agar.
3. THE VIRIDANS STREPTOCOCCI

1. State the normal habitat of the viridans streptococci and name three infections they may cause in
humans.
2. State the hemolytic reactions of the viridans streptococci on Blood agar.
B. THE GENUS ENTEROCOCCUS

DISCUSSION
1. Name the most common enterococcus that infects humans and state its normal habitat.
2. State the Lancefield group of the enterococci.
3. Name four infections commonly caused by Enterococcus faecalis.
ISOLATION AND IDENTIFICATION OF ENTEROCOCCI

1. Describe the reactions of enterococci in SF broth and on Bile Esculin agar.
2. State the gram reaction and morphology of the enterococci.
RESULTS OF THE ENTEROCOCCI

1. Identify an organism as an Enterococcus and state the reasons why when it is seen growing in SF broth
and on Bile Esculin agar.
166
LABORATORY 15:
STAPHYLOCOCCI
LABORATORY 15
ISOLATION AND IDENTIFICATION
OF STAPHYLOCOCCI
DISCUSSION
Staphylococci are often found in the human nasal cavity (and on other mucous membranes) as well as on the skin.
They are gram-positive cocci 0.5-1.0 m in diameter and occur singly, in pairs, in short chains, and most commonly,
in irregular grape-like clusters. The staphylococci are strongly catalase positive, reduce nitrates to nitrites, and
generally tolerate relatively high concentrations of sodium chloride (7.5-10%). This ability is often employed in
preparing media selective for staphylococci.
There are five species of staphylococci commonly associated with clinical infections: Staphylococcus aureus,
S. epidermidis, S. haemolyticus, S. hominis and S. saprophyticus.
A. Staphylococcus aureus (coagulase-positive staphylococci)

Staphylococcus aureus is the most pathogenic species and is implicated in a variety of infections.
Approximately 30% of adults and most children are healthy periodic nasopharyngeal carriers of S. aureus.
Around 15% of healthy adults are persistent nasopharyngeal carriers.
In the majority of S. aureus infections the source of the organism is either:
the healthy nasal carrier, or
contact with an abscess from an infected individual.
The portal of entry is usually the skin. S. aureus causes pus-filled inflammatory lesions known as
abscesses. Depending on the location and extent of tissue involvement, the abscess may be called:
1. a pustule
A pustule is an infected hair follicle where the base of the hair follicle appears red and raised with
an accumulation of pus just under the epidermis. Infected hair follicles are also referred to as
folliculitis.
2. a furuncle or boil
Furuncles appear as large, raised, pus-filled, painful nodules having an accumulation of dead,
necrotic tissue at the base. The bacteria spread from the hair follicle to adjacent subcutaneous
tissue.
3. a carbuncle
Carbuncles occur when furuncles coalesce and spread into surrounding subcutaneous and
deeper connective tissue. Superficial skin perforates, sloughs off, and discharges pus.
S. aureus also causes impetigo, a superficial blister-like infection of the skin usually occuring on the
face and limbs and seen mostly in young children. S. aureus may also spread through soft tissues and cause
cellulitis. S. aureus is also a frequent cause of accidental wound and postoperative wound infections.
Less commonly, S. aureus may escape from the local lesion and spread through the blood to other body
areas, causing a variety of systemic infections that may involve every system and organ. Such systemic
infections include septicemia, septic arthritis, endocarditis, meningitis, and osteomyelitis, as well as
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LABORATORY 15:
STAPHYLOCOCCI
abscesses in the lungs, spleen, liver, and kidneys. S. aureus pneumonia may also be a secondary
respiratory complication of viral infections such as measles and influenza. Finally, S. aureus is frequently
introduced into food by way of abscesses or the nasal cavity of food handlers. If it is allowed to grow and
produces an enterotoxin, it can cause staphylococcal food poisoning.
Virulence factors for S. aureus include exotoxins such as leukocidin (kills leukocytes), alpha and delta
toxins (damage tissue membranes), microcapsules (resist phagocytic engulfment and destruction),
coagulase and protein A (both help resist phagocytic engulfment). Some strains also produce TSST-1 (toxic
shock syndrome toxin-1) and cause toxic shock syndrome, usually associated with tampon use or wounds.
Approximately 6000 gases of toxic shock syndrome occur each year in the U.S. Some strains also produce
exfoliatin, an exotoxin that causes scalded skin syndrome, an infection usually seen in infants and young
children.
Since most S. aureus strains produce the enzyme coagulase (see the coagulase test described below),
they are often referred to as coagulase-positive staphylococci.
B. Coagulase-Negative Staphylococci
Clinically common species of staphylococci other than S. aureus are often referred to as coagulasenegative staphylococci. These staphylococci are normal flora of the skin and, as such, frequently act as
opportunistic pathogens, especially in the compromised host. S. saprophyticus is a relatively common
cause of urinary tract infections, especially in young, sexually active women, but is seldom isolated from
other sources. The great majority of infections caused by other coagulase-negative staphylococci,
including S. epidermidis, S. haemolyticus, and S. hominis, are associated with intravascular devices
(prosthetic heart valves and intra-arterial or intravenous lines) and shunts. Also quite common are
infections of prosthetic joints, wound infections, osteomyelitis associated with foreign bodies, and
endocarditis.
Staphylococcal capsules play a major role in the ability of the bacteria to adhere to and colonize
biomaterials.
Although certain reactions may vary from strain to strain, a series of biochemical tests will usually differentiate the
most common clinically encountered species of staphylococci. Today we will use a number of tests to determine if an
unknown is S. aureus, S. epidermidis, or S. saprophyticus.
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LABORATORY 15:
STAPHYLOCOCCI
ISOLATION AND IDENTIFICATION OF STAPHYLOCOCCI

A. Blood agar with a novobiocin (NB) disc
To isolate staphylococci, clinical specimens are usually grown on Blood agar (described in Lab 14).
Staphylococci produce round, raised, opaque colonies 1-2mm in diameter. The novobiocin disc is used to
detect sensitivity or resistance to the antibiotic novobiocin.
Test
*
Staphylococcus
aureus
Staphylococcus
epidermidis
Staphylococcus
saprophyticus
Hemolysis
Usually
1
beta
Usually
2
none
Usually
2
none
Pigment
Often
1
creamy gold
Usually
2
white
Usually
2
white
Novobiocin
disc
Sensitive
Sensitive
Resistant
* see Lab 14 for descriptions of hemolysis

1. some strains do not show hemolysis and/or pigment
2. some strains do show hemolysis and/or pigment
sensitive = zone of inhibition around disc
resistant = no zone of inhibition around disc
B. Gram stain
All staphylococci appear as gram-positive cocci, usually in irregular, often grape-like clusters.
C. Mannitol fermentation on Mannitol Salt agar (MSA)

Staphylococci are able to tolerate the high salt concentration found in Mannitol Salt agar and thus grow
readily. If mannitol is fermented, the acid produced turns the phenol red pH indicator from red (alkaline) to
yellow (acid).
Test
Mannitol
fermentation
Staphylococcus
aureus
Positive
Staphylococcus
epidermidis
Negative
positive = acid end products turn the phenol red pH indicator from red to yellow
negative = phenol red remains red
169
Staphylococcus
saprophyticus
Usually
positive
LABORATORY 15:
STAPHYLOCOCCI
D. Production of deoxyribonuclease (DNase) on DNase agar

DNase agar contains 0.2% DNA. To detect DNase production, the plate is inoculated and incubated. After
growth, the plate is flooded with 1N hydrochloric acid (HCl). DNase positive cultures show a distinct clear
zone around the streak where the DNA in the agar was broken down by the bacterial Dnase (Fig. 1). DNase
negative cultures appear cloudy around the growth where the acid caused the DNA in the agar to precipitate
out of solution.
Test
Staphylococcus
aureus
Positive
DNase
production
Staphylococcus
epidermidis
Negative
Staphylococcus
saprophyticus
Nnegative
positive = clear zone around growth after adding 1N HCl (no DNA remaining in the agar)
negative = cloudy around growth after adding 1N HCl (DNA remains in the agar forming a precipitate)
Fig. 1:
A positive Dnase agar test.
E. Production of coagulase
The staphylococcal enzyme coagulase will cause inoculated citrated rabbit plasma to gel or coagulate. The
coagulase converts soluble fibrinogen in the plasma into insoluble fibrin.
Test
Coagulase
production
Staphylococcus
aureus
Positive
Staphylococcus
epidermidis
Negative
positive = plasma will gel or coagulate

negative = plasma will not gel
170
Staphylococcus
saprophyticus
Negative
LABORATORY 15:
STAPHYLOCOCCI
F. The Staphyloslide Latex Test for cell-bound coagulase (clumping factor) and/or
Protein A
The Staphyloslide Latex Test is an agglutination test that detects cell-bound coagulase (clumping
factor) and/or Protein A. Approximately 97% of human strains of S. aureus possess both bound coagulase
and extracellular coagulase. Approximately 95% of human strains of S. aureus possess Protein A on their cell
surface. This test uses blue latex particles coated with human fibrinogen and the human antibody IgG. Mixing
of the latex reagent with colonies of the suspected S. aureus having coagulase and/or Protein A bound to
their surface causes agglutination of the latex particles.
Test
Cell-bound coagulase
(clumping factor) and/or
Protein A
Staphylococcus
aureus
Positive
Staphylococcus
epidermidis
Negative
Staphylococcus
saprophyticus
Negative
positive = clumping of latex particles

negative = no clumping of latex particles
Staphylococci are also being identified using chemiluminescent labelled DNA probes complementary to speciesspecific bacterial ribosomal RNA (rRNA) sequences as well as by other direct DNA techniques.
MATERIALS (per pair)

1 Blood agar plate, 2 Mannitol Salt agar plates, 1 DNase agar plate, 1 tube of citrated rabbit plasma (coagulase
test), 1 novobiocin disc, inoculating loop, swab.
ORGANISMS
A Trypticase Soy broth culture of one of the following unknowns:
Staphylococcus saprophyticus.

1. Using your inoculating loop, streak your unknown for isolation on a plate of Blood agar as described
below and shown in Fig. 2.
a. Using a sterile inoculating loop, streak your unknown for isolation on a blood agar plate so as to
get single, isolated colonies as shown in Fig. 2, step 1 and Fig. 2, step 2.
c. Using your inoculating loop, stab the agar several times in each of the 3 growth as shown in Fig.
2, step 3. This detects oxygen sensitive hemolysins.
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LABORATORY 15:
STAPHYLOCOCCI
d. Place a novobiocin antibiotic disc in the center of the area of the plate that you streaked first
and where you expect to see the heaviest growth as shown in Fig. 2, step 4.
e. Incubate at 37 C until the next lab period.
2. Streak your unknown for isolation on a plate of Mannitol Salt agar (MSA) as shown in Fig. 3.
Incubate at 37 C.
3. Streak a single line of your unknown down the center of a plate of DNase agar as shown in Fig. 4.
Incubate at 37 C.
Fig. 2:
Inoculation of a Blood agar plate with Staphylococcus aureus.
Fig. 2, step 1
Using a sterile loop, streak about 1/3 of the blood
agar plate with Staphylococcus aureus.
Fig. 2, step 2
Using a sterile loop, spread the bacteria over the
remaining 2/3 of the plate.
Fig. 2, step 3
Stab the agar several times in each
of the 3 growth areas.
Fig. 2, step 4
Place a NB disc in the center of the
first area you streaked.
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LABORATORY 15:
STAPHYLOCOCCI
Fig. 3:
Inoculation of Mannitol Salt agar.
Fig. 4:
Inoculation of Dnase agar.
4. To determine if you are a nasal carrier of S. aureus, take a second plate of Mannitol Salt agar, divide it in
half with your wax marker, and do a nasal culture on your half of the plate as follows:
a. Stick a sterile swab up your nose.
b. Streak about one-third of your portion of the plate with the swab as shown in Fig. 5, step 1.
Discard the swab in the biowaste container.
c. Spread this out over the remainder of the plate with a sterile inioculating loop (Fig. 5, step 2).
d. Incubate at 37 C until the next lab period.
5. Inoculate a tube of citrated rabbit plasma with your unknown and incubate at 37 C.
6. Next lab period, observe the demonstrations of the Staphyloslide tests performed on each of the
unknowns by mixing colonies of the bacteria with latex particles coated with human fibrinogen and human
IgG.
7. Next lab period, do a gram stain of your unknown (see Lab 6).
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LABORATORY 15:
STAPHYLOCOCCI
Fig. 5:
Nasal culture on MSA
Fig. 5, step 1
Streak one-third of your half of the
Mannitol Salt agar plate with the swab.
Fig. 5, step 2
Using a sterile loop, spread the bacteria
out over the remaining portion of your
half of the plate.
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LABORATORY 15:
STAPHYLOCOCCI
RESULTS
1. Flood the surface of your DNase agar plate with 1N HCl.
2. Observe the demonstration of the Staphyloslide test that was done on your unknown.
3. Review the expected results for each test on each unknown using the tables found earlier in this lab exercise.
Interpret the results for all unknowns and fill in the following results table.
Test
Unknown #1
Unknown #2
Hemolysis on Blood agar

(beta, alpha, gamma)
Pigment on Blood agar
(yellow-gold or white)
Novobiocin (NB) disc
(sensitive or resistant)
Mannitol fermentation
(positive or negative)
DNase production
Coagulase production
Clumping factor and/or
Protein A
175
Unknown #3
LABORATORY 15:
STAPHYLOCOCCI
4. Gram stain results
Gram stain of
Gram reaction
Shape and
arrangement
Conclusion:
Unknown #1 = _________________________
Unknown #2 = _________________________
Unknown #3 = _________________________
5. Observe the results of your nasal culture on Mannitol Salt agar. If your nasal bacteria fermented mannitol (phenol
red turned yellow), run a Staphyloslide test to confirm that the organism is Staphylococcus aureus.
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LABORATORY 15:
STAPHYLOCOCCI
LABORATORY 15
DISCUSSION
1. Name three common clinically important species of Staphylococcus and state which species is most
pathogenic.
2. State two sources and the portal of entry for most Staphylococcus aureus infections.
3. Name and describe three types of abscesses caused by Staphylococcus aureus.
4. Name four systemic Staphylococcus aureus infections.
5. State the significance of Staphylococcus aureus enterotoxin, the exotoxin TSST-1, and the exotoxin
exfoliatin.
6. Name the infection normally caused by Staphylococcus saprophyticus.
7. Name the types of infections most commonly caused by coagulase-negative staphylococci other than
Staphylococcus saprophyticus.
ISOLATION AND IDENTIFICATION OF STAPHYLOCOCCI

1. State the gram reaction and morphology of all staphylococci.
2. Describe the typical reactions of S. aureus, S. epidermidis, and S. saprophyticus on each of the following
media:
a. Blood agar (pigment, hemolysis, novobiocin resistance)
b. Mannitol Salt agar (for mannitol fermentation)
c. DNase agar (for the enzyme DNase)
d. coagulase test with citrated rabbit plasma
e. Staphyloslide test for bound coagulase and/or Protein A
RESULTS
1. Recognize staphylococci in a gram stain preparation.
2. Recognize an organism as Staphylococcus aureus and state the reasons why after seeing the results of
the following:
a. a Blood agar plate with a novobiocin disc
b. a Mannitol Salt agar plate
c. a DNase agar plate
d. a tube of citrated rabbit plasma
e. a Staphyloslide test
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LABORATORY 15:
STAPHYLOCOCCI
178
LABORATORY 16:
ISOLATION AND IDENTIFICATION OF NEISSERIAE, MYCOBACTERIA, AND OBLIGATE ANAEROBES
LABORATORY 16
NEISSERIAE, MYCOBACTERIA,
AND OBLIGATE ANAEROBES
A. The Neisseriae
B. The Mycobacteria
C. The Obligate Anaerobes
A. THE NEISSERIAE
DISCUSSION
The neisseriae are a group of gram-negative diplococci 0.6-1.5 m in diameter. Two species of
Neisseria, N. gonorrhoeae and N. meningitidis, are considered as true human pathogens. Both of these
organisms possess pili for adherence to host cells, produce endotoxins, and resist destruction within
phagocytes. N. meningitidis also produces a capsule to resist phagocytic engulfment.
Neisseria gonorrhoeae (the gonococcus) causes gonorrhea. It is estimated by CDC that over 700,000
new cases of gonorrhea occur each year in the U.S. and only about 50% of these cases are reported.
Infection usually occurs following sexual contact, with the incubation period averaging 2-7 days.
In males, the gonococcus typically invades the anterior urethra, usually producing a purulent discharge,
pain upon urination, and a frequency of urination. Approximately 5-10% of infected males are
asymptomatic but will still be infectious. The infection may spread up the reproductive tract, infecting the
prostate, vas deferens, epididymis, and testes, causing painful inflammation and scar tissue formation
that can result in sterility.
In females, 30-50% of those initially infected are asymptomatic or show mild symptoms. They are,
however, still infectious. Initially, the organism invades the cervix, the urethra, and frequently the rectum. In
about 10% - 20% of these cases, the organism spreads up the reproductive tract and infects the fallopian
tubes causing pelvic inflammatory disease (PID). The resulting inflammation and scar tissue formation
may result in sterility or abnormal (ectopic or tubal) pregnancies.
The gonococcus may also cause extragenital infections such as pharyngitis (from oral-genital sex),
ophthalmia (from inoculation of the eyes with contaminated fingers), and proctitis (from anal sex). In 1% 3% of infected women and a lower percentage of infected males, the organism invades the blood and
disseminates, causing a rash, septic arthritis, endocarditis, and/or meningitis.
Congenital gonorrhea is known as ophthalmia neonatorum and occurs as a result of the eyes of
newborns becoming infected as the baby passes through the birth canal.
Neisseria meningitidis (the meningococcus) is the causative organism of meningococcal (epidemic)
meningitis. There are between 2000 and 3000 cases of meningococcal meningitis per year in the U.S.
Approximately 50% of the cases occur in children between 1 and 4 years old. N. meningitidis infects the
nasopharynx of humans causing a usually mild or subclinical upper respiratory infection. Colonization of the
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LABORATORY 16:
nasopharynx may persist for months. However, in about 15% of these individuals, the organism invades the
blood and disseminates, leading septicemia and/or meningitis. A petechial skin rash, caused by endotoxin
in the blood, appears in about 75 percent of the septic cases and fatality rates for meningococcal septicemia
are as high as 30 percent as a result of the shock cascade. A fulminating form of the disease, called
Waterhouse-Frederichsen syndrome, can be fatal within several hours due to massive intravascular
coagulation and resulting shock, probably a result of massive endotoxin release. N. meningitidis is especially
dangerous in young children.
Diagnosis of Gonorrhea
A presumptive diagnosis of gonorrhea is made on the basis of two of the following three criteria:
1. Typical gram-negative inside of polymorphonuclear leukocytes seen in a gram stain of urethral
exudates in men and endocervical secretions in women;
2. Growth of N. gonorrhoeae from the urethra of men or the endocervix of women on a culture
medium with typical colony morphology, positive oxidase reaction, and gram-negative coccal
morphology in a gram stain; and/or
3. Detection of N. gonorrhoeae by nonculture tests such as antigen tests (e.g., Gonozyme
[Abbott]), direct specimen nucleic acid probes (e.g., Pace II [GenProbe]), or nucleic acid
amplification tests (e.g., LCR [Abbott]).
Antibiotic therapy may be started with a presumptive diagnosis.
A definitive diagnosis of gonorrhea is made on the basis of:
1. Isolation of N. gonorrhoeae from the site of exposure by culture, usually on a selective medium,
demonstration of typical colony morphology, positive oxidase reaction, and gram-negative coccal
morphology in a gram stain and
2. Conformation of isolates by biochemical, enzymatic, serologic, or nucleic acid testing, e.g.,
carbohydrate utilization, rapid enzyme substrate tests, serologic methods such as fluorescent
antibody tests, or a DNA probe culture confirmation technique.
Isolation and Identification of Neisseria gonorrhoeae

a. The GC smear
A GC smear (gonococcus smear) is a gram stain of urethral exudates in men and endocervical
secretions in women and can be part of a presumptive diagnosis of gonorrhea. One looks for gramnegative diplococci with flattened adjacent walls that are seen both inside and outside of
polymorphonuclear leukocytes (see Fig. 1). This test is quite sensitive in symptomatic males but
only 40-60% sensitive in symptomatic females. In asymptomatic males and females the gram stain
has a lower predictive value.
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LABORATORY 16:
Fig. 1:
Neisseria gonorrhoeae (arrows) inside and outside
of neutrophils.
b. Isolation of Neisseria gonorrhoeae

To diagnose genital gonorrhea in males, the sample to be cultured is taken from the urethra. In
females, cultures are taken from the cervix and the rectum. In non-genital gonorrhea, the infected
site is cultured.
The gonococcus requires an enriched medium with increased carbon dioxide tension for growth.
They are usually cultured on modified Thayer Martin (MTM) Chocolate agar or Martin-Lewis agar.
Plates are then incubated at 35-37 C under increased carbon dioxide tension (5-10% CO2) such as
that provided by a candle jar or a carbon dioxide incubator.
MTM Chocolate agar is selective for Neisseria. The medium contains enrichment factors to
promote the growth of Neisseria. In addition, it contains antibiotics to inhibit normal body flora:
vancomycin to inhibit gram-positive bacteria; colistin to inhibit gram-negative bacteria; trimethoprim to
suppress Proteus; and nystatin to inhibit yeast. The "chocolate" color is due to the hemoglobin
enrichment added to the medium. Plates are then incubated under increased carbon dioxide tension
as mentioned above. (Transgrow Medium is a convenient flask containing MTM Chocolate agar and
CO2.) N. gonorrhoeae forms small, convex, grayish-white to colorless, mucoid colonies in 48 hours at
35-37 C.
c. Identification of Neisseria gonorrhoeae

Once isolated, N. gonorrhoeae can be identified by the oxidase test, gram-staining, carbohydrate
utilization reactions, rapid enzyme substrate tests, serologic methods such as fluorescent antibody
tests, or a DNA probe culture confirmation technique.
1. Oxidase test
All Neisseria are oxidase positive. The oxidase test can be performed as in Lab 13 using
a Taxo N disc. A moistened Taxo N disc can be placed on a growing culture and a
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LABORATORY 16:
blackening of the colonies surrounding the disc indicates a positive oxidase test. All
oxidase-positive cultures would be gram stained to confirm gram-negative diplococci.
Fig. 2:
Positive oxidase test for Neisseria. Colonies
surrounding the Taxo N disc turn black.
2. Carbohydrate utilization
The various species of Neisseria can be differentiated according to carbohydrate utilization
patterns. Neisseria species do not produce acid from carbohydrate fermentation but rather
by an oxidative pathway. These tests are done using a media with single carbohydrates
(glucose, maltose, sucrose, or lactose) and a pH indicator to detect acid. The media seen
today contain phenol red as a pH indicator. If the sugar is utilized, acid end products
cause the phenol red pH indicator to turn yellow. N. gonorrhoeae produces acid only
from glucose whereas N. meningitidis produces acid from glucose and maltose.
There are a variety of Neisseria species and other genera with similar morphology that
often colonize the body. By testing for lactose and sucrose utilization as well as performing
other tests such as rapid enzyme substrate tests, serologic methods, or DNA probes, N.
gonorrhoeae and N. meningitidis can be definitively identified. Typical sugar utilization
reactions can be seen in Table 1.
d. Serologic and Nucleic Acid Tests to Identify N. gonorrhoea

Serologic tests are also available for rapidly identifying N. gonorrhoeae. These include an
ELISA test to detect gonococci in urethral pus or on a cervical swab, as well as a direct
serologic test using fluorescent monoclonal antibodies to detect N. gonorrhoeae. Serologic
testing will be covered in Labs 17 and 18.
Nucleic acid and nucleic acid amplification tests are also available for identifying N.
gonorrhoeae.
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LABORATORY 16:
Table 1
Carbohydrate Utilization by Neisseria and Related Bacteria
Neisseria species produce acid end products from an oxidative pathway
rather than from fermentation.
Organism
Glucose
Maltose
Lactose
Sucrose
Neisseria gonorrhoea
+
Kingella denitrificans
+
N. meningitidis
+
+
N. polysaccharea
+
+
N. subflava (biovars subflava/flava)
+
+
N. subflava (biovar perflava)
+
+
+
N. sicca
+
+
+
N. mucosa
+
+
+
N. lactamica
+
+
+
N. flavescens
N. elongata
-/+
N. cinera
-/+
Branhamella catarrhalis
Additional biochemical tests such as the production of hydroxyprolyaminopeptidase, the production of gammaglutamylaminopeptidase, the ability to reducte nitrate, the production of polysaccharide from sucrose, and sensitivity
or resistance to colistin can be used to determine the exact species. Nonculture tests such as antigen tests, nucleic
acid probes, and nucleic acid amplification tests can also be used for speciation.
2. Isolation and Identification of Neisseria meningitidis

a. Gram stain
A presumptive diagnosis of meningococcal meningitisis often made by doing a gram stain of
cerebrospinal fluid or petichial skin lesions and looking for gram-negative diplococci seen both
inside and outside of polymorphonuclear leukocytes. This can be followed by serologic tests,
nucleic acid probes, or culturing.
b Serologic identification
There are at least 12 different serological groups of N. meningitidis based on their capsular
polysaccharides, but over 90 percent of meningococcal meningitis cases are caused by five
serologic groups: A, B, C, Y, and W135. Serogroups A and C usually causes the epidemic form of
meningitis. Serogroup C is is the most common serogroup in North America whereas B is the most
common in Europe and Latin America. Serogroups A and C are common in China, the Middle East,
and parts of Africa. Serogroup Y has been increasing in the U.S., Israel, and Sweden.
Direct serologic testing to detect meningococcal capsular polysaccharides can be performed on
cerebrospinal fluid or on organisms from skin lesions for rapid identification. Direct serologic testing
will be discussed in more detail in Lab 17.
c. Nucleic acid identification
A polymerase chain reaction test to amplify meningococcal DNA can also be used to detect N.
meningitidis in cerebrospinal fluid or blood.
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LABORATORY 16:
d. Isolation of Neisseria meningitidis
To isolate N. meningitidis, cultures are taken from the nasopharynx, blood, cerebrospinal fluid,
and skin lesions. Typically cultures are done on an enriched, non-selective medium such as blood
agar or chocolate agar grown in 3-7% carbon dioxide. MTM Chocolate agar is also sometimes
used for isolation. Medium to large, blue-gray, mucoid, convex, colonies form in 48 hours at 35-37 C.
e Identification of Neisseria meningitidis
Once isolated, N. meningitidis, like N. gonorrhoeae discussed above, is identified by the oxidase
test, gram staining, and carbohydrate utilization reactions. N. meningitidis, like all neisseriae, is
oxidase-positive and appears in a gram stain as gram-negative diplococci. In carbohydrate
utilization tubes, N. meningitidis produces acid from both glucose and maltose but not from
lactose and sucrose (see Table-1). The acid end products turn the phenol red pH indicator from red
to yellow. N. meningitidis also produces gamma-glutamylaminopeptidase, an enzyme that can be
detected by biochemical testing.
B. THE MYCOBACTERIA
DISCUSSION
The mycobacteria are rod-shaped bacteria generally 0.4 by 3.0 m in size that are said to be acid-fast.
This means when they are stained by the acid-fast procedure (Appendix C), they will resist decolorization
with acid-alcohol and stain red, the color of the initial stain, carbol fuchsin. With the exception of a very few
other acid-fast bacteria such as Nocardia, all other bacteria will be decolorized and stain blue (the color of the
counterstain, methylene blue). The acid-fast stain is an important test for the genus Mycobacterium.
Fluorescent microscopy staining may also be used to identify Mycobacterium.
The most common species of Mycobacterium to cause human infections are M. tuberculosis, M. leprae, M.
avium complex, M. kansasii, M. fortuitum, M. chelonae, and M. abscessus. M. tuberculosis is the causative
organism of tuberculosis, M. leprae causes leprosy, and M. avium complex (MAC) frequently causes
systemic infections in people with HIV/AIDS. The other species of Mycobacterium occasionally cause
tuberculosis-like infections, especially in the debilitated or immunosuppressed host.
It is estimated by the World Health Organization that worldwide, there are over 8,800,000 million new
cases of tuberculosis each year and nearly 3,000,000 deaths. One-third of the worlds population approximately 1.9 billion people - are thought to be infected with M. tuberculosis. In the U.S. there are
approximately 20,000 new cases of tuberculosis a year.
M. tuberculosis is typically acquired by inhalation of aersolized infectious particles. In the vast majority of
people, primary infection is asymptomatic or minimally symptomatic. Approximately 5% of people
exposed to M. tuberculosis develop active disease within 2 years; another 5% - 10% develop disease
sometime later in life. Typical symptoms are malaise, cough, weight loss, and night sweats.
Primary infection typically occurs after inhalation of the organism and subsequent generation of a
peripheral lung lesion. The body responds with what is termed delayed hypersensitivity to form characteristic
lesions called granuloma (tubercles). The formation of granuloma is actually the result of cell-mediated
immune responses attempting to "wall-off" and localize infections that the body cannot effectively remove
with macrophages. Although primary infection may be self-limiting, progression of the localized lesion may
lead to pneumonia. The organisms may eventually die within the granuloma, or the tissue may undergo
caseation, liquification, and cavitation. This can result in bronchogenic spread of the M. tuberculosis. In rare
instances, the organism may enter the blood causing disseminated miliary tuberculosis.
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LABORATORY 16:
Secondary infection is usually due to a relapse of either self-resolved lesions or a previously treated
disease. Approximately 90% of tuberculosis in immunocompetent patients is a result of secondary infection.
Diagnosis of tuberculosis
The diagnosis of tuberculosis is traditionally based on clinical findings, chest radiographs, a sputum or
tissue smear showing acid-fast bacilli or fluorescing mycobacteria after using fluorochrome staining.
Confirmation can be made using cultures, DNA probes, and polymerase chain reactions to amplify
mycobacterial DNA.
1. Presumptive tests for tuberculosis
a. The PPD skin test (or other presumptive skin tests) detects delayed hypersensitivity to purified
protein from the cell wall of M. tuberculosis. A positive skin test, assessed at 48-72 hours, indicates
that the person has developed a cellular immunity to the organism as a result of either a previous or
a current infection. Recommendations for interpretation of positive skin tests are based on the size
of induration in relationship to other risk factors the patient may have:
- Induration of 5 mm or more
Contacts of persons known to be infected
Patients with abnormal chest film
Organ-transplant recipients
HIV-positive patients
Other immunosuppressed patients
Residents of prisons, nursing homes, institutions
Recent immigrants from countries with a high incidence of tuberculosis
Heatlhcare workers
Children aged <4 years or infants, children, and adolescents exposed to high-risk adults
Patients with other high-risk medical factors (eg, diabetes, renal failure, cancer, silicosis)
No risk factors.
b. Chest X-rays are used to detect confluent granuloma formation in the lungs and possible
cavitation, which could be a result of past or present infection with tuberculosis or with some other
pulmonary infection that may be mistaken for tuberculosis.
c. An Acid-fast stain of the sputum may indicate acid-fast bacilli, which is a presumptive test for
active tuberculosis. In reporting acid-fast slide results, the slide should be observed for 10-15
minutes before considered negative. Results are reported as positive or negative for acid-fast bacilli.
Sometimes the amount of acid-fast bacilli are indicated, with 3-9 per slide reported as rare, 10 or
more per slide reported as few, and more than one per oil immersion field reported as numerous.
2. Confirmation of Active Tuberculosis

a. Cultures
Active tuberculosis is confirmed by culturing the organism. Sputum is usually treated with
sodium hydroxide, which is cidal for contaminants but not for M. tuberculosis. The liquified sputum is
then neutralized, centrifuged, and the sediment is inoculated onto special enrichment media such as
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Lowenstein-Jensen agar slants, Middlebrook agar, or 7H 10 Oleic acid agar plates. Felsen Quadrant
plates with agar containing different antimicrobial agents are also inoculated to determine drug
sensitivity. Plates are incubated in a carbon dioxide atmosphere. It takes from 3-8 weeks for colonies
to form.
In recent years, more rapid culture methods for detection of M. tuberculosis have been
developed. One involves adding radioisotopic substrates to a broth growth medium in order to detect
the release of carbon dioxide during mycobacterial growth. Another uses fluorometric technology to
detect oxygen consumption during growth. These techniques usually detect mycobacterial growth in
less than two weeks.
b. Nucleic acid tests
Polymerase chain reactions to amplify mycobacterial DNA, DNA probes, and probes to detect
ribosomal RNA from M. tuberculosis are also being used with increased frequency to confirm
tuberculosis.
The above procedure represents a very simplified outline for the diagnosis of tuberculosis. Culturing of M.
tuberculosis, atypical mycobacteria, and other clinically significant mycobacteria involves a complicated
series of complex procedures carried out only in large, well-equipped labs by experienced personnel.
C. THE OBLIGATE ANAEROBES

DISCUSSION
Obligate anaerobes are organisms that grow only without oxygen and, in fact, oxygen inhibits or kills
them. They obtain energy from anaerobic respiration or fermentation. A variety of obligate anaerobic
bacteria, which are usually normal flora of the body, may cause human infections. Obligate anaerobes
primarily cause infections of anaerobic wounds, although they may participate in all varieties of infections
and involve any tissue or organ. Five organisms or groups of organisms account for about two-thirds of all
clinically significant anaerobic infections. These are Bacteroides fragilis, Bacteroides melaninogenicus,
Fusobacterium nucleatum, Clostridium perfringens, and the anaerobic cocci.
Bacteroides fragilis is the most common cause of anaerobic infections in humans. It is also a
predominant organism of the normal human intestinal tract. It mainly causes wound infections.
Bacteroides melaninogenicus is normal flora of the upper respiratory, gastrointestinal, and genitourinary
tracts.
Fusobacterium species are normal flora of the upper respiratory, gastrointestinal, and genitourinary
tracts.
Clostridium perfringens, as well as other clostridial species, are normal flora of the intestinal tract of
various animals and may cause gas gangrene. C. tetani causes tetanus and C. botulinum causes
botulism.
Anaerobic cocci such as Peptostreptococcus, Peptococcus, and Veillonella are also normal flora of the
body.
Although anaerobic procedures are no more difficult than those used in aerobic bacteriology, strict
adherence to proper technique is necessary to ensure recovery of the organism. There must be proper
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selection of the specimen, proper specimen collection, proper specimen transport to the lab, and provision of
a proper anaerobic environment.
Common ways of culturing obligate anaerobes in the lab include:
1. Brewer anaerobic jar with GasPak
A GasPak is a commercially-produced disposable hydrogen and carbon dioxide generator
envelope. When water and catalyst are added, hydrogen and carbon dioxide are produced. The
hydrogen then combines with oxygen to form water, thus creating an anaerobic atmosphere. The
cultures are placed in a Brewer jar, water is added to the GasPak, the lid of the jar is sealed, and
the jar is placed in an incubator.
2. Media containing reducing agents
Media such as Thioglycolate medium and Anaerobic agar contain chemicals which function as
reducing agents. The reducing agents absorb oxygen and create a reduced environment required by
anaerobes.
3. Carbon dioxide incubators
Carbon dioxide incubators are frequently used to culture anaerobes. After the cultures are placed
in the incubator, the air is evacuated and replaced by carbon dioxide gas.
Isolation and Identification of Clostridium perfringens

1. Direct microscopic examination of exudates
Gram stains of purulent exudates from gas gangrene show stout gram-positive bacilli frequently
surrounded by a capsule. Endospores are usually not produced on ordinary culture media or in
tissues.
2. Isolation on Blood agar
When inoculated onto Blood agar plates and grown anaerobically, C. perfringens produces
smooth, glossy colonies that are usually surrounded by a double-zone hemolysis. The double-zone
hemolysis appears as a narrow zone of beta-type hemolysis (due to theta toxin) near the colony
surrounded by a wider zone of incomplete hemolysis (due to alpha toxin).
3. Identification in Litmus Milk medium
In anaerobically-grown Litmus Milk cultures, enzymes of C. perfringens will attack the proteins and
carbohydrates of the milk producing a "stormy fermentation" with acid production (litmus turns
pink), clotting of milk proteins, and gas formation.
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PROCEDURE
A. Neisseria gonorrhoeae and Neisseria meningitidis
Observe the following demonstrations:
1. Positive GC smear for N. gonorrhoeae. Note gram-negative diplococci inside and outside of
white blood cells.
2. N. gonorrhoeae growing on MTM Chocolate agar. Note small grayish-white convex, mucoid
colonies. This medium is selective for pathogenic Neisseria.
3. Positive oxidase test for N. gonorrhoeae using a Taxo N (oxidase) disc. Note oxidase-positive
(black) colonies around the Taxo N disc.
4. Glucose, maltose, and sucrose sugar utilization tubes inoculated with N. gonorrhoeae (note
acid production is positive for glucose; negative for maltose sucrose, and lactose) and N.
meningitidis (note acid production is positive for glucose and maltose; negative for sucrose and
lactose).
B. Mycobacterium tuberculosis
Observe the following demonstrations:
1. Positive acid-fast stain of sputum from a person with active tuberculosis. Note acid-fast (red)
rods. You must look carefully for the reddish acid-fast rods in the microscopic field. All other
material in the sputum will pick up the blue counterstain.
2. 35mm projection slides showing normal guinea pig organs and organs with granuloma.
Fig. 3:
Guinea pig spleen with granuloma.
3. Positive chest X-ray for the presumptive diagnosis of tuberculosis.

4. Prepare an acid-fast stain of Mycobacterium phlei. (Ziehl-Neelsen Method)
a. Heat-fix a smear of the sample of Mycobacterium phlei on a new glass slide.
b. Cover the smear with a piece of blotting paper and flood with carbol fuchsin.
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c.
Steam for 5 minutes by passing the slide through the flame of a gas burner.
d. Allow the slide to cool and wash with water.

e. Add the acid-alcohol decolorizing slowly dropwise until the dye no longer runs off from the
smear.
f.
Rinse with water.
g. Counterstain with methylene blue for 1 minute.

h. Wash with water, blot dry, and observe using oil immersion microscopy.
i.
Repeat using Staphylococcus aureus.
Acid-fast bacteria will appear red; non-acid-fast will appear blue.

Observe the following demonstrations of Clostridium perfringens:
1. Endospore stain of C. perfringens.
2. Blood agar plate of C. perfringens grown anaerobically. Note double-zone hemolysis.
3. Litmus milk culture of C. perfringens grown anaerobically. Note stormy fermentation of milk.
To show how special techniques such as media with reducing agents must be used to culture anaerobes,
inoculate the following media with Clostridium sporogenes and incubate at 37 C:
1. Nutrient broth
2. Thioglycolate medium
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RESULTS
A. Neisseria gonorrhoeae and Neisseria meningitidis
1. GC smear for N. gonorrhoeae
Make a drawing of the GC smear, noting the gram reaction and arrangement of the bacteria and their
association with the white blood cells.
GC smear
Gram reaction
(purple = +; red =-)
Shape and
arrangement
2. N. gonorrhoeae on MTM Chocolate agar with a Taxo N disc.

Growth on selective MTM
Colony description
Oxidase reaction
Oxidase positive = black colonies around Taxo N disc
Oxidase negative = colonies around Taxo N disc are not black
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3. Acid production from carbohydrate utilization
Organism
Glucose
Maltose
Sucrose
Lactose
Neisseria meningitidis
Positive = Acid (phenol red turns yellow)
Negative = No acid (phenol red remains red)
B. Mycobacterium tuberculosis
1. Acid-fast stain of sputum
Make a drawing of the acid-fast stain, noting the acid-fast reaction and the shape of the acid-fast bacteria.
Acid-fast stain
Mycobacterium tuberculosis
Acid-fast reaction
(red = +; blue =-)
Shape
2. Describe the granuloma seen in the guinea pig organs.
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1. Clostridium perfringens
a. Blood agar (Anaerobically grown)
Colony
description
Type of hemolysis
b. Litmus Milk (Anaerobically grown)

Color
(pink or lavender)
"Stormy fermentation"
Pink = Acid (fermentation)
Blue = Alkaline (no fermentation)
Stormy fermentation = Clotting of protein and gas production
2. Observe the tubes of Nutrient broth and Thioglycolate medium inoculated with Clostridium sporogenes.
Nutrient broth
(growth or no growth)
Thioglycolate medium
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LABORATORY 16
A. THE NEISSERIAE
DISCUSSION
1. State the gram reaction and the morphology of the neisseriae.
2. State the correct scientific names for the gonococcus and the meningococcus and indicate what
disease each causes.
3. Describe how symptoms of gonorrhea differ in the male and in the female.
4. State the possible urogenital complications of gonorrhea in the male and in the female.
5. Name four possible extragenital Neisseria gonorrhoeae infections.
6. State how congenital gonorrhea usually appears.
7. Give the normal habitat for Neisseria meningitidis and briefly describe how it reaches the
meninges.
ISOLATION AND IDENTIFICATION OF PATHOGENIC NEISSERIAE
1. Describe the appearance of a positive GC smear and indicate its significance in the diagnosis of
gonorrhea.
2. State where clinical specimens are obtained in the male and in the female for the isolation of
Neisseria gonorrhoeae.
3. State where clinical specimens are obtained for the isolation of Neisseria meningitidis when it is
causing meningitis.
4. Name a selective medium useful for the isolation of pathogenic Neisseria and describe how the
resulting colonies will appear.
5. State the results of N. gonorrhoeae and N. meningitidis for the oxidase test and for acid production
from oxidation of the sugars glucose, maltose, sucrose, and lactose.
RESULTS
1. Identify a positive GC smear and state how you can tell it is positive.
2. Identify an organism as N. gonorrhoeae or N. meningitidis and state the reasons why when it is
seen growing on MTM Chocolate agar with a Taxo N (oxidase) disc and in carbohydrate utilization
tubes containing the sugars glucose, maltose, sucrose, and lactose.
B. THE MYCOBACTERIA
DISCUSSION
1. Discuss one characteristic common to the genus Mycobacterium which allows us to distinguish
this organism from most other genera of bacteria.
2. List two pathogenic species of Mycobacterium and name the infection that each causes.
3. State the significance of Mycobacterium avium complex (MAC).
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DIAGNOSIS OF TUBERCULOSIS
1. State three presumptive tests for the diagnosis of tuberculosis.
2. State two methods used for confirmation of active tuberculosis.
3. Describe the appearance of a positive acid-fast stain for tuberculosis.
RESULTS
1. Identify a positive acid-fast stain and state how you can tell it is positive.
2. Recognize granuloma when shown a slide of a tuberculoid organ.
C. THE OBLIGATE ANAEROBES

DISCUSSION
1. Name the most common obligate anaerobe to cause infections in humans, state its normal habitat,
and name the most common type of infections it causes.
2. State three ways of culturing obligate anaerobes in the lab.
3. State the normal habitat of Clostridium perfringens and name an infection it may cause.
ISOLATION AND IDENTIFICATION OF CLOSTRIDIUM PERFRINGENS
1. Describe the appearance of C. perfringens when it is anaerobically-grown on Blood agar and in
Litmus Milk.
RESULTS
1. Identify an organism as C. perfringens and state the reasons why when given anaerobically-grown
cultures of Blood agar and Litmus Milk.
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LABORATORY 17
DIRECT SEROLOGIC TESTING
LABORATORY 17
SEROLOGY, PART 1:
A. Introduction to Serologic Testing
B. Using Antigen-Antibody Reactions in the Laboratory to Identify Unknown
Antigens
C. Examples of Direct Serologic Tests to Identify Unknown Antigens
DISCUSSION
A. INTRODUCTION TO SEROLOGIC TESTING
The adaptive immune responses refer to the ability of the body (self) to recognize specific foreign antigens
(non-self) that threaten its biological integrity. There are two major branches of the adaptive immune responses:
1. humoral immunity: humoral immunity involves the production of antibody molecules in response to an
antigen and is mediated by B-lymphocytes.
2. cell-mediated immunity: Cell-mediated immunity involves the production of cytotoxic T-lymphocytes,
activated macrophages, activated NK cells, and cytokines in response to an antigen and is mediated by Tlymphocytes.
To understand the immune responses we must first understand what is meant by the term antigen. Technically, an
antigen is defined as a substance that reacts with antibody molecules and antigen receptors on lymphocytes.
An immunogen is an antigen that is recognized by the body as nonself and stimulates an adaptive immune
response. For simplicity, both antigens and immunogens are usually referred to as antigens.
Chemically, antigens are large molecular weight proteins (including conjugated proteins such as glycoproteins,
lipoproteins, and nucleoproteins) and polysaccharides (including lipopolysaccharides). These protein and
polysaccharide antigens are found on the surfaces of viruses and cells, including microbial cells (bacteria, fungi,
protozoans) and human cells.
As mentioned above, the B-lymphocytes and T-lymphocytes are the cells that carry out adaptive immune
responses. The body recognizes an antigen as foreign when that antigen binds to the surfaces of B-lymphocytes and
T-lymphocytes by way of antigen-specific receptors having a shape that corresponds to that of the antigen (similar to
interlocking pieces of a puzzle). The antigen receptors on the surfaces of B-lymphocytes are antibody molecules
called B-cell receptors or sIg; the receptors on the surfaces of T-lymphocytes are called T-cell receptors (TCRs).
The actual portions or fragments of an antigen that react with receptors on B-lymphocytes and Tlymphocytes, as well as with free antibody molecules, are called epitopes or antigenic determinants. The size of
an epitope is generally thought to be equivalent to 5-15 amino acids or 3-4 sugar residues. Some antigens, such as
polysaccharides, usually have many epitopes, but all of the same specificity. This is because polysaccharides may be
composed of hundreds of sugars with branching sugar side chains, but usually contain only one or two different
sugars. As a result, most "shapes" along the polysaccharide are the same (see Fig. 1). Other antigens such as
proteins usually have many epitopes of different specificities. This is because proteins are usually hundreds of amino
acids long and are composed of 20 different amino acids. Certain amino acids are able to interact with other amino
acids in the protein chain and this causes the protein to fold over upon itself and assume a complex three-dimensional
shape. As a result, there are many different "shapes" on the protein (see Fig. 2). That is why proteins are more
immunogenic than polysaccharides; they are chemically more complex.
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A microbe, such as a single bacterium, has many different proteins (and polysaccharides) on its surface that
collectively form its various structures, and each different protein may have many different epitopes. Therefore,
immune responses are directed against many different parts or epitopes of the same microbe.
Fig. 1:
Epitopes of a polysaccharide antigen.
Fig. 2:
Epitopes of a protein antigen.
In terms of infectious diseases, the following may act as antigens:

1. Microbial structures (cell walls, capsules, flagella, pili, viral capsids, envelope-associated glycoproteins,
etc.); and
2. Microbial exotoxins
Certain noninfectious materials may also act as antigens if they are recognized as "nonself" by the body. These
include:
1. Allergens (dust, pollen, hair, foods, dander, bee venom, drugs, and other agents causing allergic
reactions);
2. Foreign tissues and cells (from transplants and transfusions); and
2. The body's own cells that the body fails to recognize as "normal self" (cancer cells, infected cells,
cells involved in autoimmune diseases).
Antibodies or immunoglobulins are specific protein configurations produced by B-lymphocytes and plasma cells
in response to a specific antigen and capable of reacting with that antigen. Antibodies are produced in the
lymphoid tissue and once produced, are found mainly in the plasma portion of the blood (the liquid fraction of the
blood before clotting). Serum is the liquid fraction of the blood after clotting.
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There are 5 classes of human antibodies: IgG, IgM, IgA, IgD, and IgE. The simplest antibodies, such as IgG, IgD,
and IgE, are "Y"-shaped macromolecules called monomers composed of four glycoprotein chains. There are two
identical heavy chains having a high molecular weight that varies with the class of antibody. In addition, there are two
identical light chains of one of two varieties: kappa or gamma. The light chains have a lower molecular weight. The
four glycoprotein chains are connected to one another by disulfide (S-S) bonds and noncovalent bonds (see Fig. 3A).
Additional S-S bonds fold the individual glycoprotein chains into a number of distinct globular domains. The area
where the top of the "Y" joins the bottom is called the hinge. This area is flexible to enable the antibody to bind to pairs
of epitopes various distances apart on an antigen.
The two tips of the "Y" monomer are referred to as the Fab portions of the antibody (see Fig. 3A). The first 110
amino acids or first domain of both the heavy and light chain of the Fab region of the antibody provide specificity for
binding an epitope on an antigen. The Fab portions provide specificity for binding an epitope on an antigen. The
bottom part of the "Y" is called the Fc portion and this part is responsible for the biological activity of the antibody
(see diagram of IgG; Fig. 3A). Depending on the class of antibody, biological activities of the Fc portion of antibodies
include the ability to activate the complement pathway (IgG & IgM), bind to phagocytes (IgG, IgA), or bind to mast
cells and basophils (IgE).
Two classes of antibodies are more complex. IgM is a pentamer (see Fig. 3B), consisting of 5 "Y"-like molecules
connected at their Fc portions, and secretory IgA is a dimer consisting of 2 "Y"-like molecules (see Fig. 3C).
Fig. 3:
Antibody structure (IgG)
For more information on antigens, antibodies, and antibody production, see the following Learning Objects in your
Lecture Guide:
Serology refers to using antigen-antibody reactions in the laboratory for diagnostic purposes. Its name comes
from the fact that serum, the liquid portion of the blood where antibodies are found is used in testing. Serologic
testing may be used in the clinical laboratory in two distinct ways:
Serologic testing may be used in the clinical laboratory in two distinct ways:
a. To identify unknown antigens such as microorganisms. This is called direct serologic testing. Direct
serologic testing uses a preparation known antibodies, called antiserum, to identify an unknown
antigen such as a microorganism and is the principle behind Lab 17.
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b. To detect antibodies being made against a specific antigen in the patient's serum. This is called
indirect serologic testing. Indirect serologic testing is the procedure by which antibodies in a person's
serum being made by that individual against an antigen associated with a particular disease are
detected using a known antigen. This is the principle behind Lab 18.
B. USING ANTIGEN-ANTIBODY REACTIONS IN THE LABORATORY TO IDENTIFY

UNKNOWN ANTIGENS SUCH AS MICROORGANISMS.
This type of serologic testing uses a known antiserum (serum containing specific known antibodies). The
preparation of known antibodies is prepared in one of two ways: in animals or by hybridoma cells.
1. Preparation of known antisera in animals.
Preparation of known antiserum in animals involves inoculating animals with specific known antigens such
as a specific strain of a bacterium. After the animals immune responses have had time to produce antibodies
against that antigen, the animal is bled and the blood is allowed to clot. The resulting liquid portion of the
blood is the serum and it will contain antibodies specific for the injected antigen.
However, one of the problems of using antibodies prepared in animals (by injecting the animal with a
specific antigen and collecting the serum after antibodies are produced) is that up to 90% of the antibodies in
the animal's serum may be antibodies the animal has made "on its own" against environmental antigens,
rather than those made against the injected antigen. The development of monoclonal antibody technique has
largely solved that problem.
2. Preparation of known antibodies by monoclonal antibody technique.
One of the major breakthroughs in immunology occurred when monoclonal antibody technique was
developed. Monoclonal antibodies are antibodies of a single specific type. In this technique, an animal is
injected with the specific antigen for the antibody desired. After appropriate time for antibody production, the
animal's spleen is removed. The spleen is rich in plasma cells and each plasma cell produces only one
specific type of antibody. However, plasma cells will not grow artificially in cell culture. Therefore, a plasma
cell producing the desired antibody is fused with a myeloma cell (a cancer cell from bone marrow which
will grow rapidly in cell culture) to produce a hybridoma cell. The hybridoma cell has the characteristics of
both parent cells. It will produce the specific antibodies like the plasma cell and will also grow readily in
cell culture like the myeloma cell. The hybridoma cells are grown artificially in huge vats where they
produce large quantities of the specific antibody (see Fig. 4).
Monoclonal antibodies are now used routinely in medical research and diagnostic serology and are being
used experimentally in treating certain cancers and a few other diseases.
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Fig. 4:
Preparation of monoclonal antibodies.
Fig. 4, Step 1
Fig. 4, Step 2
Fig. 4, Step 3
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3. The concept and general procedure for direct serologic testing.

The concept and general procedure for using antigen-antibody reactions to identify unknown antigens are
as follows:
Concept:
This testing is based on the fact that antigen- antibody reactions are very specific. Antibodies usually
react only with the antigen that stimulated their production in the first place, and are just as specific as
an enzyme-substrate reaction. Because of this, one can use known antiserum (prepared by animal
inoculation or monoclonal antibody technique as discussed above) to identify unknown antigens such as a
microorganism.
General Procedure:
A suspension of the unknown antigen to be identified is mixed with known antiserum for that antigen.
One then looks for an antigen-antibody reaction.
Examples of serologic tests used to identify unknown microorganisms include the serological typing of
Shigella and Salmonella (Lab 13), the Lancefield typing of beta streptococci (Lab 14), and the serological
identification of Neisseria gonorrhoeae and Neisseria meningitidis (Lab 16). Serological tests used to identify
antigens that are not microorganisms include blood typing, tissue typing, and pregnancy testing.
4. Detection of antigen-antibody reactions in the laboratory
Antigen-antibody reactions may be detected in the laboratory by a variety of techniques. Some of the
commonly used techniques for observing in vitro antigen-antibody reactions are briefly described below.
a. Agglutination
Known antiserum causes bacteria or other particulate antigens to clump together or agglutinate.
Molecular-sized antigens can be detected by attaching the known antibodies to larger, insoluble
particles such as latex particles or red blood cells in order to make the agglutination visible to the
naked eye.
b. Precipitation
Known antiserum is mixed with soluble test antigen and a cloudy precipitate forms at the zone of
optimum antigen-antibody proportion.
c. Complement-fixation
Known antiserum is mixed with the test antigen and complement is added. Sheep red blood cells
and hemolysins (antibodies that lyse the sheep red blood cells in the presence of free complement)
are then added. If the complement is tied up in the first antigen-antibody reaction, it will not be
available for the sheep red blood cell-hemolysin reaction and there will be no hemolysis. A negative
test would result in hemolysis.
d. Enzyme immunoassay (EIA)
Test antigens from specimens are passed through a tube (or a membrane) coated with the
corresponding specific known antibodies and become trapped on the walls of the tube (or on the
membrane). Known antibodies to which an enzyme has been chemically attached are then passed
through the tube (or membrane) where they combine with the trapped antigens. Substrate for the
attached enzyme is then added and the amount of antigen-antibody complex formed is proportional
to the amount of enzyme-substrate reaction as indicated by a color change.
e. Radioactive binding techniques
Test antigens from specimens are passed through a tube coated with the corresponding specific
known antibodies and become trapped on the walls of the tube. Known antibodies to which a
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radioactive isotope has been chemically attached are then passed through the tube where they
combine with the trapped antigens. The amount of antigen-antibody complex formed is proportional
to the degree of radioactivity.
f. Fluorescent antibody technique
A fluorescent dye is chemically attached to the known antibodies. When the fluorescent antibody
reacts with the antigen, the antigen will fluoresce when viewed with a fluorescent microscope.
C. EXAMPLES OF DIRECT SEROLOGIC TEST TO IDENTIFY UNKNOWN

ANTIGENS
As stated above, this type of serologic testing uses known antiserum (antibodies) to identify unknown
antigens. Four such tests will be looked at in lab today.
1. Serological Typing of Shigella
Discussion
There are four different serological subgroups of Shigella, each corresponding to a different species:
subgroup A = Shigella dysenteriae
subgroup B = Shigella flexneri
subgroup C = Shigella boydii subgroup D = Shigella sonnei
Known antiserum is available for each of the 4 subgroups of Shigella listed above and contains antibodies
against the cell wall ("O" antigens) of Shigella. The suspected Shigella (the unknown antigen) is placed in
each of 4 circles on a slide and a different known antiserum (A, B, C or D) is then added to each circle. A
positive antigen-antibody reaction appears as a clumping or agglutination of the Shigella (Fig. 5).
Fig. 5:
Agglutination of Shigella using known antiserum.
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2. Serological Typing of Streptococci
Discussion
The OSOM Strep A Exact Test is a qualitative serologic test for detecting Group A Streptococcal
antigen (the unknown antigen) directly from throat swabs and is used as an aid in diagnosing
streptococcal pharyngitis caused by Streptococcus pyogenes (Group A Beta Streptococci).
The test consists of a membrane strip that is precoated with rabbit anti-Strep A antibody-blue latex
conjugate (known antibody with blue latex particles attached) located in a pad at the beginning of
the strip. It is also precoated with rabbit anti-Strep A antibody (known antibody without attached blue
latex) that is immobilized at the test line where the test results are read (see Fig. 6A). The blue latex
particles attached to the rabbit anti-Strep A antibody is what ultimately causes the positive blue band.
When the test strip is immersed in the extracted sample, the Group A Streptococcal antigen extracted
from the Streptococcus pyogenes on the throat swab of a person with strep throat begins to move
chromatographically up the membrane and binds to the blue-colored known antibody-latex conjugate
in the pad located at the beginning of the strip, forming a Strep A antigen-antibody complex (see Fig.
6B). This Strep A antigen-antibody complex continues to moves up the membrane to the test line region
where the immobilized rabbit anti-Strep A antibodies are located.
If Group A Streptococcal antigen is present in the throat swab, a blue-colored sandwich of
antibody/Strep A antigen/blue latex conjugate antibody forms in the test result region of the strip
(see Fig. 6C). The red color at the control line region lets you know the test is finished. As a result,
a positive test for Group A Strep antigen appears as a blue band in the test result area and a red
band in the control area (see Fig. 6C).
Fig. 6A:
Strep A Test Strip
Fig. 6B:
Strep A Antigen/Gold Conjugate Antibody Complex
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If there is no Group A Streptococcal antigen present in the throat swab no blue band appears in the test
result region of the strip and a single red band appears in the control line region, indicating a
negative test for Group A Strep antigen (see Fig. 6D).
3. Serological Testing to Diagnose Pregnancy

Discussion
The hormone human chorionic gonadotropin (HCG), produced by the placenta, appears in the serum
and urine of pregnant females. The HCG is composed of two subunits - alpha and beta. The QuickVue+
HCG-Combo Test is a one step pregnancy test that detects measurable levels of HCG as early as early as
7-10 days after conception. HCG, the unknown antigen for which one is testing, is identified in the urine by
using known monoclonal antibody against human HCG.
This test uses a color immunochromatographic assay to detect the antigen-antibody reaction. Inside the
plastic card is a membrane strip along which the urine flows and on which the reaction occurs. The urine is
placed in the "add urine" well on the right side of the card and flows along the card from right to left.
The membrane just to the left of the sample well is coated with red latex beads to which known
antibodies against the beta chain of human HCG have been attached. If there is HCG in the urine, the
beta subunit of the HCG will react with the known anti-beta HCG antibody/red latex conjugate and this
complex of HCG-antibody/red latex will become mobilized and flow with the urine towards the left side of
the card. In the "read results" window of the card is a vertical line to which is immobilized known
antibodies against the alpha subunit of human HCG. As the urine containing the antibody/red latex
conjugate bound to the beta subunit of HCG flows past the vertical line, the alpha subunit of the HCG binds to
the immobilized antibodies located on the line, trapping the complex and causing a vertical red line to appear.
The vertical line crosses the horizontal blue line preprinted in the "read results" window to form a (+) sign
(Fig. 7, steps 1 and 2).
If the woman is not pregnant and there is no HCG in the urine, then there will be no antigen to react with the
anti-beta HCG antibody/red latex conjugate to the left of the sample well and likewise, no reaction with the
anti-alpha HCG antibodies immobilized along the vertical line in the "read results" window. The antibody/red
latex conjugate will continue to flow to the left of the slide until it reaches the "test complete" window. Since no
vertical red line forms, a (-) sign appears in the "read results" window.
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LABORATORY 17
Fig. 7:
Serological Testing to Diagnose Pregnancy
Fig. 7, step 1
Fig. 7, step 2
The HCG molecule has tw chains: an alpha chain and

a beta chain. Known antibodies can be made against
both of these parts of HCG.
Known antibodies against the beta chain of the HCG in

the urine react with the HCG. Red latex particles are
attached to these antibodies.
Fig. 7, step 3
Known antibodies against the alpha chain of the HCG are fixed to the membrane above
and below the printed blue "minus" sign. As the HCG molecules with bound antibody and
red latex move across the membrane with the urine, the alpha chain of the HCGs bind to
the fixed antibodies on the membrane creating the "plus" sign.
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LABORATORY 17
4. Identification of Microorganisms Using the Direct Fluorescent Antibody Technique

Discussion
Certain fluorescent dyes can be chemically attached to the known antibody molecules in antiserum.
The known fluorescent antibody is then mixed with the unknown antigen (such as a microorganism) fixed
to a slide. After washing, to remove any fluorescent antibody not bound to the antigen, the slide is viewed
with a fluorescent microscope. If the fluorescent antibody reacted with the unknown antigen, the antigen
will glow or fluoresce under the fluorescent microscope. If the fluorescent antibody did not react with the
antigen, the antibodies will be washed off the slide and the antigen will not fluoresce.
For example, in the direct fluorescent antibody test for Neisseria gonorrhoeae, mentioned briefly in lab
16, the unknown antigen, suspected Neisseria gonorrhoeae,is fixed to a microscope slide. Known
fluorescent antibodies made against N. gonorrhoeae are then added (see Fig. 8, step-1) and the slide is
then washed to remove any fluorescent antibody not bound to the antigen. The slide is then viewed under
a fluorescent microscope.
If the unknown antigen is Neisseria gonorrhoeae, the known antibodies against N. gonorrhoeae
with attached fluorescent dye will bind to the bacterium and will not wash off. The bacteria will
fluoresce when viewed under a fluorescent microscope (see Fig. 8, step-2). If the unknown antigen is not
N. gonorrhoeae, the known fluorescent antibodies against will wash off the slide and the bacteria will not
fluoresce when viewed under a fluorescent microscope.
Many bacteria, viruses, and fungi can be identified using this technique.
Fig. 8:
Direct Fluorescent Antibody Test for Neisseria gonorrhoeae
Fig. 8, step 1
Fig. 8, step 2
The unknown antigen, suspected Neisseria

gonorrhoeae, is fixed to a microscope slide. Known
fluorescent antibodies made against N. gonorrhoeae
are added. The slide is then washed and viewed under
205
If the unknown antigen is Neisseria gonorrhoeae, the

known antibodies against N. gonorrhoeae with attached
fluorescent dye will bind to the bacterium and will not
wash off. The bacteria will fluoresce when viewed under
LABORATORY 17
PROCEDURE
A. Serologic Typing of Shigella
1. Using a wax marker, label four circles of a serology slide A, B, C, and D, as shown below.
2. Add one drop of the suspected Shigella (unknown antigen) to each circle. (The Shigella has
been treated with formalin to make it noninfectious but still antigenic.)
3. Now add one drop of known Shigella subgroup A antiserum to the "A" circle, one drop of known
Shigella subgroup B antiserum to the "B" circle, one drop of known Shigella subgroup C antiserum
to the "C" circle, and one drop of known Shigella subgroup D antiserum to the "D" circle.
4. Rotate the slide carefully for 30-60 seconds and look for agglutination of the bacteria,
indicating a positive reaction (Fig. 9).
5. Dispose of all pipettes and slides in the disinfectant container.
Fig. 9:
Agglutination of Shigella.
B. Serologic Typing of Streptococci

1. Add 3 drops of Extraction Reagent #1 to the extraction tube. This reagent contains 5M sodium
nitrite and should be pink to purple in color.
2. Add 3 drops of Extraction Reagent #2 to the extraction tube. This reagent contains 0.03M citric
acid. The solution must turn yellow in color.
3. Place the throat swab in the extraction tube and roll it with a circular motion inside the tube. Let
stand for at least 1 minute.
4. Squeeze the swab firmly against the extraction tube to expel as much liquid as possible from the
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LABORATORY 17
swab and discard the swab in the biowaste container.
5. Immerse the test strip into the extraction tube with the arrows pointing toward the extracted
sample solution. Leave the strip in the tube and start timing.
6. Read results in 5 minutes. A red band in both the control region and the test region indicates a
positive test (See Fig. 6C). A single red band in the control region only indicates a negative test
(See Fig. 6D). No colored band in the control region indicates an invalid test.
Fig. 6C:
Positive Strep A Antigen Test
Fig. 6D:
Negative Strep A Antigen Test
C. Serologic Testing to Detect Pregnancy

1. Fill the disposable pipette to the line with urine and dispense the urine into the "add urine" well of
the QuickVue+ HCG-Combo Test.
2. Shortly after the urine is added, a blue color will be seen moving across the "read results" window.
3. The test results can be read in the "read results" window when a distinct blue line appears in the
"test complete" window (approximately 5 minutes). A (+) sign indicates a positive test.
D. The Direct Fluorescent Antibody Technique

Observe the demonstration of a positive direct fluorescent antibody test for Neisseria gonorrhoeae.
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LABORATORY 17
RESULTS
A. Serologic Typing of Shigella
Make a drawing of your results.
Shigella typing slides
B. Serologic Identification of Group A Streptococci

Make a drawing of your results.
Strep A strip
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LABORATORY 17
C. Serologic Testing to Diagnose Pregnancy

Make a drawing of a positive pregnancy test.
QuickVue+ HCG-Combo Test
D. The Direct Fluorescent Antibody Technique

Make a drawing and describe a positive direct fluorescent antibody test.
A positive direct fluorescent antibody test for Neisseria gonorrhoeae.
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LABORATORY 17
LABORATORY 17
A. INTRODUCTION TO SEROLOGICAL TESTING

1. Define serology.
2. Define antigen and state what may act as an antigen.
3. Define antibody and state where they are primarily found in the body.
4. Define direct serologic testing and indirect serologic testing.
B. USING ANTIGEN-ANTIBODY REACTIONS IN THE LAB TO IDENTIFY UNKNOWN

ANTIGENS SUCH AS MICROORGANISMS
1. Define antiserum.
2. Describe two ways of producing known antiserum.
3. Describe the concept and general procedure for using serologic testing to identify unknown antigens (direct
serologic testing).
C. EXAMPLES OF SEROLOGIC TESTS TO IDENTIFY UNKNOWN ANTIGENS

DISCUSSION
1. Describe how to determine serologically whether an organism is a subgroup A, B, C, or D Shigella.
2. Describe how to serologically identify Lancefield group A Streptococcus causing pharyngitis.
3. Describe how to diagnose pregnancy serologically.
4. Briefly describe the direct fluorescent antibody technique.
RESULTS
1. Correctly interpret the results of the following serological tests:
a. serological typing of Shigella
b. serological identification of Group A Streptococcal antigen
c. serological testing for pregnancy
a direct fluorescent antibody test
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LABORATORY 18
INDIRECT SEROLOGIC TESTING
LABORATORY 18
SEROLOGY, PART 2:
A. Using Antigen-Antibody Reactions in the Laboratory to Indirectly Diagnose
Disease by Detecting Antibodies in a Person's Serum Produced Against a
Disease Antigen
B. Examples of Indirect Serologic Tests to Detect Antibodies in the Patient's
Serum
DISCUSSION
A. USING ANTIGEN-ANTIBODY REACTIONS IN THE LABORATORY TO INDIRECTLY
DIAGNOSE DISEASE BY DETECTING ANTIBODIES IN A PERSON'S SERUM PRODUCED
AGAINST A DISEASE ANTIGEN
As stated in the introduction to serological testing in Lab 17, indirect serologic testing is the procedure whereby
antibodies in a person's serum being made by that individual against an antigen associated with a particular
disease are detected using a known antigen.
1. The concept and general procedure for indirect serologic testing.
The concept and general procedure for this type of serological testing are as follows:
Concept:
This type of testing is based on the fact that antibodies are only produced in response to a
specific antigen. In other words, a person will not be producing antibodies against a disease
antigen unless that antigen is in the body stimulating antibody production.
General Procedure:
A sample of the patient's serum (the liquid portion of the blood after clotting and containing
antibodies against the disease antigen if the person has or has had the disease) is mixed with the
known antigen for that suspected disease. One then looks for an antigen-antibody reaction.
Examples of serologic tests to diagnose disease by the detection of antibodies in the patient's
serum include the following: the various serological tests for syphilis or STS (such as the RPR, the
VDRL, and the FTA-ABS tests), the tests for infectious mononucleosis, the tests for the Human
Immunodeficiency Virus (HIV), the tests for systemic lupus erythematosus, and tests for variety of
other viral infections.
2. Qualitative and quantitative serologic tests.
Indirect serologic tests may be qualitative or quantitative. A qualitative test only detects the presence or
absence of specific antibodies in the patient's serum and is often used for screening purposes. A
quantitative test gives the titer or amount of that antibody in the serum. Titer indicates how far you can
dilute the patient's serum and still have it contain enough antibodies to give a detectable
antigen-antibody reaction. In other words, the more antibodies being produced by the body, the more you
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LABORATORY 18
can dilute the person's serum and still see a reaction. Quantitative serological tests are often used to follow
the progress of a disease by looking for a rise and subsequent drop in antibody titer.
3. Detection of antigen-antibody reactions in the laboratory
Antigen-antibody reactions may be detected in the laboratory by a variety of techniques. Some of the
commonly used techniques are briefly described below.
a. Agglutination
Antibodies in the patient's serum cause the known particulate antigens or cells to clump or
agglutinate. Molecular-sized known antigens can be attached to larger, insoluble particles such as
latex particles, red blood cells, or charcoal particles in order to observe agglutination with the naked
eye.
b. Precipitation
The patient's serum is mixed with soluble known antigen and a cloudy precipitate forms at the zone
of optimum antigen-antibody proportion.
c. Complement-fixation
The patient's serum is mixed with the known antigen and complement is added. Sheep red blood
cells and hemolysins (antibodies that lyse the sheep red blood cells in the presence of free
complement) are then added. If the complement is tied up in the first antigen-antibody reaction, it will
not be available for the sheep red blood cell-hemolysin reaction and there will be no hemolysis. A
negative test would result in hemolysis.
d. Enzyme immunoassay (EIA)
The patient's serum is placed in a tube or well coated with the corresponding known antigen and
becomes trapped on the walls of the tube. Enzyme-labeled anti-human gamma globulin or anti-HGG
(antibodies made in another animal against the Fc portion of human antibody and to which an
enzyme has been chemically attached), is then passed through the tube where it combines with the
trapped antibodies from the patient's serum. Substrate for the enzyme is then added and the amount
of antibody-antigen complex formed is proportional to the amount of enzyme-substrate reaction as
indicated by a color change.
e. Radioactive binding techniques
The patient's serum is passed through a tube coated with the corresponding known antigen and
becomes trapped on the walls of the tube. Radioisotope-labeled anti-human gamma globulin or antiHGG (antibodies made in another animal against the Fc portion of human antibody and to which a
radioactive isotope has been chemically attached), is then passed through the tube where it
combines with the trapped antibodies from the patient's serum. The amount of antibody-antigen
complex formed is proportional to the degree of radioactivity measured.
f. Fluorescent antibody technique
The patient's serum is mixed with known antigen fixed to a slide. Fluorescent anti-human gamma
globulin or anti-HGG (antibodies made against the Fc portion of human antibody and to which a
fluorescent dye has been chemically attached) is then added. It combines with the antibodies from
the patient's serum bound to the antigen on the slide causing the antigen to fluoresce when viewed
with a fluorescent microscope.
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B. EXAMPLES OF INDIRECT SEROLOGIC TESTS TO DETECT

ANTIBODIES IN THE PATIENT'S SERUM
1. The RPR Test for Syphilis
Discussion
Syphilis is a sexually transmitted disease caused by the spirochete Treponema pallidum. The RPR (Rapid
Plasma Reagin) Card test is a presumptive serologic screening test for syphilis. The serum of a person
with syphilis contains a nonspecific antilipid antibody (traditionally termed reagin), which is not found in
normal serum. The exact nature of the antilipid (reagin) antibody is not known but it is thought that a syphilis
infection instigates the breakdown of the patient's own tissue cells. Fatty substances which are released then
combine with protein from Treponema pallidum to form an antigen which stimulates the body to produce
antibodies against both the body's tissue lipids (nonspecific or nontreponemal) as well as the T.
pallidum protein (specific or treponemal). The RPR Card test detects the nonspecific antilipid antibody
and is referred to as a nontreponemal test for syphilis.
It must be remembered that tests for the presence of these nonspecific anti-lipid antibodies are meant as a
presumptive screening test for syphilis. Similar regain-like antibodies may also be present as a result of other
diseases such as malaria, leprosy, infectious mononucleosis, systemic lupus erythematosus, viral
pneumonia, measles, and collagen diseases and may give biologic false-positive results (BFP). Confirming
tests should be made for the presence of specific antibodies against the T. pallidum itself. The confirming test
for syphilis is the FTA-ABS test discussed below. Any serologic test for syphilis is referred to commonly as an
STS (Serological Test for Syphilis).
The known RPR antigen consists of cardiolipin, lecithin, and cholesterol bound to charcoal particles
in order to make the reaction visible to the naked eye. If the patient has syphilis, the antilipid antibodies in his
or her serum will cross-react with the known RPR lipid antigens giving a visible clumping of the charcoal
particles (see Fig. 1).
We will do a quantitative RPR Card test today in lab. Keep in mind that a quantitative test allows one to
determine the titer or amount of a certain antibody in the serum. In this test, a constant amount of RPR
antigen is added to dilutions of the patient's serum. The most dilute sample of the patient's serum still
containing enough antibodies to give a visible antigen-antibody reaction is reported as the titer.
Fig. 1:
A positive RPR test.
Note clumping of carbon particles.
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2. Serologic Tests for Infectious Mononucleosis

Discussion
During the course of infectious mononucleosis, caused by the Epstein-Barr virus (EBV), the body produces
nonspecific heterophile antibodies that are not found in normal serum. As it turns out, these heterophile
antibodies will also cause horse or sheep erythrocytes (red blood cells) to agglutinate (Fig. 2).
Fig. 2:
A positive test for mononucleosis.
Note clumping of red blood cells.
The infectious mononucleosis serologic test demonstrated today is a rapid qualitative test for infectious
mononucleosis that uses specially treated horse erythrocytes (acting as the "known antigen") that are
highly specific for mononucleosis heterophile antibodies. Agglutination of erythrocytes after adding the
patient's serum indicates a positive test. Quantitative tests may be done to determine the titer of heterophile
antibodies and follow the progress of the disease.
3. Serologic Tests for Systemic Lupus Erythematosus (SLE)

Discussion
Systemic lupus erythematosus or SLE is a systemic autoimmune disease. Immune complexes become
deposited between the dermis and the epidermis, and in joints, blood vessels, glomeruli of the kidneys, and
the central nervous system. It is four times more common in women than in men. In SLE, autoantibodies are
made against components of DNA. This test is specific for the serum anti-deoxyribonucleoprotein
antibodies associated with SLE. The known antigen is deoxyribonucleoprotein adsorbed to latex
particles to make the reaction more visible to the eye (see Fig. 3). This is a qualitative test used to screen
for the presence of the disease and to monitor its course.
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Fig. 3:
A positive test for SLE. Note agglutination of
latex particles
to which the known antigen is adsorbed.
4. Detecting Antibody Using the Indirect Fluorescent Antibody Technique: The FTA-ABS test for
syphilis
Discussion
The indirect fluorescent antibody technique involves three different reagents:
1) The patient's serum (containing antibodies against the disease antigen if the disease is present)
2) Known antigen for the suspected disease
3) Fluorescent anti-human gamma globulin antibodies (antibodies made in another animal
against the Fc portion of human antibodies (see Fig. 9) by injecting an animal with human serum. A
fluorescent dye is then chemically attached to the anti-human gamma globulin (anti-HGG)
antibodies.
The FTA-ABS test (Fluorescent Treponemal Antibody Absorption Test) for syphilis is an example of an
indirect fluorescent antibody procedure. This is the confirming test for syphilis since it tests specifically for
antibodies in the patient's serum made in response to the syphilis spirochete, Treponema pallidum.
In this test, killed T. pallidum,(the known antigen), is fixed on a slide (Fig. 4, step 1). The patient's serum is
then added. If the patient has syphilis, antibodies against the T. pallidum will react with the antigen on the
slide (Fig. 4, step 2). The slide is then washed to remove any antibodies not bound to the spirochete.
To make this reaction visible, a second animal-derived antibody made against human antibodies and
labelled with a fluorescent dye (fluorescent anti-human gamma globulin) is added. These fluorescent antiHGG antibodies react with the patient's antibodies that have reacted with the T. pallidum on the slide (Fig. 4,
step 3). The slide is washed to remove any unbound fluorescent anti-HGG antibodies and observed with a
fluorescent microscope. If the spirochetes glow or fluoresce, the patient has made antibodies against T.
pallidum and has syphilis (Fig. 5).
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LABORATORY 18
Fig. 9:
IgG
Fig. 4:
The FTA-ABS test for syphilis (Indirect fluorescent antibody test)
Fig. 4, step 1:
Fig. 4, step 2:
The known antigen, Treponema pallidum, is fixed to the
The patients serum is added to the slide. The slide is then
slide.
washed.
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LABORATORY 18
Fig. 4, step 3:
Fluorescent anti-HGG is added to the slide. The slide is
then washed and viewed by means of a fluorescent
microscope.
Fig. 5:
A positive FTA-ABS test for syphilis.
5. The EIA and Western Blot serologic tests for antibodies against the Human Immunodeficiency
Virus (HIV)
Discussion
In the case of the current HIV antibody tests, the patient's serum is mixed with various HIV antigens
produced by recombinant DNA technology. If the person is seropositive (has repeated positive
antigen-antibody tests), then HIV must be in that person's body stimulating antibody production. In other
words, the person must be infected with HIV. The two most common tests currently used to detect antibodies
against HIV are the enzyme immunoassay or EIA (also known as the enzyme-linked immunosorbant
assay or ELISA) and the Western blot or WB. A person is considered to be seropositive for HIV infection
only after an EIA screening test is repeatedly reactive and another test such as the WB has been performed
to confirm the results.
The EIA is less expensive, faster, and technically less complicated than the WB and is the procedure
initially done as a screening test for HIV infection. The various EIA tests give a spectrophotometric reading of
the amount of antibody binding to known HIV antigens.
The EIA test kit contains plastic wells to which various HIV antigens have been adsorbed (Fig. 6, step
1). The patient's serum is added to the wells and any antibodies present in the serum against HIV antigens
will bind to the corresponding antigens in the wells (Fig. 6, step 2). The wells are then washed to remove all
antibodies in the serum other than those bound to HIV antigens. Enzyme-linked anti-human gamma
globulin (anti HGG) antibodies are then added to the wells (Fig. 6, step 3). These antibodies, made in
another animal against the Fc portion of human antibodies by injecting the animal with human serum, have
an enzyme chemically attached. They react with the human antibodies bound to the known HIV antigens.
The wells are then washed to remove any anti-HGG that has not bound to serum antibodies. A substrate
specific for the enzyme is then added and the resulting enzyme-substrate reaction causes a color change
in the wells (Fig. 6, step 4). If there are no antibodies in the patient's serum against HIV, there will be nothing
for the enzyme-linked anti-HGG to bind to and it will be washed from the wells. When the substrate is added,
there will be no enzyme present in the wells to give a color change.
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LABORATORY 18
Fig. 6:
Enzyme Immunoassay
Fig. 6, step 1:
The test well contains known HIV antigens.
Fig. 6, step 3:
Anti-HGG with attached enzyme is added to the wells.
The wells are then washed.
Fig. 6, step 2:
The patients serum is added to the wells. The wells
are then washed.
Fig. 6, step 4:
Substrate is added for the enzyme-linked anti-HGG.
The enzyme-substrate reaction causes a color
change in the wells.
If the initial EIA is reactive it is automatically repeated to reduce the possibility that technical laboratory
error caused the reactive result. If the EIA is still reactive, it is then confirmed by the Western blot test.
The Western blot WB is the test most commonly used as a confirming test if the EIA is repeatedly positive.
The WB is technically more complex to perform and interpret, is more time consuming, and is more
expensive than the EIAs.
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LABORATORY 18
With the WB, the various protein and glycoprotein antigens from HIV are separated according to their
molecular weight by gel electrophoresis (a procedure that separates charged proteins in a gel by applying an
electric field). Once separated, the various HIV antigens are transferred to a nitrocellulose strip (Fig. 7, step 1
and step 2). The patient's serum is then incubated with the strip and any HIV antibodies that are present will
bind to the corresponding known HIV antigens on the strip (Fig. 7, step 3). As with the EIA mentioned above,
antigen-antibody reactions can then be detected using enzyme-linked anti-human gamma globulin antibodies
(anti-HGG), as shown in Fig. 7, step 4 and step 5).
Fig. 7:
The Western Blot Test
Fig. 7, step 1
Fig. 7, step 2:
A section of the strip containing the known HIV
antigen gp120.
Fig. 7, step 3:
The patients serum is added to the strip. The strip is
then washed.
Fig. 7, step 4:
Enzyme-linked anti-HGG is added to the strip. The
strip is then washed.
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LABORATORY 18
Fig. 7, step 5:
Substrate is added for the enzyme-linked anti-HGG. The
enzyme-substrate reaction causes a color change on the strip.
It should be mentioned that all serologic tests are capable of giving occasional false-positive and falsenegative results. The most common cause of a false-negative HIV antibody test is when a person has been
only recently infected with HIV and his or her body has not yet made sufficient quantities of
antibodies to give a visible positive serologic test. It generally takes between 2 weeks and 3 months after
a person is initially infected with HIV to convert to a positive HIV antibody test.
A number of commercial rapid HIV tests have also been improved for detecting antibody against HIV.
They include:
OraQuick Advance HIV1/2: uses either a finger-stick blood speciman or an oral speciman.
Uni-Gold Recombigen: uses either a finger-stick or whole blood speciman.
Reveal G2: Uses serum or plasma.
Multispot HIV-1/HIV-2: Uses serum or Plasma.
PROCEDURE
A. The RPR Card Test for Syphilis (demonstration)
1. Label 6 test tubes as follows: 1:1, 1:2, 1:4, 1:8, 1:16, and 1:32.
2. Using a 1.0 ml pipette, add 0.5 ml of 0.9% saline solution into tubes 1:2, 1:4, 1:8, 1:16, and
1:32.
3. Add 0.5 ml of the patient's serum to the 1:1 tube (undiluted serum).
4. Add another 0.5 ml of serum to the saline in the 1:2 tube and mix. Remove 0.5 ml from the 1:2
tube and add it to the 1:4 tube and mix. Remove 0.5 ml from the 1:4 tube, add to the 1:8 tube and
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LABORATORY 18
mix. Remove 0.5 ml from the 1:8 tube, add to the 1:16 tube and mix. Remove 0.5 ml from the 1:16
tube, add to the 1:32 tube and mix. Remove 0.5 ml from the 1:32 tube and discard. The dilution of
the serum is summarized in Fig. 8.
Fig. 8:
Diluting the patients serum in a quantitative RPR card test.
5. Using the capillary pipettes provided with the kit, add a drop of each serum dilution to separate
circles of the RPR card. Spread the serum over the entire inner surface of the circle with the tip of the
pipette, using a new pipette for each serum dilution.
6. Using the RPR antigen dispenser, add a drop of known RPR antigen to each circle. Do not let
the needle of the dispenser touch the serum. Using disposable stirrers, mix the known RPR antigen
with the serum in each circle.
7. Place the slide on a shaker and rotate for a maximum of 4 minutes.
8. Read the results as follows:
- A definite clumping of the charcoal particles is reported as reactive (R) (see Fig. 1).
- No clumping is reported as nonreactive (N).
The greatest serum dilution that produces a reactive result is the titer. For example, if the dilutions turned
out as follows, the titer would be reported as 1:4 or 4 dils.
1:1
1:2
1:4
1:8
1:16
1:32
B. The Serologic Tests for Infectious Mononucleosis (demonstration)

1. Place one drop of each of the patient's serum in circles on the test slide.
2. Add one drop of treated horse erythrocytes (the known antigen) to each circle and mix with
disposable applicator sticks.
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3. Rock the card gently for 1 minute, then leave undisturbed for 1 minute, and observe for
agglutination of the red blood cells. Agglutination of the horse erythrocytes (see Fig. 2) indicates the
presence of heterophile antibodies.
C. The Serologic Tests for Systemic Lupus Erythematosus (SLE)

1. Add one drop of each of the patient's serum to separate circles on the test slide.
2. Add one drop of the Latex-Deoxyribonucleoprotein reagent to each serum sample and mix
with disposable applicator sticks. The known antigen, deoxyribonucleoprotein adsorbed to latex
particles to make agglutination visible to the naked eye (Fig. 3).
3. Rock the slide gently for 1 minute and observe for agglutination. Agglutination indicates the
presence of antinuclear antibodies associated with SLE.
D. The FTA-ABS Test for Syphilis (Indirect Fluorescent Antibody Technique)

Observe the 35mm slide of a positive FTA-ABS test.
E. The EIA and WB Tests for HIV Antibodies
Observe Figures 6 and 7.
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RESULTS
A. RPR Card Test for Syphilis (Quantitative)
Detects non-treponemal anti-lipid antibodies (reagin)
Record your results:
Dilution
Result
1:1
1:2
1:4
1:8
1:16
1:32
titer
R = Reactive (distinct clumps)
N = Non-reactive (no clumps)
B. MONO-TEST for Infectious Mononucleosis (Qualitative)

Detects heterophile antibodies.
Draw the results of a positive and a negative test.
Mono-Test
(+) = Agglutination of RBCs
(-) = No agglutination of RBCs
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C. Serologic test for SLE (Qualitative)

Detects anti-deoxyribonucleoprotein antibodies.
Draw the results of a positive and a negative test.
SLE Test
(+) = Agglutination
(-) = No agglutination
D. FTA-ABS Test for Syphilis (Confirming)

Detects antibodies against Treponema pallidum
Draw the results of a positive FTA-ABS test.
Positive FTA-ABS Test for Syphilis

(Fluorescent spirochetes)
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LABORATORY 18
DISCUSSION
1. State the principle and the general procedure behind indirect serologic testing.
2. State the difference between a qualitative serological test and a quantitative serological test.
3. Define titer.
4. State what disease the RPR and the FTA-ABS procedures test for. Indicate which of these is a
presumptive test, which is a confirming test, and why.
5. State the significance of non-treponemal anti-lipid (reagin) antibodies in serological testing.
6. State the significance of heterophile antibodies in serological testing.
7. State the significance of anti-deoxyribonucleoprotein antibodies in serological testing.
8. Briefly describe the indirect fluorescent antibody technique.
9. Briefly describe the EIA test for HIV antibodies and state the significance of a positive HIV antibody test.
10. State the most common reason for a false-negative HIV antibody test.
RESULTS
1. Interpret the results of the following serological tests:
a. serologic test for infectious mononucleosis
b. serologic test for SLE
c. FTA-ABS test
2. Determine the titer of a quantitative RPR Card test.
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LABORATORY 19
USING PHYSICAL AGENTS TO CONTROL MICROORGANISMS
LABORATORY 19
USING PHYSICAL AGENTS TO
CONTROL OF MICROORGANISMS
A. Introduction to the Control of Microorganisms
B. Temperature
C. Desiccation
D. Osmotic Pressure
E. Radiation
F. Filtration
A. INTRODUCTION TO THE CONTROL OF MICROORGANISMS

The next three labs deal with the inhibition, destruction, and removal of microorganisms. Control of microorganisms
is essential in order to prevent the transmission of diseases and infection, stop decomposition and spoilage, and
prevent unwanted microbial contamination.
Microorganisms are controlled by means of physical agents and chemical agents. Physical agents include such
methods of control as high or low temperature, desiccation, osmotic pressure, radiation, and filtration. Control by
chemical agents refers to the use of disinfectants, antiseptics, antibiotics, and chemotherapeutic antimicrobial
chemicals.
Basic terms used in discussing the control of microorganisms include:
1. Sterilization
Sterilization is the process of destroying all living organisms and viruses. A sterile object is one free of all life
forms, including bacterial endospores, as well as viruses.
2. Disinfection
Disinfection is the elimination of microorganisms from inanimate objects or surfaces.
3. Decontamination
Decontamination is the treatment of an object or inanimate surface to make it safe to handle.
4. Disinfectant
A disinfectant is an agents used to disinfect inanimate objects but generally to toxic to use on human
tissues.
5. Antiseptic
An antiseptic is an agent that kills or inhibits growth of microbes but is safe to use on human tissue.
6. Sanitizer
A sanitizer is an agent that reduces, but may not eliminate, microbial numbers to a safe level.
7. Antibiotic
An antibiotic is a metabolic product produced by one microorganism that inhibits or kills other
microorganisms.
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LABORATORY 19
8. Chemotherapeutic antimicrobial chemical

Chemotherapeutic antimicrobial chemicals are synthetic chemicals that can be used therapeutically.
9. Cidal
An agent that is cidal in action will kill microorganisms and viruses.
10. Static
An agent that is static in action will inhibit the growth of microorganisms.
These three labs will demonstrate the control of microorganisms with physical agents, disinfectants and antiseptics,
and antimicrobial chemotherapeutic agents. Keep in mind that when evaluating or choosing a method of controlling
microorganisms, you must consider the following factors that may influence antimicrobial activity:
1. The concentration and kind of a chemical agent used
2. The intensity and nature of a physical agent used
3. The length of exposure to the agent
4. The temperature at which the agent is used
5. The number of microorganisms present
6. The organism itself
7. The nature of the material bearing the microorganism
B. TEMPERATURE
Microorganisms have a minimum, an optimum, and a maximum temperature for growth. Temperatures below the
minimum usually have a static action on microorganisms. They inhibit microbial growth by slowing down metabolism
but do not necessarily kill the organism. Temperatures above the maximum usually have a cidal action, since they
denature microbial enzymes and other proteins. Temperature is a very common and effective way of controlling
microorganisms.
1. High Temperature
Vegetative microorganisms can generally be killed at temperatures from 50 C to 70 C with moist heat.
Bacterial endospores, however, are very resistant to heat and extended exposure to much higher
temperature is necessary for their destruction. High temperature may be applied as either moist heat or dry
heat.
a. Moist heat
Moist heat is generally more effective than dry heat for killing microorganisms because of its ability
to penetrate microbial cells. Moist heat kills microorganisms by denaturing their proteins (causes
proteins and enzymes to lose their three-dimensional functional shape). It also may melt lipids in
cytoplasmic membranes.
1. Autoclaving
Autoclaving employs steam under pressure. Water normally boils at 100 C; however,
when put under pressure, water boils at a higher temperature. During autoclaving, the
materials to be sterilized are placed under 15 pounds per square inch of pressure in a
pressure-cooker type of apparatus. When placed under 15 pounds of pressure, the boiling
point of water is raised to 121 C, a temperature sufficient to kill bacterial endospores.
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The time the material is left in the autoclave varies with the nature and amount of material
being sterilized. Given sufficient time (generally 15-45 minutes), autoclaving is cidal for both
vegetative organisms and endospores, and is the most common method of sterilization for
materials not damaged by heat.
2. Boiling water
Boiling water (100 C) will generally kill vegetative cells after about 10 minutes of exposure.
However, certain viruses, such as the hepatitis viruses, may survive exposure to boiling
water for up to 30 minutes, and endospores of certain Clostridium and Bacillus species may
survive even hours of boiling.
b. Dry heat
Dry heat kills microorganisms through a process of protein oxidation rather than protein
coagulation. Examples of dry heat include:
1. Hot air sterilization
Microbiological ovens employ very high dry temperatures: 171 C for 1 hour; 160 C for 2
hours or longer; or 121 C for 16 hours or longer depending on the volume. They are
generally used only for sterilizing glassware, metal instruments, and other inert materials like
oils and powders that are not damaged by excessive temperature.
2. Incineration
Incinerators are used to destroy disposable or expendable materials by burning. We also
sterilize our inoculating loops by incineration.
c. Pasteurization
Pasteurization is the mild heating of milk and other materials to kill particular spoilage organisms
or pathogens. It does not, however, kill all organisms. Milk is usually pasteurized by heating to
71.6 C for at least 15 seconds in the flash method or 62.9 C for 30 minutes in the holding method.
2. Low Temperature
Low temperature inhibits microbial growth by slowing down microbial metabolism. Examples include
refrigeration and freezing. Refrigeration at 5 C slows the growth of microorganisms and keeps food fresh for
a few days. Freezing at -10 C stops microbial growth, but generally does not kill microorganisms, and keeps
food fresh for several months.
C. DESICCATION
Desiccation, or drying, generally has a static effect on microorganisms. Lack of water inhibits the action of microbial
enzymes. Dehydrated and freeze-dried foods, for example, do not require refrigeration because the absence of water
inhibits microbial growth.
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D. OSMOTIC PRESSURE
Microorganisms, in their natural environments, are constantly faced with alterations in osmotic pressure. Water
tends to flow through semipermeable membranes, such as the cytoplasmic membrane of microorganisms, towards
the side with a higher concentration of dissolved materials (solute). In other words, water moves from greater water
(lower solute) concentration to lesser water (greater solute) concentration.
When the concentration of dissolved materials or solute is higher inside the cell than it is outside, the cell is said to
be in a hypotonic environment and water will flow into the cell (Fig. 1). The rigid cell walls of bacteria and fungi,
however, prevent bursting or plasmoptysis. If the concentration of solute is the same both inside and outside the
cell, the cell is said to be in an isotonic environment (Fig. 2). Water flows equally in and out of the cell. Hypotonic
and isotonic environments are not usually harmful to microorganisms. However, if the concentration of dissolved
materials or solute is higher outside of the cell than inside, then the cell is in a hypertonic environment (Fig. 3).
Under this condition, water flows out of the cell, resulting in shrinkage of the cytoplasmic membrane or plasmolysis.
Under such conditions, the cell becomes dehydrated and its growth is inhibited.
The canning of jams or preserves with a high sugar concentration inhibits bacterial growth through hypertonicity.
The same effect is obtained by salt-curing meats or placing foods in a salt brine. This static action of osmotic
pressure thus prevents bacterial decomposition of the food. Molds, on the other hand, are more tolerant of
hypertonicity. Foods, such as those mentioned above, tend to become overgrown with molds unless they are first
sealed to exclude oxygen. (Molds are aerobic.)
Fig. 1:
Bacterium in an hypotonic environment.
Fig. 2:
Bacterium in a isotonic environment.
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LABORATORY 19
Fig. 3:
Bacterium in a hypertonic environment.
E. RADIATION
1. Ultraviolet Radiation
The ultraviolet portion of the light spectrum includes all radiations with wavelengths from 100 nm to 400 nm.
It has low wave-length and low energy. The microbicidal activity of ultraviolet (UV) light depends on the
length of exposure: the longer the exposure the greater the cidal activity. It also depends on the
wavelength of UV used. The most cidal wavelengths of UV light lie in the 260 nm - 270 nm range where it
is absorbed by nucleic acid.
In terms of its mode of action, UV light is absorbed by microbial DNA and causes adjacent thymine bases
on the same DNA strand to covalently bond together, forming what are called thymine-thymine dimers (see
Fig. 4). As the DNA replicates, nucleotides do not complementary base pair with the thymine dimers and this
terminates the replication of that DNA strand. However, most of the damage from UV radiation actually
comes from the cell trying to repair the damage to the DNA by a process called SOS repair. In very
heavily damaged DNA containing large numbers of thymine dimers, a process called SOS repair is activated
as kind of a last ditch effort to repair the DNA. In this process, a gene product of the SOS system binds to
DNA polymerase allowing it to synthesize new DNA across the damaged DNA. However, this altered DNA
polymerase loses its proofreading ability resulting in the synthesis of DNA that itself now contains many
misincorporated bases. In other words, UV radiation causes mutation and can lead to faulty protein
synthesis. With sufficient mutation, bacterial metabolism is blocked and the organism dies. Agents such as
UV radiation that cause high rates of mutation are called mutagens.
The effect of this incorrect base pairing may be reversed to some extent by exposing the bacteria to strong
visible light immediately after exposure to the UV light. The visible light activates an enzyme that breaks the
bond that joins the thymine bases, thus enabling correct complementary base pairing to again take place.
This process is called photoreactivation.
UV lights are frequently used to reduce the microbial populations in hospital operating rooms and sinks,
aseptic filling rooms of pharmaceutical companies, in microbiological hoods, and in the processing
equipment used by the food and dairy industries.
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An important consideration when using UV light is that it has very poor penetrating power. Only
microorganisms on the surface of a material that are exposed directly to the radiation are susceptible to
destruction. UV light can also damage the eyes, cause burns, and cause mutation in cells of the skin.
Fig. 4:
Thymine-thymine dimer from U.V. radiation
2. Ionizing Radiation
Ionizing radiation, such as X-rays and gamma rays, has much more energy and penetrating power than
ultraviolet radiation. It ionizes water and other molecules to form radicals (molecular fragments with unpaired
electrons) that can disrupt DNA molecules and proteins. It is often used to sterilize pharmaceuticals and
disposable medical supplies such as syringes, surgical gloves, catheters, sutures, and petri plates. It can also
be used to retard spoilage in seafoods, meats, poultry, and fruits.
F. FILTRATION
Microbiological membrane filters provide a useful way of sterilizing materials such as vaccines, antibiotic
solutions, animal sera, enzyme solutions, vitamin solutions, and other solutions that may be damaged or
denatured by high temperatures or chemical agents. The filters contain pores small enough to prevent the
passage of microbes but large enough to allow the organism-free fluid to pass through. The liquid is then
collected in a sterile flask (see Fig. 5). Filters with a pore diameter from 25nm to 0.45m are usually used in this
procedure. Filters can also be used to remove microorganisms from water and air for microbiological testing (see
Appendix D).
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Fig. 5:
Micropore filter apparatus
A. OSMOTIC PRESSURE
MEDIA
2 plates of Trypticase Soy agar, 2 plates of 5% glucose agar, 2 plates of 10% glucose agar, 2 plates of 25%
glucose agar, 2 plates of 5% NaCl agar, 2 plates of 10% NaCl agar, and 2 plates of 15% NaCl agar.
ORGANISMS
Trypticase Soy broth cultures of Escherichia coli and Staphylococcus aureus; a spore suspension of the
mold Aspergillus niger.
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PROCEDURE (to be done by tables)

1. Divide one plate of each of the following media in half. Using your inoculating loop, streak one half of
each plate with E. coli and the other half with S. aureus. Incubate at 37 C until the next lab period.a.
Trypticase Soy agar (control).
a. Trypticase Soy agar

b. Trypticase Soy agar with 5% glucose
c. Trypticase Soy agar with 10% glucose
d. Trypticase Soy agar with 25% glucose
e. Trypticase Soy agar with 5% NaCl
f. Trypticase Soy agar with 10% NaCl
g. Trypticase Soy agar with 15% NaCl
2. Using a sterile swab, streak one plate of each of the following media with a spore suspension of the mold
A. niger. Incubate at room temperature for 1 week.
a. Trypticase Soy agar
b. Trypticase Soy agar with 5% glucose
c. Trypticase Soy agar with 10% glucose
d. Trypticase Soy agar with 25% glucose
e. Trypticase Soy agar with 5% NaCl
f. Trypticase Soy agar with 10% NaCl
g. Trypticase Soy agar with 15% NaCl
B. ULTRAVIOLET RADIATION
MEDIA
5 plates of Trypticase Soy agar
ORGANISM
Trypticase Soy broth culture of Serratia marcescens

1. Using sterile swabs, streak all 5 Trypticase Soy agar plates with S. marcescens as follows:
a. Dip the swab into the culture.
b. Remove all of the excess liquid by pressing the swab against the side of the tube.
c. Streak the plate so as to cover the entire agar surface with organisms.
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LABORATORY 19
2. Expose 3 of the plates to UV light as follows:
a. Remove the lid of each plate and place a piece of cardboard with the letter "V" cut out of it over
the top of the agar.
b. Expose the first plate to UV light for 1 second, the second plate for 3 seconds, and the third plate
for 10 seconds.
c. Replace the lids and incubate at room temperature until the next lab period.
3. Leaving the lid on, lay the cardboard with the letter "V" cut out over the fourth plate and expose to UV
light for 30 seconds. Incubate at room temperature with the other plates.
4. Use the fifth plate as a non-irradiated control and incubate at room temperature with the other plates.
NOTE: Do not look directly at the UV light as it may harm the eyes.
C. FILTRATION (Demonstration)
MEDIUM
2 plates of Trypticase Soy agar
ORGANISM
Trypticase Soy broth cultures of Micrococcus luteus
PROCEDURE (demonstration
1. Using alcohol-flamed forceps, aseptically place a sterile membrane filter into a sterile filtration
device.
2. Pour the culture of M. luteus into the top of the filter set-up.
3. Vacuum until all the liquid passes through the filter into the sterile flask.
4. With alcohol-flamed forceps, remove the filter and place it organism-side-up on the surface of a
Trypticase Soy agar plate.
5. Using a sterile swab, streak the surface of another Trypticase Soy agar plate with the filtrate from
the flask.
6. Incubate the plates at 37 C until the next lab period.
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RESULTS
A. Osmotic Pressure
Observe the 2 sets of plates from the osmotic pressure experiment and record the results below.
Plate
Escherichia
coli
Staphylococcus
aureus
Control (TSA)
5% NaCl
10% NaCl
15% NaCl
5% glucose
10% glucose
25% glucose
+ = Scant growth
++ = Moderate growth
+++ = Abundant growth
- = No growth
Conclusions:
B. Ultraviolet Radiation
1. Make drawings of the 5 plates from the ultraviolet light experiment.
Non-irradiated control
1 second; lid off
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Aspergillus
niger
LABORATORY 19
3 seconds; lid off
10 seconds; lid off
30 seconds; lid on
Conclusions:
2. Observe the plates exposed to UV light for any non-pigmented colonies. Aseptically pick-off one of
these non-pigmented colonies and streak it in a plate of Trypticase Soy agar. Incubate at room temperature
until the next lab period.
3. After incubation, observe the plate you streaked with the nonpigmented colony.
Does the organism still lack chromogenicity?
What would account for this?
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LABORATORY 19
C. FILTRATION
Observe the two filtration plates and describe the results below.
Plate containing the filter
Plate streaked with filtrate
Conclusions:
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LABORATORY 19
LABORATORY 19
A. INTRODUCTION TO THE CONTROL OF MICROORGANISM

1. Define the following terms: sterilization, disinfection, decontamination, static, and cidal.
B. TEMPERATURE
1. State whether moist or dry heat is more effective in controlling microorganisms, and indicate why.
2. State specifically how moist heat kills microorganisms.
3. State two methods of applying moist heat.
4. Briefly describe the process of autoclaving (pressure, time, and temperature).
5. State whether or not boiling is an effective means of sterilization and state why or why not.
6. State specifically how dry heat kills microorganisms.
7. State two methods of applying dry heat.
8. Define pasteurization.
9. State whether low temperature has a static or cidal effect on microorganisms, and indicate why.
C. DESICCATION
1. State whether desiccation has static or cidal effect on microorganisms, and indicate how it affects the cell.
D. OSMOTIC PRESSURE
1. Describe osmosis in terms of water flow through a semipermeable membrane.
2. Define the following terms: hypotonic, hypertonic, isotonic, plasmoptysis, and plasmolysis.
3. State why hypotonicity does not normally harm bacteria.
4. Describe how bacterial growth is inhibited in jams and salt-cured meats.
5. State why jams still must be sealed even though bacteria will not grow in them.
6. State whether hypertonicity has a static or a cidal effect on microorganisms.
E. RADIATION
1. State how the wavelength and the length of exposure influence the bacteriocidal effect of UV light.
2. Describe specifically how UV light kills microorganisms.
3. State why UV light is only useful as a means of controlling surface contaminants and give several practical
applications.
4. Describe how ionizing radiation kills microorganisms and state several common applications.
F. FILTRATION
1. State the concept behind sterilizing solutions with micropore membrane filters.
2. State why filters are preferred over autoclaving for such materials as vaccines, antibiotic solutions, sera,
and enzyme solutions.
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LABORATORY 20
DISINFECTANTS, ANTISEPTICS, AND SANITIZERS
LABORATORY 20
CONTROL OF MICROORGANISMS USING
A. Disinfectants, Antiseptics, and Sanitizers
B. Evaluation of Disinfectants and Antiseptics
C. Effectiveness of Hand Washing
A. DISINFECTANTS, ANTISEPTICS, AND SANITIZERS

Disinfection is the elimination of microorganisms from inanimate objects or surfaces, whereas decontamination
is the treatment of an object or inanimate surface to make it safe to handle.
a. The term disinfectant is used for an agent used to disinfect inanimate objects or surfaces but is
generally to toxic to use on human tissues
b. The term antiseptic refers to an agent that kills or inhibits growth of microbes but is safe to use on
human tissue.
c. The term sanitizer describes an agent that reduces, but may not eliminate, microbial numbers to a
safe level.
Because disinfectants and antiseptics often work slowly on some viruses - such as the hepatitis viruses, bacteria with
an acid-fast cell wall such as Mycobacterium tuberculosis, and especially bacterial endospores, produced by the
genus Bacillus and the genus Clostridium, they are usually unreliable for sterilization - the destruction of all life
forms.
There are a number of factors that influence the antimicrobial action of disinfectants, antiseptics, and sanitizers
including:
1. The concentration of the chemical agent.
2. The temperature at which the agent is being used. Generally, the lower the temperature, the longer it
takes to disinfect or decontaminate.
3. The kinds of microorganisms present. Endospore producers such as Bacillus species, Clostridium
species, and acid-fast bacteria like Mycobacterium tuberculosis are harder to eliminate.
4. The number of microorganisms present. The more microorganisms present, the harder it is to disinfect
or decontaminate.
5. The nature of the material bearing the microorganisms. Organic material such as dirt and excreta
interferes with some agents.
The best results are generally obtained when the initial microbial numbers are low and when the surface to be
disinfected is clean and free of possible interfering substances.
There are 2 common antimicrobial modes of action for disinfectants, antiseptics, and sanitizers:
1. They may damage the lipids and/or proteins of the semipermeable cytoplasmic membrane of
microorganisms resulting in leakage of cellular materials needed to sustain life.
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LABORATORY 20
2. They may denature microbial enzymes and other proteins, usually by disrupting the hydrogen and
disulfide bonds that give the protein its three-dimensional functional shape. This blocks metabolism.
A large number of such chemical agents are in common use. Some of the more common groups are listed below:
1. Phenol and phenol derivatives
Phenol (5-10%) was the first disinfectant commonly used. However, because of its toxicity and odor, phenol
derivatives are now generally used. These include orthophenylphenol, hexachlorophene, hexylresorcinol, and
chlorhexidine. Orthophenylphenol is the agent in Lysol, O-syl, Staphene, and Amphyl.
Hexachlorophene in a 3% solution is combined with detergent and is found in PhisoHex. Triclosan is a
chlorine-containing phenolic antiseptic very common in antimicrobial soaps and other products.
Hexylresorcinol is in throat lozenges and ST-37. A 4% solution of chlorhexidine in isopropyl alcohol and
combined with detergent (Hibiclens and Hibitane) is a common hand washing agent and surgical
handscrub. These agents kill most bacteria, most fungi, and some viruses, but are usually ineffective against
endospores. They alter membrane permeability and denature proteins.
2. Soaps and detergents
Soaps are only mildly microbicidal. Their use aids in the mechanical removal of microorganisms by
breaking up the oily film on the skin (emulsification) and reducing the surface tension of water so it spreads
and penetrates more readily. Some cosmetic soaps contain added antiseptics to increase antimicrobial
activity.
Detergents may be anionic or cationic. Anionic (negatively charged) detergents, such as laundry powders,
mechanically remove microorganisms and other materials but are not very microbicidal. Cationic
(positively charged) detergents alter membrane permeability and denature proteins. They are effective
against many vegetative bacteria, some fungi, and some viruses. However, bacterial endospores and certain
bacteria such as Mycobacterium tuberculosis and Pseudomonas species are usually resistant. Soaps and
organic materials like excreta also inactivate them. Cationic detergents include the quaternary ammonium
compounds such as benzalkonium chloride , zephiran, diaprene, roccal, ceepryn, and phemerol.
3. Alcohols
70% solutions of ethyl or isopropyl alcohol are effective in killing vegetative bacteria, enveloped viruses,
and fungi. However, they are usually ineffective against endospores and non-enveloped viruses. Once they
evaporate, their cidal activity will cease. Alcohols denature membranes and are often combined with other
disinfectants, such as iodine, mercurials, and cationic detergents for increased effectiveness.
4. Acids and alkalies
Acids and alkalies alter membrane permeability and denature proteins and other molecules. Salts of
organic acids, such as calcium propionate, potassium sorbate, and methylparaben, are commonly used as
food preservatives. Undecylenic acid (Desenex) is used for dermatophyte infections of the skin. An example
of an alkali is lye (sodium hydroxide).
5. Heavy metals
Heavy metals, such as mercury, silver, and copper, denature proteins. Mercury compounds
(mercurochrome, metaphen, merthiolate) are only bacteriostatic and are not effective against endospores.
Silver nitrate (1%) is sometimes put in the eyes of newborns to prevent gonococcal ophthalmia. Copper
sulfate is used to combat fungal diseases of plants and is also a common algicide. Selinium sulfide kills fungi
and their spores.
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6. Chlorine
Chlorine gas reacts with water to form hypochlorite ions, which in turn denature microbial enzymes.
Chlorine is used in the chlorination of drinking water, swimming pools, and sewage. Sodium hypochlorite
is the active agent in household bleach. Calcium hypochlorite, sodium hypochlorite, and chloramines
(chlorine plus ammonia) are used to sanitize glassware, eating utensils, dairy and food processing
equipment, hemodialysis systems, and treating water supplies.
7. Iodine and iodophores
Iodine also denatures microbial proteins. Iodine tincture contains a 2% solution of iodine and sodium
iodide in 70% alcohole. Aqueous iodine solutions containing 2% iodine and 2.4% sodium iodide are
commonly used as a topical antiseptic. Iodophores are a combination of iodine and an inert polymers such as
polyvinylpyrrolidone that reduces surface tension and slowly releases the iodine. Iodophores are less
irritating than iodine and do not stain.They are generally effective against vegetative bacteria, Mycobacterium
tuberculosis, fungi, some viruses, and some endospores. Examples include Wescodyne, Ioprep, Ioclide,
Betadine, and Isodine.
8. Aldehydes
Aldehydes, such as formaldehyde and glutaraldehyde, denature microbial proteins. Formalin (37%
aqueous solution of formaldehyde gas) is extremely active and kills most forms of microbial life. It is used in
embalming, preserving biological specimens, and in preparing vaccines. Alkaline glutaraldehyde (Cidex),
acid glutaraldehyde (Sonacide), and glutaraldehyde phenate solutions (Sporocidin) kill vegetative bacteria
in 10-30 minutes and endospores in about 4 hours. A 10 hour exposure to a 2% glutaraldehyde solution can
be used for cold sterilization of materials.
9. Ethylene oxide gas
Ethylene oxide is one of the very few chemicals that can be relied upon for sterilization (after 4-12 hours
exposure). Since it is explosive, it is usually mixed with inert gases such as freon or carbon dioxide. Gaseous
chemosterilizers, using ethylene oxide, are commonly used to sterilize heat-sensitive items such as plastic
syringes, petri plates, textiles, sutures, artificial heart valves, heart-lung machines, and mattresses. Ethylene
oxide has very high penetrating power and denatures microbial proteins. Vapors are toxic to the skin,
eyes, and mucous membranes and are also carcinogenic. Another gas that is used as a sterilant is chlorine
dioxide which denatures proteins in vegetative bacteria, bacterial endospores, viruses, and fungi.
B. EVALUATION OF DISINFECTANTS, ANTISEPTICS, AND SANITIZERS

It is possible to evaluate disinfectants, antiseptics, and sanitizers using either in vitro or in vivo tests. An in vitro test
is one done under artificial, controlled laboratory conditions. An in vivo test is one done under the actual
conditions of normal use.
A common in vitro test is to compare the antimicrobial activity of the agent being tested with that of phenol. The
resulting value is called a phenol coefficient and has some value in comparing the strength of disinfectants under
standard conditions. Phenol coefficients may be misleading, however, because as mentioned earlier, the killing rate
varies greatly with the conditions under which the chemical agents are used. The concentration of the agent, the
temperature at which it is being used, the length of exposure to the agent, the number and kinds of
microorganisms present, and the nature of the material bearing the microorganisms all influence the
antimicrobial activity of a disinfectant. If a disinfectant is being evaluated for possible use in a given in vivo
situation, it must be evaluated under the same conditions in which it will actually be used.
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LABORATORY 20
Today we will do a test to see how thermometers might carry microorganisms if not properly disinfected or
decontaminated.
C. EFFECTIVENESS OF HAND WASHING

There are 2 categories of microorganisms, or flora, normally found on the hands. Resident flora are the normal
flora of the skin. Transient flora are the microorganisms you pick up from what you have been handling. It is routine
practice to wash the hands prior to and after examining a patient and to do a complete regimented surgical scrub prior
to going into the operating room. This is done in order to remove the potentially harmful transient flora, reduce the
number of resident flora, and disinfect the skin.
Actual sterilization of the hands is not possible since microorganisms live not only on the surface of the skin but also
in deeper skin layers, in ducts of sweat glands, and around hair follicles. These normal flora are mainly nonpathogenic
staphylococci (Lab 15) and diphtheroid bacilli.
Today we will qualitatively evaluate the effectiveness washing time on the removal of microorganisms from the
hands.
A. EVALUATIONS OF DISINFECTANTS, ANTISEPTICS, AND SANITIZERS

MATERIALS (per group of 3)
7 sterile glass rods ("thermometers")
9 plates of Trypticase Soy agar (TSA); 3 each
112 tubes of sterile water; 4 each
3 tubes of a particular antiseptic; 1 each. Each different group uses a different antiseptic.
1 bottle of dishwashing detergent per class
ORGANISMS (per group of 4)

Trypticase Soy broth culture of a mixture of common fecal opportunists: Escherichia coli, Enterobacter
cloacae, and Enterococcus faecalis.)
Trypticase Soy broth culture of Bacillus subtilis
oral sample (your mouth)
ANTISEPTICS
3 tubes of one of the following antiseptics per group of 3:
70% isopropyl alcohol
3% hydrogen peroxide
brand "X" mouthwash
brand "Y" mouthwash
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LABORATORY 20
PROCEDURE
Each group of 3 will test one particular antiseptic against each of the 3 organisms or samples. One person
will test the normal flora of his or her own mouth, one will test a mixture of common fecal opportunists, and
one will test B. subtilis.
1. Take 2 plates of TSA and, using your wax marker, divide each plate in half. Label the 4 halves
as follows: control, 5 seconds, 30 seconds, and 3 minutes. Also place the name of the antiseptic your
group is testing, the name of the specimen being tested, and your group name or symbol on each
plate. Take the third TSA plate and label it "soap and water."
2. Holding the sterile glass rod by one tip only, place it in your mouth, in the mixture of common fecal
opportunists, or in the B. subtilis for 3 minutes.
3. After 3 minutes, place the rod in your first tube of sterile water to rinse it briefly.
4. Remove the rod from the water, let the excess water drip off, and streak the tip of the rod on the
control sector of the TSA plate. Be careful that the inoculum does not enter the other sector of
the plate.
5. Place the rod in the mouth (use a new sterile glass rod for the mouth), the mixture of common
fecal opportunists, or the B. subtilis a second time for 3 minutes. Then place it in your tube of
antiseptic for 5 seconds. Remove the rod from the antiseptic and rinse it briefly in your second
tube of sterile water. Streak the tip of the rod on the 5-second sector of the TSA plate.
6. Place the rod in the specimen a third time (use a new sterile rod for the mouth) for 3 minutes.
Then place it in your antiseptic tube for 30 seconds. Rinse it briefly in your third tube of sterile
water, and streak the tip on the 30-second sector of the TSA plate.
7. Place the rod a fourth time in the specimen (use a new sterile rod for the mouth) for 3 minutes.
Then place it in your tube of antiseptic for 3 minutes. Rinse it briefly in your fourth tube of
sterile water, and streak the tip on the 3-minute sector of the TSA plate.
8. Place the rod a final time in the specimen (use a new sterile rod for the mouth) for 3 minutes.
Squeeze a small amount of dishwashing detergent on the rod and clean the rod using a wet
paper towel. Rinse the rod under running water and streak the tip of the rod on the TSA plate
labelled "soap and water."
9. Incubate the TSA plates at 37 C until the next lab period.
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LABORATORY 20
B. EFFECTIVENESS OF HAND WASHING

MATERIALS
2 plates of Trypticase Soy agar (TSA)
Sterile scrub brush
Soap

1. Using your wax marker, divide each TSA plate in half and label the halves 1 through 4.
2. Rub your fingers over sector 1 prior to washing your hands.
3. Using a scrub brush, soap, and water, scrub your hands for 2 minutes. Rub your damp fingers
over sector 2.
4. Again scrub your hands with soap and water for 2 minutes and rub your fingers over sector 3.
5. Again scrub your hands with soap and water for 2 minutes and rub your fingers over sector 4.
6. Incubate the TSA plates at 37 C until the next lab period.
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LABORATORY 20
RESULTS
A. Evaluation of Disinfectants, Antiseptics, and Sanitizers
Record your group's results and the results of the other groups who used different agents below:
(++) = Abundant growth
Organism
Mixture of common
fecal opportunists
Time
(+) = Some growth

70%
isopropyl
alcohol
Control
5 sec.
30 sec.
3 min.
Soap & water
B.subtilis
Control
5 sec.
30 sec.
3 min.
Soap & water
Mouth
Control
5 sec.
30 sec.
3 min.
Soap & water
247
3%
hydrogen
peroxide
(-) = No growth
Mouthwash
X
Mouthwash
Y
LABORATORY 20
B. Effectiveness of Hand Washing

Record your results of the 2 TSA "hand washing" plates:
(++) = Abundant growth
(+) = Some growth
Sector
Growth
Sector 1
(no washing)
Sector 2
(2 min. of washing)
sector 3
(4 min. of washing)
Sector 4
(6 min. of washing)
248
(-) = No growth
LABORATORY 20
LABORATORY 20
A. DISINFECTANTS, ANTISEPTICS, AND SANITIZERS

1. Define the following terms: sterilization, disinfection, decontamination, disinfectant, antiseptic, and sanitizer.
2. State why chemical agents are usually unreliable for sterilization.
3. List five factors that may influence the antimicrobial action of disinfectants, antiseptics, and sanitizers.
4. Describe two modes of action of disinfectants, antiseptics, and sanitizers (i.e., how they harm the
microorganisms).
5. Name two chemical agents that are reliable for sterilization.
B. EVALUATION OF DISINFECTANTS, ANTISEPTICS, AND SANITIZERS

1. State why the results of an in vitro test to evaluate chemical agents may not necessarily apply to in vivo
situations.
C. EVALUATION OF HAND WASHING

1. Define transient flora and resident flora and compare the two groups in terms of ease of removal.
249
250
LABORATORY 21
ANTIMICROBIAL CHEMOTHERAPY
LABORATORY 21
CONTROL OF MICROORGANISMS USING
A. Antimicrobial Chemotherapeutic Agents
B. Microbial Resistance to Chemotherapeutic Agents
C. Antibiotic Susceptibility Testing
A. ANTIMICROBIAL CHEMOTHERAPEUTIC AGENTS

Antimicrobial chemotherapy is the use of chemicals to inhibit or kill microorganisms in or on the host.
Chemotherapy is based on selective toxicity. This means that the agent used must inhibit or kill the
microorganism in question without seriously harming the host.
In order to be selectively toxic, a chemotherapeutic agent must interact with some microbial function or microbial
structure that is either not present or is substantially different from that of the host. For example, in treating infections
caused by prokaryotic bacteria, the agent may inhibit peptidoglycan synthesis or alter bacterial (prokaryotic)
ribosomes. Human cells do not contain peptidoglycan and possess eukaryotic ribosomes. Therefore, the drug shows
little if any effect on the host (selective toxicity). Eukaryotic microorganisms, on the other hand, have structures and
functions more closely related to those of the host. As a result, the variety of agents selectively effective against
eukaryotic microorganisms such as fungi and protozoans is small when compared to the number available against
prokaryotes. Also keep in mind that viruses are not cells and, therefore, lack the structures and functions altered by
antibiotics so antibiotics are not effective against viruses.
Based on their origin, there are 2 general classes of antimicrobial chemotherapeutic agents:
1. Antibiotics: substances produced as metabolic products of one microorganism which inhibit or kill other
microorganisms.
2. Antimicrobial chemotherapeutic chemicals: chemicals synthesized in the laboratory which can be used
therapeutically on microorganisms.
Today the distinction between the 2 classes is not as clear, since many antibiotics are extensively modified in the
laboratory (semisynthetic) or even synthesized without the help of microorganisms.
Most of the major groups of antibiotics were discovered prior to 1955, and most antibiotic advances since then have
come about by modifying the older forms. In fact, only 3 major groups of microorganisms have yielded useful
antibiotics: the actinomycetes (filamentous, branching soil bacteria such as Streptomyces), bacteria of the genus
Bacillus, and the saprophytic molds Penicillium and Cephalosporium.
To produce antibiotics, manufacturers inoculate large quantities of medium with carefully selected strains of the
appropriate species of antibiotic-producing microorganism. After incubation, the drug is extracted from the
medium and purified. Its activity is standardized and it is put into a form suitable for administration.
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LABORATORY 21
Some antimicrobial agents are cidal in action: they kill microorganisms (e.g., penicillins, cephalosporins,
streptomycin, neomycin). Others are static in action: they inhibit microbial growth long enough for the body's own
defenses to remove the organisms (e.g., tetracyclines, erythromycin, sulfonamides).
Antimicrobial agents also vary in their spectrum. Drugs that are effective against a variety of both gram-positive
and gram-negative bacteria are said to be broad-spectrum (e.g., tetracycline, streptomycin, cephalosporins,
ampicillin, sulfonamides). Those effective against just gram-positive bacteria, just gram-negative bacteria, or
only a few species are termed narrow-spectrum (e.g., penicillin G, erythromycin, clindamycin, gentamicin).
If a choice is available, a narrow spectrum is preferable since it will cause less destruction to the body's normal flora.
In fact, indiscriminate use of broad-spectrum antibiotics can lead to superinfection by opportunistic
microorganisms, such as Candida (yeast infections) and Clostridium difficile (antibiotic-associated ulcerative colitis),
when the body's normal flora is destroyed. Other dangers from indiscriminate use of antimicrobial chemotherapeutic
agents include drug toxicity, allergic reactions to the drug, and selection for resistant strains of
microorganisms.
Below are examples of commonly used antimicrobial chemotherapeutic agents arranged according to their mode of
action:
1. Antimicrobial agents that inhibit peptidoglycan synthesis (also see Table 1)
Inhibition of peptidoglycan synthesis in actively dividing bacteria results in osmotic lysis.
a. Penicillins (produced by the mold Penicillium)
There are several classes of penicillins:
1. Natural penicillins are highly effective against gram-positive bacteria (and a very few
gram-negative bacteria) but are inactivated by the bacterial enzyme penicillinase. Examples
include penicillin G, F, X, K, O, and V.
2. Semisynthetic penicillins are effective against gram-positive bacteria but are not
inactivated by penicillinase. Examples include methicillin, dicloxacillin, and nafcillin.
3. Semisynthetic broad-spectrum penicillins are effective against a variety of
gram-positive and gram-negative bacteria but are inactivated by penicillinase. Examples
include ampicillin, carbenicillin, and oxacillin. Some of the newer semisynthetic penicillins
include azlocillin, mezlocillin, and piperacillin.
4. Semisynthetic broad-spectrum penicillins combined with beta lactamase inhibitors
such as clavulanic acid and sulbactam. Although the clavulanic acid and sulbactam have
no antimicrobial action of their own, they inhibit penicillinase thus protecting the penicillin
from degradation. Examples include amoxicillin plus clavulanic acid, ticarcillin plus
clavulanic acid, and ampicillin plus sulbactam.
b. Cephalosporins (produced by the mold Cephalosporium)
Cephalosporins are effective against a variety of gram-positive and gram-negative bacteria and are
resistant to penicillinase (although some can be inactivated by other beta-lactamase enzymes similar
to penicillinase). Three "generations" of cephalosporins have been developed over the years in an
attempt to counter bacterial resistance:
1. First generation cephalosporins include cephalothin, cephapirin, and cephalexin.
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LABORATORY 21
2. Second generation cephalosporins include cefamandole, cefaclor, cefazolin,
cefuroxime, and cefoxitin.
3. Third generation cephalosporins include cefotaxime, cefsulodin, cefetamet, cefixime,
ceftriaxone, cefoperazone, ceftazidine, and moxalactam.
4. Fourth generation cephalosporins include cefepime and cefpirome.
c. Carbapenem
Carbapenems consist of a broad-spectrum beta lactam antibiotic to inhibit peptidoglycan synthesis
combined with cilastatin sodium, an agent that prevents degradation of the antibiotic in the kidneys.
An example is imipenem.
d. Monobactems
Monobactems are broad-spectrum beta lactam antibiotics resistant to beta lactamase. An example
is aztreonam.
e. Carbacephem
A synthetic cephalosporin. An example is loracarbef.
f. Glycopeptides (produced by the bacterium Streptomyces)
Vancomycin, a glycopeptide, is effective against gram-positive bacteria.
g. Bacitracin (produced by the bacterium Bacillus)
Bacitracin is used topically against gram-positive bacteria.
h. Fosfomycin (Monurol )
2. Antimicrobial agents that alter the cytoplasmic membrane (also see Table 1)
Alteration of the cytoplasmic membrane of microorganisms results in leakage of cellular materials.
a. Polymyxin B (produced by the bacterium Bacillus)
Polymyxin B is used in severe Pseudomonas infections.
b. Amphotericin B (produced by the bacterium Streptomyces)
Amphotericin B is used for systemic fungal infections.
c.
Nystatin (produced by the bacterium Streptomyces)

Nystatin is used mainly for Candida yeast infections.
d. Imidazoles (produced by the bacterium Streptomyces)

The imidazoles are antifungal antibiotics used for yeast infections, dermatophytic infections, and
systemic fungal infections. Examples include clotrimazole, miconazole, ketoconazole,
itraconazole, and fluconazole.
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LABORATORY 21
3. Antimicrobial agents that inhibit protein synthesis (also see Table 1)
These agents prevent bacteria from synthesizing structural proteins and enzymes.
a. Agents that block transcription (prevent the synthesis of mRNA off of DNA).
1. Rifaximin (produced by the bacterium Streptomyces)
Rifaximins are effective against some gram-positive and gram-negative bacteria and
Mycobacterium tuberculosis. They inhibit the enzyme RNA polymerase.
b. Agents that block translation (alter bacterial ribosomes to prevent mRNA from being translated
into proteins).
1. Agents that bind irreversibly to the 30s ribosomal subunit and cause a misreading of the
mRNA (the aminoglycosides produced by the bacterium Streptomyces). Examples include
streptomycin, kanamycin, tobramycin, and amikacin. Most are effective against grampositive and gram-negative bacteria.
2. Agents that bind reversibly to the 30s ribosomal subunit and interfere with the binding of
charged tRNA to the bacterial ribosome. Examples include tetracycline, minocycline, and
doxycycline, produced by the bacterium Streptomyces. They are effective against a variety
of gram-positive and gram-negative bacteria.
3. Agents that bind reversibly to the 50s ribosomal subunit and block peptide bond formation
during protein synthesis. Examples include lincomycin and clindamycin, produced by the
bacterium Streptomyces. Most are used against gram-positive bacteria.
4. Agents that bind reversibly to the 50s ribosomal subunit and prevent the release of
uncharged tRNA from the bacterial ribosome. Erythromycin, roxithromycin,
clarithromycin, and azithromycin are examples and are used against gram-positive
bacteria and some gram-negative bacteria.
5. The oxazolidinones (linezolid) bind to the 50S ribosomal subunit appear to interfere with
the initiation of translation.
6. The streptogramins (a combination of quinupristin and dalfopristin) bind to different sites
on the 50S ribosomal subunit and work synergistically to inhibit translocation.
4. Antimicrobial agents that interfere with DNA synthesis (also see Table 1)
a. Fluoroquinolones (synthetic chemicals):
The fluoroquinolones block bacterial DNA replication by inhibiting bacterial DNA gyrase and
DNA topoisomerase enzymes needed for the unwinding, replication, separation, and supercoiling
of bacterial DNA. They are broad spectrum and examples include norfloxacin, ciprofloxacin,
enoxacin, temafloxacin, levofloxacin, and trovafloxacin.
b. Sulfonamides and trimethoprim (synthetic chemicals):
Co-trimoxazole is a combination of sulfamethoxazole and trimethoprim. Both of these drugs block
the bacterial synthesis of folic acid, a coenzyme needed to make DNA bases.
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LABORATORY 21
c. Metronidazole
Metronidazole is a drug that is activated by the microbial proteins flavodoxin and feredoxin found in
microaerophilc and anaerobic bacteria and certain protozoans. Once activated, the metronidazole
puts nicks in the microbial DNA strands.
Table 1: Common Antibacterial Antibiotics

Selected antibiotics and their modes of action.
(U.S. Brand names are in parentheses; .)
1. Inhibit synthesis of peptidoglycan causing osmotic lysis.
a. Penicillins: penicillin G (Pfizerpen; Bicillin; Wycillin), penicillin V (Betapen; Pen-Vee K), methicillin (Staphcillin), ampicillin (Omnipen;
Polycillin), oxacillin (Bactocill ), amoxicillin (Amoxil; Biomox; Polymox), ticarcillin (Ticar), carbenicillin (Geocillin), piperacillin (Pipracil),
mezlocillin (Mezlin), bacampicillin (Spectrobid), dicloxacillin (Dynapen), nafcillin (Nallpen; Unipen).
b. Penicillins plus beta lactamase inhibitors or compounds preventing antibiotic degradation on the kidneys: amoxicillin +
clavulanate (Augmentin), ticarcillin + clavulanate (Timentin), ampicillin + sulbactam (Unasyn), piperacillin + tazobactam (Zosyn),
imipenem + cilastatin (Primaxin) .
c. Cephalosporins: cefaclor (Ceclor), cefadroxil (Duricef), cefazolin (Ancef; Kefzol), cefixime (Sulprax), cefepime (Maxipime),
ceftibuten (Cedax), cefprozil (Cefzil), cefpodoxime (Vantin), cefotaxime (Claforan), cefotetan (Cefotan), cefoxitin (Cefoxitin; Mefoxin),
ceftazidime (Ceptaz; Fortaz; Tazicef; Tazidime), ceftizoxime (Cefizox), ceftriaxone (Rocephin), cefuroxime (Ceftin; Kefurox; Zinacef),
cephalexin (Biocef; Keflex; Keftab), cephradine (Velosef), cefdinir (Omnicef), cefditoren pivoxil (Spectracef), loracarbef (Lorabid).
d. Carbapenems: imipenem (Primaxin), meropenem (Merrem), ertapenem (Invanz) .
e. Monobactems: aztreonam (Azactam).
f. Glycopeptides: vancomycin (Lyphocin; Vancocin).
g. Bacitracin (AK-Tracin; Baci-IM; Baci-Rx; Ocu-Tracin; Ziba-Rx)
h. Fosfomycin (Monurol )
2. Alter cytoplasmic membrane causing cellular leakage

a. Polymyxins: colistimethate(Coly Mycin M), polymyxin B (Aerosporin; also mixed with other antibiotics in ointments such as
Cortisporin, Neosporin, and LazerSporin).
b. Daptomycin (Cubicin)
3. Alter bacterial ribosomes, blocking translation and causing faulty protein synthesis
a. Causing faulty protein synthesis by binding to the 30S ribosomal subunit
1. Aminoglycosides: amikacin (Amikin), tobramycin (Nebcin), gentamicin (Garamycin; Genoptic; Gentacidin; Gentak;
Gentasol; Ocu-Mycin), kanamycin (Kantrex), neomycin (mixed with other antibiotics in antibiotic ointments such as Neosporin,
Cortisporin, and LazerSporin), paromomycin (Humatin), tobramycin (AK-Tob; Tobrasol; Tobrex; Nebcin; Tobi).
2. Tetracyclines: tetracycline (Ala-Tet; Brodspec; Panmycin; Sumycin; Tetracon), minocycline (Arestin; Dynacin; Minocin;
Vectrin), doxycycline (Adoxa; Atridox; Doryx; Monodox; Vibramycin), demeclocycline (Declomycin).
3. Spectinomycin (Trobicin)
b. Causing faulty protein synthesis by binding to the 50S ribosomal subunit
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LABORATORY 21
1. Macrolides: erythromycin (A/T/S; Akne-Mycin; E.E.S.; Emgel; E-Mycin; Eryc; Erycette; Erygel; Erymax;
EryPed; Ery-Tab; Erythra-Derm; Erythrocin; Erythrocot; PCE; Romycin; Roymicin; Staticin; Theramycin; TStat), azithromycin (Zithromax), clarithromycin (Biaxin), dirithromycin ( Dynabac).
2. Lincosamides: lincomycin (Bactramycin; Lincocin; Lincomycin), clindamycin (Cleocin; Clinda-Derm;
Clindagel; Clindamax ).
3. Chloramphenicol: (AK-Chlor; Chloromycetin; Chloroptic; Ocu-Chlor)
4. Oxazolidinones: linezolid (Zyvox)
5. Streptogramins: a combination of quinupristin and dalfopristin (Synercid)
6. Telithromycin (Ketek)
4. Inhibiting bacterial nucleic acid synthesis

a. Inhibit DNA replication by inhibiting one or more of a group of enzymes called topoisomerases that are essiential for
bacterial DNA replication and transcription
Fluroquinolones: norfloxacin (Noroxin, Chibroxin), ciprofloxacin (Cipro; Ciloxan; Ciprodex), ofloxacin (Floxin; Ocuflox),
enoxacin (Penetrex), lomefloxacin (Maxaquin), levofloxacin (Levaquin; Quixin), gatifloxacin (Tequin), moxifloxacin (Avelox),
nalidixic acid (NegGram), gemifloxacin (Factive), sparfloxacin (Zagam).
b. Inhibit bacterial DNA synthesis by blocking synthesis of tetrahydrafolate, a cofactor needed to make nucleotide
bases
1. Sulfonamides: sulfanilamide (AVC), sulfisoxazole (Gantrisin; Truxazole), sulfacetamide (AK-Sulf; Bleph-10; Isopto
Cetamide; Klaron; Ocu-Sul; Ocusulf; Ovace; S.O.S.S.; Sebizon; Sodium Sulamyd; Sulf-10; Sulfac 10%; Sulfacet; Avar; Clenia;
Nicosyn; Novacet; Plexion ; Prascion Rosac; Rosanil; Rosula; Sulfacet-R; Zetacet), Sulfadiazine (Sulfadiazine),
sulfabenzamide + sulfacetamide + sulfathiazole (Gyne Sulf; Triple Sulfa), sulfisoxazole + erythromycin (Pediazole; Eryzole).
2. Trimethoprim (Primsol; Proloprim; Trimpex), trimethoprim + polymyxin B (Polytrim; Proloprim; Trimpex)
3. Trimethoprim + sulfamethoxazole ( Bactrim; Bethaprim; Septra; SMX-TMP Plain; Sulfatrim; Uroplus).
4. Trimetrexate (NeuTrexin)
c. Drugs that are activated by the microbial proteins flavodoxin and feredoxin found in microaerophilc and anaerobic bacteria
and certain protozoans. Once activated, the drug puts nicks in the microbial DNA strands.
Metronidazole (Flagyl; RTU; MetroCream; Metro; Metronidazole; Noritate; Protostat; Rozex )
d. Drugs that inhibit bacterial RNA synthesis by binding to RNA polymerase.
Rifaximin (Xifaxan)
5. Antituberculosis drugs
Rifampin (Rimactane, Rifadin), rifapentine (Priftin), isoniazid (Nydrazid), ethambutol (Myambutol), capreomycin (Capastat), cycloserine (Seromycin),
ethionamide (Trecator), rifabutin (Mycobutin), aminosalicylic acid (Paser D/R), clofazimine (Lamprene), rifampin + isoniazid (Rifamate), rifampin +
isoniazid + pyrazinamide (Rifater).
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LABORATORY 21
B. MICROBIAL RESISTANCE TO ANTIMICROBIAL CHEMOTHERAPEUTIC

AGENTS
A common problem in antimicrobial chemotherapy is the development of resistant strains of bacteria. Most bacteria
become resistant to antimicrobial agents by one or more of the following mechanisms:
1. Producing enzymes that detoxify or inactivate the antibiotic, e.g., penicillinase and other betalactamases.
2. Altering the target site in the bacterium to reduce or block binding of the antibiotic, e.g., producing a
slightly altered ribosomal subunit that still functions but to which the drug can't bind.
3. Preventing transport of the antimicrobial agent into the bacterium, eg., producing an altered
cytoplasmic membrane or outer membrane.
4. Developing an alternate metabolic pathway to by-pass the metabolic step being blocked by the
antimicrobial agent, e.g., overcoming drugs that resemble substrates and tie-up bacterial enzymes.
5. Increasing the production of a certain bacterial enzyme, e.g., overcoming drugs that resemble
substrates and tie-up bacterial enzymes.
These changes in the bacterium that enable it to resist the antimicrobial agent occur naturally as a result of
mutation or genetic recombination of the DNA in the nucleoid, or as a result of obtaining plasmids from other bacteria.
Exposure to the antimicrobial agent then selects for these resistant strains of organism.
As an example, many gram-negative bacteria possess R (resistance) plasmids that have genes coding for
multiple antibiotic resistance through the mechanisms stated above, as well as transfer genes coding for a sex
pilus. Such an organism can conjugate with other bacteria and transfer an R plasmid to them. Escherichia coli,
Proteus, Serratia, Salmonella, Shigella, and Pseudomonas are examples of bacteria that frequently have R plasmids.
Because of the problem of antibiotic resistance, antibiotic susceptibility testing is usually done in the clinical
laboratory to determine which antimicrobial chemotherapeutic agents will most likely be effective on a particular strain
of microorganism. This is discussed in the next section.
To illustrate how plasmids carrying genes coding for antibiotic resistance can be picked up by antibiotic-sensitive
bacteria, in today's lab we will use plasmid DNA to transform an Escherichia coli sensitive to the antibiotic
ampicillin into one that is resistant to the drug.
The E. coli will be rendered more "competent" to take up plasmid DNA (pAMP), which contains a gene coding for
ampicillin resistance, by treating them with a solution of calcium chloride, cold incubation, and a brief heat shock.
They will then be plated on 2 types of media: Lauria-Bertani agar (LB) and Lauria-Bertani agar with ampicillin
(LB/amp). Only E. coli that have picked up a plasmid coding for ampicillin resistance will be able to form colonies on
the LB/amp agar.
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LABORATORY 21
C. ANTIBIOTIC SUSCEPTIBILITY TESTING

For some microorganisms, susceptibility to chemotherapeutic agents is predictable. However, for many
microorganisms (Pseudomonas, Staphylococcus aureus, and gram-negative enteric bacilli such as Escherichia coli,
Serratia, Proteus, etc.) there is no reliable way of predicting which antimicrobial agent will be effective in a given case.
This is especially true with the emergence of many antibiotic-resistant strains of bacteria. Because of this, antibiotic
susceptibility testing is often essential in order to determine which antimicrobial agent to use against a specific strain
of bacterium.
Several tests may be used to tell a physician which antimicrobial agent is most likely to combat a specific pathogen:
1. Tube dilution tests
In this test, a series of culture tubes are prepared, each containing a liquid medium and a different
concentration of a chemotherapeutic agent. The tubes are then inoculated with the test organism and
incubated for 16-20 hours at 35C. After incubation, the tubes are examined for turbidity (growth). The lowest
concentration of chemotherapeutic agent capable of preventing growth of the test organism is the minimum
inhibitory concentration (MIC).
Subculturing of tubes showing no turbidity into tubes containing medium but no chemotherapeutic agent
can determine the minimum bactericidal concentration (MBC). MBC is the lowest concentration of the
chemotherapeutic agent that results in no growth (turbidity) of the subcultures. These tests, however, are
rather time consuming and expensive to perform.
2. The agar diffusion test (Bauer-Kirby test)
A procedure commonly used in clinical labs to determine antimicrobial susceptibility is the Bauer-Kirby disc
diffusion method. In this test, the in vitro response of bacteria to a standardized antibiotic-containing disc has
been correlated with the clinical response of patients given that drug.
In the development of this method, a single high-potency disc of each chosen chemotherapeutic agent was
used. Zones of growth inhibition surrounding each type of disc (Fig. 1) were correlated with the minimum
inhibitory concentrations of each antimicrobial agent (as determined by the tube dilution test). The MIC for
each agent was then compared to the usually-attained blood level in the patient with adequate dosage.
Categories of "Resistant," "Intermediate," and "Susceptible" were then established.
Fig. 1:
Zones of inhibition surrounding antibiotic discs.
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LABORATORY 21
The basic steps for the Bauer-Kirby method of antimicrobial susceptibility testing are given below. This
outline of procedure is intended to be used as an adjunct to clinical laboratory instruction. The procedure is
highly regulated and controlled by the Clinical and Laboratory Standards Institute (CLSI) and must be
accompanied by a rigorous quality assurance program including performance by certified and/or licensed
personnel when the results are to be reported in clinical settings.
a. Prepare a standard turbidity inoculum of the test bacterium so that a certain density of
bacteria will be put on the plate.
Select 3-5 isolated colonies of the bacterium that is being tested.
If the organism is a Staphylococcus or is fastidious and grows unpredictably in broth like the
streptococci, suspend the colonies is saline, Mueller Hinton broth or trypticase soy broth. If
the organism grows rapidly in broth, place the colonies in Mueller Hinton broth or trypticase
soy broth and incubate 2-8 hours.
Match the turbidity of the test suspension or culture with a 0.5 McFarland standard.
(McFarland standards are tubes containing either latex particles or barium sulfate and
adjusted to a standard turbity.)
o If the bacterial suspension is too turbid, add more saline or broth.
o If the bacterial suspension is too light, pick off more colonies and suspend them in
the broth or incubate longer.
b. Inoculate a 150mm Mueller-Hinton agar plate with the standardized inoculum so as to cover the
entire agar surface with bacteria.
Dip a sterile swab into the previously standardized tube of the bacterium being tested.
Squeeze the swab against the inner wall of the tube to remove excess liquid.
Swab the entire plate from top to bottom, edge-to-edge leaving no gaps.
Rotate the plate approximately 60 degrees and using the same swab, again swab the entire
plate from top to bottom.
Rotate the plate approximately 60 degrees and using the same swab, and swab the entire
plate from top to bottom a third time.
c. Place standardized antibiotic-containing discs on the plate.

d. Incubate the plate agar side up. For nonfastidious bacteria, incubate at 35 C for 16-18 hours. For
fastidious bacteria, follow CLSI standards.
e. Measure the diameter of any resulting zones of inhibition in millimeters (mm) as shown in Fig.
2.
f. Determine if the bacterium is susceptible, moderately susceptible, intermediate, or resistant to
each antimicrobial agent using a standardized table (see Table 2). (The latest interpretation tables
can be found in CLSI document M100 which is updated every January.)
If there is a double zone of inhibition, measure the diameter of the innermost zone.
If there is a zone containing colonies, measure the diameter of the colony free zone.
If there is a feathered zone, measure the diameter of the point where there is an obvious
demarcation between growth and no growth.
When testing swarming Proteus mirabilis, ignore the swaming.
When testing Staphylococcus aureus, the haze around an oxacillin should not be ignored.
Measure the diameter of the zone free of growth or haze.
The term intermediate generally means that the result is inconclusive for that drug-organism
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LABORATORY 21
combination. The term moderately susceptible is usually applied to those situations where a drug
may be used for infections in a particular body site, e.g., cystitis because the drug becomes highly
concentrated in the urine.
3. Automated tests
Computerized automated tests have been developed for antimicrobial susceptibility testing. These tests
measure the inhibitory effect of the antimicrobial agents in a liquid medium by using light scattering to
determine growth of the test organism. Results can be obtained within a few hours. Labs performing very
large numbers of susceptibility tests frequently use the automated methods but the equipment is quite
expensive.
A. MICROBIAL RESISTANCE TO ANTIMICROBIAL CHEMOTHERAPEUTIC

AGENTS
MATERIALS
Plasmid DNA (pAMP) on ice, calcium chloride solution on ice, 2 sterile culture tubes, 1 tube of LB broth, 2
plates of LB agar, 2 plates of LB agar with ampicillin (LB/amp), sterile 1 ml transfer pipettes, sterile plastic
inoculating loops, bent glass rod, turntable, alcohol, beaker of ice, water bath at 42 C.
ORGANISM
LB agar culture of Escherichia coli
PROCEDURE (demonstration; see Fig. 3)

1. Label one LB agar plate "Transformed Bacteria, Positive control" and the other LB agar plate "Wild-Type
Bacteria, Positive Control."
Label one LB/amp agar plate "Transformed Bacteria, Experiment" and the other LB/amp agar plate "WildType Bacteria, Negative Control."
2. Label one sterile culture tube "(+) AMP" and the other "(-) AMP." Using a sterile 1ml transfer pipette, add
250 l of ice-cold calcium chloride to each tube. Place both tubes on ice.
3. Using a sterile plastic inoculating loop, transfer 1-2 large colonies of E. coli into the (+) AMP tube and
vigorously tap against the wall of the tube to dislodge all the bacteria. Immediately suspend the cells by
repeatedly pipetting in and out with a sterile transfer pipette until no visible clumps of bacteria remain. Return
tube to the ice.
4. Repeat step 3 this time using the (-) AMP tube and return to the ice.
5. Using a sterile plastic inoculating loop, add one loopful of pDNA (plasmid DNA) solution to the (+) AMP
tube and swish loop to mix the DNA. Return to the ice.
6. Incubate both tubes on ice for 15 minutes.
7. After 15 minutes, "heat-shock" both tube of bacteria by immersing them in a 42 C water bath for 90
seconds. Return both tubes to the ice for 1 minute or more.
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LABORATORY 21
8. Using a sterile 1ml transfer pipette, add 250l of LB broth to each tube. Tap tubes with your fingers to
mix. Set tubes in a test tube rack at room temperature.
9. Using a sterile 1ml transfer pipette, add 100 l of E. coli suspension from the (-) AMP tube onto the
LB/amp agar plate labeled "Wild-Type Bacteria, Negative Control." Add another 100 l of E. coli from the (-)
AMP to the LB agar plate labeled "Wild-Type Bacteria, Positive Control."
10. Using a bent glass rod dipped in alcohol and flamed, spread the bacteria thoroughly over both agar
plates. Make sure you re-flame the glass rod between plates.
11. Using a sterile 1ml transfer pipette, add 100 l of E. coli suspension from the (+) AMP tube onto the
LB/amp agar plate labeled "Transformed Bacteria, Experiment." Add another 100 l of E. coli from the (+)
AMP to the LB agar plate labeled "Transformed Bacteria, Positive Control."
12. Immediately spread as in step 10.
13. Incubate all plates at 37 C.
14. The procedure is summarized in Fig. 21C.
Fig. 3:
Transfer of plasmid-mediated resistance to ampicillin in E. coli
261
LABORATORY 21

MATERIALS
150mm Mueller-Hinton agar plates (3)
Sterile swabs (3)
An antibiotic disc dispenser containing discs of antibiotics commonly effective against gram-positive bacteria,
and one containing discs of antibiotics commonly effective against gram-negative bacteria
ORGANISMS
Trypticase Soy broth cultures of Staphylococcus aureus (gram-positive), Enterococcus faecalis (grampositive), and Pseudomonas aeruginosa (gram-negative)
PROCEDURE
The basic steps for the Bauer-Kirby method of antimicrobial susceptibility testing are given below. This
outline of procedure is intended to be used as an adjunct to general microbiology laboratory instruction. The
procedure is highly regulated and controlled by the Clinical and Laboratory Standards Institute (CLSI) and
must be accompanied by a rigorous quality assurance program including performance by certified and/or
licensed personnel when the results are to be reported in clinical settings.
1. Take 3 Mueller-Hinton agar plates. Label one S. aureus, one E. faecalis, and one P. aeruginosa.
2. Using your wax marker, divide each plate into thirds to guide your streaking.
3. Dip a sterile swab into the previously standardized tube of S. aureus. Squeeze the swab against the
inner wall of the tube to remove excess liquid.
4.Streak the swab perpendicular to each of the 3 lines drawn on the plate overlapping the streaks to
assure complete coverage of the entire agar surface with inoculum.
5. Repeat steps 3 and 4 for the E. faecalis and P. aeruginosa plates.
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LABORATORY 21
6. Using the appropriate antibiotic disc dispenser, place gram-positive antibiotic-containing discs on the
plates of S. aureus and E. faecalis; gram-negative antibiotic-containing discs on the plate of P.
aeruginosa.
7. Incubate the 3 plates upside-down at 35 C until the next lab period.
8. Using a metric ruler, measure the diameter in mm of the zone of inhibition around each disc on each
plate by placing the ruler on the bottom of the plate (Fig. 2).
If there is a double zone of inhibition, measure the diameter of the innermost zone (see Fig.
4).
If there is a zone containing colonies, measure the diameter of the colony free zone (see
Fig. 5).
If there is a feathered zone, measure the diameter of the point where there is an obvious
demarcation between growth and no growth.
When testing Staphylococcus aureus, the haze around an oxacillin should not be ignored.
Measure the diameter of the zone free of growth or haze.
9. Determine whether each organism is susceptible, moderately susceptible, intermediate, or resistant

to each chemotherapeutic agent using the standardized table (Table 2) and record your results.
Fig. 2:
Measuring the diameter of zones of inhibition in mm.
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LABORATORY 21
Fig. 4:
Double Zone of Iinhibition
Fig. 5:
Zone Containing Colonies
If there is a double zone of inhibition, measure the

diameter of the innermost zone (arrowed line).
If there is a zone containing colonies, measure the

diameter of the colony free zone (arrowed line).
264
LABORATORY 21
Table 2
Zone Size Interpretive Chart for Bauer-Kirby Test
Antimicrobial
agent
Disc
code
Amikacin
AN-30
Amoxicillin/
Clavulanic Acid
- Staphylococcus
-other organisms
AmC-30
Ampicillin
- Staphylococcus
-G- enterics
AM-10
Azlocillin
R=
mm or
less
I=
mm
MS=
mm
15
15-16
16
19
13
14-17
20
18
28
11
12-13
29
14
AZ-75
14
15-17
13
Aztreonam
ATM-30
15
16-21
22
Carbenicillin
-Enterobacteriaceae
Pseudomonas
CB-100
17
13
18-22
14-16
23
17
Cefamandole
MA-30
14
15-17
18
Cefazolin
CZ-30
14
15-17
18
Cefonicid
CID-30
14
15-17
18
Cefoperazone
CFP-75
15
16-20
21
Cefotaxime
CTX-30
14
15-22
23
Cefotetan
CTT-30
12
13-15
16
Cefoxitin
FOX-30
13
15-17
18
Ceftazidime
CAZ-30
14
15-17
18
Ceftizoxime
-Pseudomonas
-other organisms
ZOX-30
10
14
11
15-19
Ceftriaxone
CRO-30
13
14-20
21
Cefuroxime
CXM-30
14
15-17
18
Cephalothin
CF-30
14
15-17
18
Chloramphenicol
C-30
12
13-17
18
Cinoxacin
CIN-100
14
15-18
19
Ciprofloxacin
CIP-5
15
16-20
21
Clindamycin
CC-2
14
15-20
21
265
S=
mm or
more
20
LABORATORY 21
Table 2, continued
Zone Size Interpretive Chart for Bauer-Kirby Test
Antimicrobial
agent
Disc
code
Doxycycline
D-30
Erythromycin
I=
mm
MS=
mm
12
13-15
16
E-15
13
14-22
23
Gentamicin
GM-10
12
13-14
15
Imipenem
IPM-10
13
14-15
16
Kanamycin
K-30
13
14-17
18
Methicillin
- Staphylococcus
DP-5
9
10-13
14
Mezlocillin
MZ-75
12
13-15
16
Minocycline
MI-30
14
15-18
19
Moxalactam
MOX-30
14
15-22
23
Nafcillin
- Staphylococcus
NF-1
10
11-12
13
Nalidixic Acid
NA-30
13
14-18
19
Netilmicin
NET-30
12
13-14
17
Nitrofurantoin
F/M-300
14
15-16
17
Norfloxacin
NOR-10
12
13-16
17
Oxacillin
- Staphylococcus
OX-1
10
11-12
13
28
29
17
17
18-20
-
21
18
Penicillin
- Staphylococcus
R=
mm or
less
P-10
S=
mm or
more
Piperacillin/Tazobactum
-Enterobactereaceae
- Staphylococcus or P. aeruginosa
TZP-110
Sulfamethoxazole
+ Trimethoprim
SXT
10
11-15
16
Tetracycline
Te-30
14
15-18
19
Ticarcillin
TIC-75
11
12-14
15
Ticarcillin/
Clavulanic Acid
TIM-85
11
12-14
15
Tobramycin
NN-10
12
13-14
15
Vancomycin
Va-30
10-11
12
266
LABORATORY 21
RESULTS
A. MICROBIAL RESISTANCE TO ANTIMICROBIAL CHEMOTHERAPEUTIC
AGENTS
Count the number of colonies on each plate. If the growth is too dense to count individual colonies, record
"lawn" (bacteria cover nearly the entire agar surface).
Plate
Number of colonies
LB/amp
"Transformed Bacteria,
Experiment"
LB
"Transformed Bacteria,
Positive Control"
LB/amp
"Wild-Type Bacteria,
Negative Control"
LB
"Wild-Type Bacteria,
Positive Control"
267
Conclusion
LABORATORY 21
B. ANTIBIOTIC SUSCEPTIBILITY TESTING: BAUER-KIRBY METHOD

Interpret the results following steps 9 and 10 of the procedure and record your results in the tables below.
Disc
code
Antimicrobial
agent
AmC-30
Amoxicillin/
Clavulanic Acid
CTX-30
Cefotaxime
FOX-30
Cefoxitin
CIP-5
Ciprofloxacin
CC-2
Clindamycin
E-15
Erythromycin
K-30
Kanamycin
OX-1
Oxacillin
SXT
Sulfamethoxazole
Zone in
mm
+ Trimethoprim
Te-30
Tetracycline
TZP-110
Va-30
Vancomycin
R = Resistant
I = Intermediate
MS = Moderately Susceptible
S = Susceptible
268
MS
LABORATORY 21
Enterococcus faecalis
Disc
code
Antimicrobial
agent
AmC-30
Amoxicillin/
Clavulanic Acid
CTX-30
Cefotaxime
FOX-30
Cefoxitin
CIP-5
Ciprofloxacin
CC-2
Clindamycin
E-15
Erythromycin
K-30
Kanamycin
OX-1
Oxacillin
SXT
Sulfamethoxazole
Zone in
mm
+ Trimethoprim
Te-30
Tetracycline
TZP-110
Va-30
Vancomycin
R = Resistant
I = Intermediate
S = Susceptible
269
MS
LABORATORY 21
Disc
code
Antimicrobial
agent
AN-30
Amikacin
AmC-30
Amoxicillin/
Clavulanic Acid
AM-10
Ampicillin
CB-100
Carbenicillin
CIP-5
Ciprofloxacin
CTX-30
Cefotaxime
FOX-30
Cefoxitin
GM-10
Gentamicin
K-30
Kanamycin
SXT
Sulfamethoxazole
Zone in
mm
+ Trimethoprim
Te-30
Tetracycline
TZP-110
R = Resistant
I = Intermediate
S = Susceptible
270
MS
LABORATORY 21
LABORATORY 21
A. ANTIMICROBIAL CHEMOTHERAPEUTIC AGENTS

1. Define the following: antibiotic, antimicrobial chemotherapeutic chemical, narrow spectrum antibiotic,
broad-spectrum antibiotic.
2. Discuss the meaning of selective toxicity in terms of antimicrobial chemotherapy.
3. List four genera of microorganisms that produce useful antibiotics.
4. Describe four different major modes of action of antimicrobial chemotherapeutic chemicals and give three
examples of drugs fitting each mode of action.
B. MICROBIAL RESISTANCE TO ANTIMICROBIAL AGENTS

DISCUSSION
1. State five mechanisms by which microorganisms may resist antimicrobial chemotherapeutic agents.
2. Briefly describe R-plasmids and name four bacteria that commonly possess these plasmids.
RESULTS
1. Interpret the results of the Escherichia coli plasmid transformation experiment.

DISCUSSION
1. State why antimicrobial susceptibility testing is often essential in choosing the proper chemotherapeutic
agent to use in treating an infection.
2. State what is meant by MIC.
RESULTS
1. Interpret the results of a Bauer-Kirby antimicrobial susceptibility test when given a Mueller-Hinton agar
plate, a metric ruler, and a standardized zone-size interpretation table.
271
272
LABORATORY 22
PARASITOLOGY
LABORATORY 22
PARASITOLOGY
A. Parasitic Protozoans
B. Parasitic Helminths
A. PARASITIC PROTOZOANS
Protozoans are unicellular eukaryotic microorganisms belonging to the Kingdom Protista. They reproduce
asexually by fission (one cell splits into two), schizogony (multiple fission; the nucleus divides many times and the
nuclei are separated into daughter cells), or budding (pinching off of a bud from a parent cell). Some protozoans also
reproduce sexually by fusion of haploid sex cells called gametes.
The vegetative form (motile, feeding, reproducing form) of a protozoan is called a trophozoite. Under certain
conditions, some protozoans produce a protective form called a cyst that enables them to survive harsh
environments. Cysts allow some pathogens to survive outside their host. Favorable conditions in a new host result in
excystation that once again produces a trophozoite.
The parasitic protozoans can be divided into 4 groups based primarily on their means of locomotion.
1. The Sarcomastigophora (Amoeboflagellates)
a. The amoebas (subphylum Sarcodina) move by extending lobe-like projections of their cytoplasm
called pseudopodia. Food is obtained by phagocytosis.
1. One important pathogen in this group is Entamoeba histolytica, the causative agent of
amoebic dysentery. The organism is transmitted by the fecal-oral route. Cysts are
excreted in the feces of an infected individual or carrier and ingested through fecallycontaminated food, water, objects, etc. After excystation, the trophozoites penetrate the
walls of the large intestines causing ulceration and frequently causing the symptoms of
dysentery. Involvement of the liver and other organs may occur if the protozoan invades the
blood. The disease is diagnosed by microscopically looking for cysts of E. histolytica
in a fecal smear (Fig. 1).
2. Acanthamoeba, another infectious amoeba, can infect the eye, blood, spinal cord, and
brain and is transmitted by waterborne cysts picked up while swimming in contaminated
water, crossing the mucous membranes.
b. The flagellates (subphylum Mastigophora) move by means of flagella. Some also have an
undulating membrane. Important pathogens in this class include:
1. Trypanosoma gambiense, Trypanosoma rhodesiense, and Trypanosoma cruzi
T. gambiense and T. rhodesiense cause the disease African sleeping sickness or African
trypanosomiasis. They are transmitted to humans by the bite of an infected tsetse fly (a
vector). The disease primarily involves the lymphatic and nervous systems of humans and is
diagnosed by microscopically looking for Trypanosoma (Fig. 2) in the blood, in
aspirated fluid from lymph nodes, or in spinal fluid.
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LABORATORY 22
PARASITOLOGY
T. cruzi causes South American sleeping sickness or Chagas' disease and is transmitted
by infected Triatomid bugs (kissing bugs).
Fig. 1:
Cysts of Entamoeba in a fecal smear.
Fig. 2:
Trophozoite of Trypanosoma in the blood.
2. Giardia lamblia
Giardia lamblia (G. intestinalis) causes a gastroenteritis-type of disease called giardiasis.
Giardiasis is the most common protozoan intestinal disease in the U.S. and is transmitted by the
fecal-oral route. Cysts of the organism are ingested through fecally-contaminated food, water, etc.
Giardiasis is diagnosed by microscopically looking for cysts of G. intestinalis in fecal smears
(Fig. 3).
3. Trichomonas vaginalis
This protozoan causes genitourinary trichomoniasis. There are an estimated 2.5 million cases
per year in the U.S. In females, it usually appears as vaginitis with itching and a white discharge. In
males it is often asymptomatic but may cause urethritis. It is transmitted mainly by venereal
contact and is diagnosed by microscopically looking for T. vaginalis trophozoites in vaginal
discharge and urine (Fig. 4).
2. The Ciliophora
This group of protozoans is characterized by a covering of cilia used for motility and direction of food
particles into the mouth or cytosome. In the trophozoite, a large macronucleus, small micronucleus, cilia, and
contractile vacuoles may be seen.
The only pathogen in this group is Balantidium coli, which causes a diarrhea-type infection called
balantidiasis. The protozoan is transmitted to humans by the fecal-oral route and invades the large
intestines causing ulceration. It is diagnosed by microscopically looking for B. coli in a fecal smear (Fig.
5).
274
LABORATORY 22
PARASITOLOGY
Fig. 3:
Cyst of Giardia lamblia in a fecal smear.
Fig. 4:
Trophozoite of Trichomonas vaginalis.
Fig. 5:
Balantidium coli in a fecal smear.
Fig. 7:
Blood smear showing red blood cells infected with
Plasmodium.
3. The Apicomplexans
The sporozoa are not motile in their mature forms, reproduce both asexually and sexually, and often
have complex life cycles for transmission from host to host. They possess a complex of organelles at their
apex (apical complexes) that contain enzymes used in penetrating host tissues.Threecommon pathogens
in this group are:
a. Toxoplasma gondii
This protozoan causes the disease toxoplasmosis. In adults, the disease is usually mild and
resembles infectious mononucleosis. However, new-born infants who contracted toxoplasmosis in
utero commonly have severe central nervous system damage. It also causes severe disease in
immunosuppressed individuals such as people with AIDS. Domestic cats, who pick up the organism
from eating infected rodents, may act as carriers of T. gondii, and their feces may contain oocysts of
the protozoan. However, the organism may be found in practically every mammal. The disease is
275
LABORATORY 22
PARASITOLOGY
transmitted to humans by ingesting raw meat of an infected mammal or by inhaling or
ingesting cysts of T. gondii from cat feces. Pregnant women should be especially careful to avoid
raw meat and cat feces. The disease is diagnosed by serologic testing and by growing the
organism in cell culture.
b. Plasmodium
Four Plasmodium species, P. falciparum, P. malariae, P. ovale, and P. vivax cause malaria. The
vector involved in the transmission of the disease from human to human or from animal to human is
an infected female Anopheles mosquito.
Asexual reproduction (or schizogony) of the Plasmodium occurs within liver cells and red blood
cells of the infected human. With malaria caused by P. vivax and P. ovale, a dormant form or
hypnozoite remains in the liver and may cause later relapses. The infected cells in which the
organism is reproducing by schizogony are called schizonts (Fig. 7). The sexual cycle (or
sporogeny) occurs in the mosquito. The typical recurring malarial fever is a result of the lysis of
the infected red blood cells, causing release of merozoites and their metabolic by-products. Fever
cycles of 24, 48, or 72 hours usually occur depending on the infecting species. The life cycle is
shown in Fig. 6. Malaria is diagnosed by microscopically looking for the parasite within
infected red blood cells (schizonts).
c. Cryptosporidium
Cryptosporidium is an intracellular parasite that causes diarrhea, although in people who are
immunosuppressed it can also cause respiratory and gallbladder infections. It is transmitted by
the fecal-oral route.
Fig. 6:
Malaria life cycle.
276
LABORATORY 22
PARASITOLOGY
B. PARASITIC HELMINTHS
Helminthology is the study of worms, or helminths. Helminths are multicellular, often macroscopic worms having
both rudimentary organs and organ systems. We will look at three groups of pathogenic helminths: nematodes,
cestodes, and trematodes
1. The Nematodes (Roundworms)
Nematodes are elongated, unsegmented, cylindrical worms having separate sexes. The various
systems of the roundworms can be seen in Fig. 8, and a generalized drawing of a nematode is given in Fig.
9. We will look at several pathogenic nematodes.
Fig. 8
Organ systems of a typical Nematode (roundworm)
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LABORATORY 22
PARASITOLOGY
Fig. 9:
Female and male nematodes
a. Ascaris lumbricoides (Fig. 11A)

These worms range from 20-45 cm long and are 5 mm in diameter in the adult form, the female
being larger than the male. The life cycle is seen in Fig. 10. The disease is called ascariasis.
Humans become infected by ingesting water or food contaminated with feces that contains
Ascaris ova or from fingers contaminated with polluted soil. The disease is diagnosed by
microscopically looking for Ascaris ova in a fecal smear. The Ascaris ova have a bumpy or
serrated edge (Fig. 11). A similar roundworm, Toxocara, parasitizes dogs and cats. Visceral larva
migrans is the migration of larvae of these worms in human tissues such as lung, liver, and brain,
where they may cause tissue damage and allergic reactions.
b. Enterobius vermicularis (pinworms) Fig. 13A
E. vermicularis is a small worm, the female being 8-13 mm long and 0.3-0.5 mm wide; the male
being 2-5 mm long and 0.1 mm wide. The life cycle is shown in Fig. 12. Humans, frequently children,
become infected by inhaling E. vermicularis ova or from transfer of ova to the mouth from
fecally-contaminated fingers. The female worm migrates to the perianal region of the infected
individual, releasing masses of ova and causing an itching sensation. The disease is diagnosed by
applying tape to the perianal region and microscopically looking for pinworm ova that have
stuck to the tape. The pinworm ova have a smooth edge (Fig. 13)
c. Trichinella spiralis
T. spiralis causes a disease called trichinosis. Humans become infected mainly by eating poorly
cooked infected pork containing encysted larva 1-2 mm long (Fig. 15). The life cycle is shown in
Fig. 14. The larvae excyst and develop into adult worms in the intestines. After mating, the female
releases larvae which enter the blood and are distributed throughout the body where they become
encysted in muscle tissue. The disease is diagnosed by serological tests and microscopic
examination of biopsy specimens.
278
LABORATORY 22
PARASITOLOGY
2. The Cestodes (Tapeworms)

Tapeworms are flat, segmented worms which are hermaphroditic (contain both male and female sexual
organs). Adult tapeworms have several distinct regions. The scolex is a head-like structure with distinct
suckers and possibly hooks used for attachment to the intestinal wall (Fig. 16 and Fig. 17). Behind the scolex
is a constricted neck region consisting of germinative tissue from which new segments, or proglottids, are
formed (Fig. 18). Finally, there is a long strobila or chain of proglottids of varying stages of maturity.
Proglottids containing thousands of ova are excreted in the feces. When ingested by intermediate hosts (such
as cattle, pigs, and fish), the larva hatch from the ingested ova and migrate to muscle where they encyst as
cysticerci. The life cycle is shown in Fig. 19.
Humans become infected with tapeworms by eating poorly cooked infected beef, pork, or fish
containing cysticerci. Taenia saginata, the beef tapeworm often reaches 6 meters in length; Taenia solium,
the pork tapeworm is normally 2-7 meters in length; and Diphyllobothrium latum, the fish tapeworm may
reach 3-6 meters in length. These tapeworms are diagnosed by looking for proglottids and ova in the
feces.
When humans ingest tapeworm eggs instead of cysts, embryos are released, penetrate the intestinal wall,
and enter the blood. The embryos migrate to various tissues (frequently the brain) and develop into cysticerci.
Humans also act as intermediate hosts for Echinococcus granulosus found in dogs and cats. Larva hatch
from ingested ova and migrate to the liver and lungs and form hydatid cysts.
Fig. 10:
Life cycle of Ascaris lumbricoides
279
LABORATORY 22
PARASITOLOGY
Fig. 11:
Ascaris ova
Fig. 11A:
Ascaris
Fig. 12:
Life cycle of Enterobius vermicularis
280
LABORATORY 22
PARASITOLOGY
Fig. 13:
Enterobius ovum
Fig. 13A:
Female Enterobius filled with ova (arrows)
Fig. 14:
Life cycle of Trichinella spiralis
281
LABORATORY 22
PARASITOLOGY
Fig. 15:
Trichinella encysted in muscle
Fig. 16:
Cestode (tapeworm) morphology
282
LABORATORY 22
PARASITOLOGY
Fig. 17:
Scolex of a tapeworm
Fig. 18:
Gravid proglottid of a tapeworm filled with ova
Fig. 19:
Life cycle of Taenia solium
283
LABORATORY 22
PARASITOLOGY
3. The Trematodes (Flukes)

Flukes are unsegmented, flat, leaf-shaped worms having a variety of organ systems (Fig. 20). Most
flukes are hermaphroditic. They attach to the host by means of an oral sucker and a ventral sucker (Fig.
20A). Flukes, as adults, may infect either the portal blood vessels, intestines, liver, or lungs of humans and
are named according to the tissue they infect. Humans become infected with liver flukes, lung flukes, and
intestinal flukes by ingesting poorly cooked fish, crayfish, crabs, snails, or water vegetables infested
with flukes. Blood flukes directly penetrate the skin.
In their life cycle (Fig. 21), fluke ova leave the body of the infected human or animal by means of feces,
urine, or sputum (depending on the type of fluke). The ova enter water and infect the first intermediate host,
certain species of water snails. A free-swimming form of the fluke called the cercaria, then leaves the snail
and infects second intermediate hosts (fish, crayfish, water vegetables, etc.) which are ingested by humans.
The cercariae of the blood fluke Schistosoma (Fig. 22 and Fig. 22A) can directly penetrate the skin of
humans and cause schistosomiasis, a major problem in Africa, South America, and Asia.
Fig. 20:
Morphology of a liver fluke
Fig. 20A:
Fasciola hepatica (liver fluke)
Fig. 22:
Morphology of a blood fluke
Fig. 22A:
The blood fluke Schistosoma
284
LABORATORY 22
PARASITOLOGY
Fig. 21:
Life cycle of trematodes (flukes)
285
LABORATORY 22
PARASITOLOGY
PROCEDURE AND RESULTS

1. Observe the prepared slides of the following parasitic protozoans and compare them with the indicated figures
in this lab exercise.
a. The Sarcodina
Fecal smear containing cysts of Entamoeba histolytica (the cause of amoebic dysentery). Note that it
contains several nuclei. See Fig. 1.
b. The Mastigophora
1. Blood smear containing Trypanosoma gambiense (the cause of African sleeping sickness). Note
the nucleus, the undulating membrane, and the red blood cells in the background. See Fig. 2.
2. Fecal smear containing cysts and/or trophozoites of Giardia lamblia (the cause of giardiasis). Note
the bilateral symmetry and macronuclei of the organism thay look like "eyes." See Fig. 3.
286
LABORATORY 22
PARASITOLOGY
3. Vaginal discharge containing Trichomonas vaginalis (the cause of genitourinary trichomoniasis).
Note the bundle of flagella, the undulating membrane, and the nucleus. See Fig. 4.
c. The Ciliophora
Fecal smear containing Balantidium coli (the cause of balantidiasis). Note the large dumbbell-shaped
macronucleus. See Fig. 5.
d. The Sporozoa
1. Sporozoites of Plasmodium from the salivary glands of an infected mosquito. See Fig. 6.
2. Blood smear containing red blood cells infected with merozoites of Plasmodium (the cause of
malaria). See Fig. 6 and 7.
287
LABORATORY 22
PARASITOLOGY
2. Observe the prepared slides of the following parasitic helminths and compare them with the indicated figures
in this lab exercise.
a. The Nematodes (roundworms)
1. Fecal smear containing ova of Ascaris lumbricoides (the cause of ascariasis). Note the "bumpy"
edge of the ova. See Fig. 10 and Fig. 11.
2. Ascaris lumbricoides larva. Note the organ systems. See Figs. 8, 9, and 10.
3. Fecal smear containing ova of Enterobius vermicularis (pinworm). Note the "smooth" edge of the
ova. See Fig. 13.
288
LABORATORY 22
PARASITOLOGY
4. Enterobius vermicularis larva. Note the organ systems. See Figs. 8, 9, and 12.
5. Muscle tissue containing encysted larvae of Trichinella spiralis (the cause of trichinosis). Note the
spiral-shaped larva within the cyst. See Fig. 14 and Fig. 15.
b. The Cestodes (tapeworms)

1. Scolex of Taenia pisiformis (dog tapeworm). Note hooks and suckers. See Fig. 16 and Fig. 17.
289
LABORATORY 22
PARASITOLOGY
2. Gravid proglottid of Taenia pisiformis. Note the uterus and ova. See Fig. 18.
c. The Trematodes (flukes)

1. Fasciola hepatica (liver fluke). Note the organ systems. See Fig. 20 and Fig. 21, and 21A.
2. Schistosoma mansoni (blood fluke). Note the oral and ventral suckers. See Fig. 22 and 22A.
1. Observe the preserved helminths.
290
LABORATORY 22
PARASITOLOGY
LABORATORY 22
A. PARASITIC PROTOZOANS
DISCUSSION
1. Define the following: protozoan, trophozoite, cyst.
2. State how the following diseases may be transmitted to humans and briefly discuss how the diseases are
diagnosed in the clinical laboratory:
a. amoebic dysentery
b. African sleeping sickness
c. giardiasis
d. genitourinary trichomoniasis
e. balantidiasis
f. malaria
g. toxoplasmosis
3. Describe the following in terms of the malarial life cycle: sporozoite, schizont, asexual cycle, sexual cycle.
4. State what causes the recurring fever of malaria.
RESULTS
1. Recognize the following organisms when seen through a microscope and state what disease they are
associated with:
a. Entamoeba histolytica cysts in a fecal smear
b. Trypanosoma gambiense in a blood smear
c. Giardia lamblia cysts in a fecal smear
d. Trichomonas vaginalis in vaginal discharge
e. Balantidium coli in a fecal smear
f. Plasmodium merozoites in infected red blood cells
B. PARASITIC HELMINTHS
DISCUSSION
1. Define the following: helminth, ova, hermaphroditic.
2. List the three classes of parasitic helminths and state the common name for each class.
3. State how the following diseases may be transmitted to humans and state how each disease may be
diagnosed in the clinical laboratory:
a. ascariasis
b. pinworms
c. trichinosis
d. tapeworms
e. flukes
4. Compare protozoans and helminths in terms of their size and structural complexity.
291
LABORATORY 22
PARASITOLOGY
RESULTS
1. Recognize the following organisms or structures when seen through a microscope:
a. roundworms
b. Ascaris ova
c. pinworm ova
d. Trichinella in muscle tissue
e. tapeworms
f. scolex of a tapeworm
g. ova and uterus in a gravid proglottid of a tapeworm
h. flukes
292
APPENDIX A
LAB 2
APPENDIX A
LAB 2
Colony Morphology on Agar Plate Cultures
A. Form of colony
Punctiform
Under 1 mm in diameter
Circular
Filamentous
Long, irregular, interwoven threads
Rhizoid
Irregular, branched
Irregular
B. Elevation of colony
Effuse
Very thin, spreading
Flat
Raised
Convex
Umbonate
293
APPENDIX A
LAB 2
C. Margin (or edge) of colony
Entire
Undulate
Erose
Filamentous
Curled
D. Surface of colony
Smooth
Contoured
Undulating
Radiate
Radiating ridges
Concentric
Concentric rings
Rugose
Wrinkled
E. Pigmentation
Specific color and solubility of pigment or lack of color
F. Optical characteristics
Opaque, translucent, dull, mucoid, etc.
294
APPENDIX B
LAB 4
APPENDIX B
LAB 4
I. Scientific Notation
When doing scientific calculations or writing, scientific notation is commonly used. In scientific notation,
one digit (a number between 1 and 9) only is found to the left of the decimal point. The following
examples are written in scientific notation:
3
3.17 x 10
-2
5.2 x 10
Note that exponents (the powers of 10) are used in these conversions.
Multiples of 10 are expressed in positive exponents:
0
10 = 1
1
10 = 10
2
10 = 100 = 10 x 10
3
10 = 1000 = 10 x 10 x 10
4
10 = 10,000 = 10 x 10 x 10 x 10
5
10 = 100,000 = 10 x 10 x 10 x 10 x 10
6
10 = 1,000,000 = 10 x 10 x 10 x 10 x 10 x 10
Fractions of 10 are expressed as negative exponents:
-1
= 0.1
-2
= 0.01 = 0.1 x 0.1
-3
= 0.001 = 0.1 x 0.1 x 0.1
-4
= 0.0001 = 0.1 x 0.1 x 0.1 x 0.1
-5
= 0.00001 = 0.1 x 0.1 x 0.1 x 0.1 x 0.1
-6
= 0.000001 = 0.1 x 0.1 x 0.1 x 0.1 x 0.1 x 0.1
10
10
10
10
10
10
A. Procedure for converting numbers that are multiples of 10 to scientific notation

1. Convert 365 to scientific notation.
a. Move the decimal point so that there is only one digit between 1 and 9 to the left of the
point (from 365.0 to 3.65).
295
APPENDIX B
LAB 4
b. 3.65 is a smaller number than the original. To equal the original you would have to
2
multiply 3.65 by 100. As shown above, 100 is represented by 10 . Therefore, the proper
2
scientific notation of 365 would be 3.65 x 10 .
c. A simple way to look at these conversions is that you add a positive power of 10 for
each place the original decimal is moved to the left. Since the decimal was moved two
2
2
places to the left to get 3.65, the exponent would be 10 , thus 3.65 x 10 .
2. Convert 6,500,000 to scientific notation.
a. Move the decimal point so there is only one digit to the left of the point (6,500,000
becomes 6.5).
6
b. To equal the original number, you would have to multiply 6.5 by 1,000,000 or 10 . (Since
6
you moved the decimal point 6 places to the left, the exponent would be 10 .)
6
c. Therefore, the proper scientific notation of 6,500,000 would be 6.5 x 10 .
B. Procedure for converting numbers that are fractions of 10 to scientific notation.

1. Convert 0.0175 to scientific notation.
a. Move the decimal so there is one digit between 1 and 9 to the left of the decimal point
(0.0175 becomes 1.75).
-2
b. To equal the original number, you would have to multiply 1.75 by 0.01 or 10 . Therefore,
-2
the proper scientific notation for 0.0175 would be 1.75 x 10 .
c. A simpler way to look at these conversions is that you add a negative power of 10 for
each place you move the decimal to the right. Since the decimal point was moved 2
-2
-2
places to the right, the exponent becomes 10 , thus 1.75 x 10 .
2. Convert 0.000345 to scientific notation.
a. Move the decimal point so only one digit (between 1 and 9) appears to the left of the
decimal (0.000345 becomes 3.45).
-4
b. To equal the original number, you would have to multiply 3.45 by 0.0001 or 10 . (Since
-4
you moved the decimal point 4 places to the right, the exponent becomes 10 .)
-4
c. Therefore, the proper scientific notation of 0.000345 is 3.45 x 10 .
C. Other examples
7
12,420,000 = 1.242 x 10
4
21,300 = 2.13 x 10
-3
0.0047 = 4.7 x 10
-6
0.000006 = 6.0 x 10
296
APPENDIX B
LAB 4
II. Dilutions: Examples

A. 1 ml of bacteria is mixed with 1 ml of sterile saline. The total ml in the tube would be 2 ml, of which 1
ml is bacteria. This is a 1:2 dilution (also written 1/2, meaning 1/2 as many bacteria per ml as the original
ml).
B. 1 ml of bacteria is mixed with 3 ml of sterile saline. The total ml in the tube would be 4 ml, of which 1
ml is bacteria. This is then a 1:4 dilution (also written 1/4, meaning 1/4 as many bacteria per ml as the
original ml).
C. 1 ml of bacteria is mixed with 9 ml of sterile saline. The total ml in the tube would be 10 ml, of which 1
-1
-1
ml is bacteria. This is then a 1:10 dilution (also written 1/10 or 10 , meaning 1/10 or 10 as many bacteria per
ml as the original ml).
D. For dilutions greater than 1:10, usually serial dilutions (dilutions of dilutions) are made. The following
represents a serial ten-fold dilution (a series of 1:10 dilutions):
-1
The dilution in tube #1 would be 1/10 or 10 .

-2
The dilution in tube #2 would be 1/100 or 10 (1/10 of 1/10).
-3
The dilution in tube #3 would be 1/1000 or 10 (1/10 of 1/100).
-4
The dilution in tube #4 would be 1/10,000 or 10 (1/10 of 1/1000).
The dilution factor is the inverse of the dilution. (Inverse means you flip the two numbers of the fraction; with
scientific notation you use the positive exponent.)
For a dilution of 1/2, the dilution factor would be 2/1 or 2.
For a dilution of 1/4, the dilution factor would be 4/1 or 4.
-1
1
For a dilution of 1/10 or 10 , the dilution factor would be 10/1 or 10 or 10 .
-6
6
For a dilution of 1/1,000,000 or 10 , the dilution factor would be 1,000,000/1 or 1,000,000 or 10 .
In other words, the dilution factor tells you what whole number you have to multiply the dilution by to get back to
the original 1 ml.
297
APPENDIX C
LAB 16
298
APPENDIX C
LAB 16
APPENDIX C
LAB 16
PROCEDURE FOR THE ACID-FAST STAIN (Ziehl-Neelsen Method)
1. Heat-fix a smear of the sample to be stained on a new glass slide.
2. Cover the smear with a piece of blotting paper and flood with carbol fuchsin.
3. Steam for 5 minutes by passing the slide through the flame of a gas burner.
4. Allow the slide to cool and wash with water.
5. Add the acid-alcohol decolorizing slowly dropwise until the dye no longer runs off from the smear.
6. Rinse with water.
7. Counterstain with methylene blue for 1 minute.
8. Wash with water, blot dry, and observe using oil immersion microscopy.
Acid-fast bacteria will appear red; non-acid-fast material will appear blue.
299
APPENDIX D
LAB 12
300
APPENDIX D
LAB 12
APPENDIX D
LAB 19
BACTERIAL EXAMINATION OF WATER: COLIFORM COUNTS
Discussion
The purpose of the bacteriological examination of water is to determine if there is a possibility of pathogens being
present. Infectious diseases such as salmonellosis, typhoid fever, shigellosis, cholera, hepatitis A, amoebic dysentery,
Campylobacter gastroenteritis, giardiasis, and other fecal-oral route diseases may be transmitted by fecallycontaminated water. The identification of pathogens, however, is quite difficult. Pathogens may not survive long in
water and are usually present only in small quantity. Therefore, one usually tests for the presence of coliforms in
water.
Coliforms are gram-negative, lactose-fermenting rods of the family Enterobacteriaceae. Escherichia coli, a fecal
coliform, is normal flora of the intestines in humans and animals and is, therefore, a direct indicator of fecal
contamination of the water. The presence of coliforms would then indicate the possibility of fecal pathogens being
present.
Two tests are frequently performed to monitor water: the fecal coliform count and the total coliform count.
1. The fecal coliform count tests specifically for the fecal coliform E. coli. M-FC medium is used in this test
and the plates are incubated at 45.5 C. This temperature is selective for fecal coliforms (nonfecal coliforms
will not grow at this temperature) that produce blue colonies. This test, however, requires a special water bath
incubator to assure a temperature of 45.5 C.
2. The total coliform count will detect any coliforms (fecal and nonfecal) present in the water. It is not as
specific an indicator of fecal contamination, but is a useful screening test. M-coliform medium is used in this
test and the plates are incubated at 37 C. Both fecal and nonfecal coliforms will grow and produce
metallic green colonies. Coliforms would indicate the possibility of fecal contamination of the water.
Both of these tests use the micropore membrane filter method. Different amounts of the water sample being
tested are passed through a membrane filter (Lab 19). The water passes through and the bacteria are trapped on
the surface of the filter. The filter is then placed in a petri plate on pads containing either M-FC or M-coliform
medium. Colonies then form on the filter. By counting the number of colonies and knowing the volume of water
sample used, the number of fecal coliforms or total coliforms per ml of water can be determined.
PROCEDURE
1. Take three 50mm petri plates and aseptically place a sterile pad in the bottom of each. Label the plates
0.1ml, 1.0ml, and 10.0ml.
2. Using a 10ml pipette, add 2.0ml of M-coliform broth to each pad.
3. Using alcohol-flamed forceps, remove a 0.45m pore-diameter gridded membrane filter and place it
grid-side-up in the filter set-up.
4. Secure the funnel to the filter set-up.
301
APPENDIX D
LAB 12
5. Pour about one inch of sterile saline into the filter set-up.
6. Using a 1.0ml pipette, add 0.1ml of the water sample being tested to the sterile water and mix.
7. Vacuum the water through the filter.
8. Add another inch of sterile saline to the funnel and swirl. This washes the bacteria off the sides of the
funnel onto the filter.
9. Vacuum.
10. Using alcohol-flamed forceps, remove the filter and place it grid-side-up in the plate labeled 0.1ml.
Make sure the entire filter makes contact with the M-coliform-containing pad.
11. Repeat using 1.0ml of the water sample.
12. Repeat using 10.0ml of the water sample.
13. Incubate the 3 plates at 37 C until the next lab period.
14. Observe the M-coliform plates. Both fecal and non-fecal coliforms will produce metallic green
colonies. If there are a feasible number of coliform colonies for counting, determine the number of total
coliforms per ml of water.
302

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INTRODUCTION

LAB 1: INTRODUCTION TO THE MICROSCOPE

LAB 2: ASEPTIC TECHNIQUE AND TRANSFER OF

LAB 3: OBTAINING PURE CULTURES FROM A MIXED

LAB 4: ENUMERATION OF MICROORGANISMS

LAB 5: DIRECT STAIN AND INDIRECT STAIN

LAB 6: GRAM STAIN AND CAPSULE STAIN

LAB 7: ENDOSPORE STAIN AND BACTERIAL MOTILITY

LAB 8: IDENTIFICATION OF BACTERIA THROUGH

LAB 9: FUNGI PART 1 - THE YEASTS

LAB 10: FUNGI PART 2 - THE MOLDS

LAB 11: VIRUSES - THE BACTERIOPHAGES

LAB 12: ISOLATION AND IDENTIFICATION OF

The Enterobacteriaceae: Fermentative,

Using the EnterotubeII

LAB 13: ISOLATION AND IDENTIFICATION OF

LAB 14: ISOLATION AND IDENTIFICATION OF

LAB 15: ISOLATION AND IDENTIFICATION OF

LAB 16: ISOLATION AND IDENTIFICATION OF

The Neisseriae (Neisseria gonorrhoeae and

LAB 17: SEROLOGY, PART 1: DIRECT SEROLOGIC

Introduction to Serological Testing

LAB 18: SEROLOGY, PART 2: INDIRECT SEROLOGIC

LAB 19: USING PHYSICAL AGENTS TO CONTROL

LAB 20: USING DISINFECTANTS AND ANTISEPTICS

LAB 21: USING ANTIMICROBIAL CHEMOTHERAPEUTIC

LAB 22: PARASITOLOGY

APPENDIX A: Bacterial Growth on an Agar Surface

APPENDIX B: Scientific Notation and Dilutions

APPENDIX C: The Acid-Fast Stain

APPENDIX D: Bacteriological Examination of Water

A. Using Performance Objectives

E. Metric Length and Fluid Volume

centimeter (cm) = 10 m or 1/100 m

Escherichia coli, a rod-shaped bacterium.

Staphylococcus aureus, a coccus-shaped bacterium.

F. Using the Microscope (Olympus Model CH-2 Microscope)

Fig. 3: An Olympus CH-2 Microscope

Fig. 4: An Olympus CH-2 Microscope

7. Focusing from lower power to higher power

Fig. 5: The Oil Immersion Lens

The immersion oil has the same refractive index

A. USING PERFORMANCE OBJECTIVES

F. USING THE MICROSCOPE

A. BACTERIAL SHAPES AND ARRANGEMENTS

Note budding (arrows).

D. FOCUSING WITH OIL IMMERSION - Olympus CH-2 Microscope (see Fig. 7)

Fig. 6: An Olympus CH-2 Microscope

Fig. 7: Olympus CH-2 Microscope

A. ASEPTIC TECHNIQUE (Figs. 1 & 2)

2. Remove the inoculum.

b. Transferring the inoculum onto a petri plate:

B. FORMS OF CULTURE MEDIA

A. Sterilize the loop.

D. Remove the inoculum.

B. Remove the cap of the broth

C. Pass the lip of the tube through the

E. Pass the lip of the tube through

F. Replace the cap.

A. Remove the cap of the broth