General

Page | 1
 Introduction To
Microorganisms
 Microorganisms are generally unicellular → the whole organism is one cell.
 a single microbial cell performs all the functions required to maintain itself and propagate.

Microorganisms may be classified in the following large biological groups:

1. Algae. 5. Bacteria.
2. Protozoa. 6. Archaebacteria.
3. Slime molds. 7. Viruses.
4. Fungi. 8. Prions.

Prokaryote Eukaryote
Pro = before EU = True
Size Smaller Larger
Development Simple More developed
Nucleus No True nucleus True nucleus
One chromosome is called
Nucleoid or Nuclear region
Nuclear No nuclear membrane Surrounded by nuclear membrane
membrane
Mitochondria No mitochondria Contain mitochondria
Organelles No membrane bound Contain membrane bound
organelles organelles
Ribosomes 70S 80S
Cytoplasmic No sterol (except Contain sterol
membrane mycoplasma)
Bacteria Algae (except blue green)
Examples Mycoplasma Protozoa
Rickettsia Slime molds
Chlamydia Fungi
Blue green algae Plants
Archaebacteria Animals

Page | 2
 Viruses  Smallest infective agent
 Have no cell structure
 Obligate intracellular parasites →
require host cells
Viroids Single stranded RNA (no protein)
Causes diseases in plants
Prions Infectious protein particles (no nucleic acids)
Blue green algae Do not cause infections
May produce potent toxins (drinking polluted waters)

MCQs
1- Which of the following microorganisms has a nuclear
membrane?
a- Viruses
b- Fungi
c- Prions
d- Bacteria
e- Viroids

2- Viruses have all the following characteristics EXCEPT:

a- They are one of the smallest infectious agents.
b- They have no cell structure.
c- They are obligate intracellular parasites.
d- They require the host biological machinery for their replication.
e- They are prokaryotic.

3- Prions:
a- Are single stranded circular RNA
b- Are devoid of proteins
c- Are infectious proteins devoid of nucleic acids
d- Are prokaryotic cells
e- Cause diseases in plants

Page | 3
 Bacteria:
Their Structure and Organization
 Bacteria were first discovered by Leeuwenhoek 1674.
 They are among the most widely distributed forms of life.
 They are found in air, water and soil.
 They are also found in or on the human body, animals and plants.

Bacterial Morphology
Bacteria are classified based on their morphological features such as:
1) Shape
2) Size
3) arrangement
4) staining characteristics.

Bacterial Size
Most bacteria range in size from
0.2-1.2 µm in width and 0.4-14 µm
in length.

Bacterial Shape and Arrangement:

Cocci Bacilli Spiral

bacteria
Definition Spherical organisms Rod shaped (Stick)
Singular = coccus Singular = bacillus
Types Diplococci: pairs of cells → Neisseria. May occur single, in Spirilla: rigid
Irregular grape-like clusters, → pairs, or chains Spirochetes:
staphylococci. Coccobacilli: Short flexible
Chains of four or more → streptococci. Vibrio: curved

Page | 4
 The arrangement of cells is determined by
the planes of division.
the cocci that divide along a single plane
produce diplococci or chains →
streptococci
those that divide on many planes produce
clusters → staphylococci.

Staining Characteristics

Simple staining Differential staining

Using a single dye Requires more than one dye
Stained structures give the same color Distinguish between different types of
bacteria by giving different colors
Used for revealing the characteristics of Gram stain:
size, shape, arrangement The most important stain in microbiology
Divides bacteria into:
1- gram positive (violet)
2- gram negative (red)

Ziehl-neelsen stain:
Used to stain mycobacteria (acid fast
bacilli)

Page | 5
 Bacterial Ultra-Structures and their Functions

All bacteria have a nucleoid, ribosomes and a cytoplasmic membrane.

Most bacteria also have a cell wall and some are further enveloped by a capsule or
slime layer.
Some types of bacteria have also various appendages as flagella and pili.

Cytoplasm
Few morphologically distinct components can be found within the cytoplasm

Nucleoid:
❖ Genetic information of a bacterial cell is contained in a single circular molecule of
double-stranded DNA, which constitutes the bacterial chromosome.
❖ It is 1 mm long and is packed into a supercoiled state inside the cell.

Plasmids:
❖ In many bacteria, additional genetic
information is contained on plasmids
which are small circular extrachromosomal
DNA molecules that can replicate independently of the chromosome.

Ribosomes:
❖ They are the site of protein synthesis in the cell.
❖ Ribosomes consist of protein and RNA.
❖ Prokaryotic ribosomes have a sedimentation constant of
70S, smaller than the 8OS ribosomes of eukaryotes.
❖ This difference makes bacterial ribosomes a selective target for antibiotic action.

Page | 6
Inclusion granules:
❖ These are granules of nutrient materials, usually
phosphates, sulphur, carbohydrates and lipids.
❖ Energy reserves are usually stored as glycogen,
starch or poly-ꞵ-hydroxybutyrate.
❖ Phosphate is stored in metachromatic or volutin granules, which are used for
synthesis of ATP.

Mesosomes:
❖ These are complex invagination of the cytoplasmic membrane.
❖ They are involved in cell division and sporulation.
❖ They also have a function analogous to the mitochondria in eukaryotes providing a
membranous support for respiratory enzymes

Cytoplasmic Membrane

Definition: It is a phospholipid protein bilayer similar to that of eukaryotic cells except

that, in bacteria, it lacks sterols.

It has the following functions:

1. Selective transport:
molecules move across the cytoplasmic membrane by simple diffusion, facilitated
diffusion and active transport.

2. Excretion of extracellular enzymes:

a. Hydrolytic enzymes: which digest large food molecules into subunits small enough
to penetrate the cytoplasmic membrane.
b. Enzymes used to destroy harmful chemicals
Example: penicillin-degrading enzymes.

3. Respiration: The respiratory enzymes are located in the cytoplasmic membrane, which
is thus a functional analogue of the mitochondria in eukaryotes.

Page | 7
4. Cell wall biosynthesis:
The cytoplasmic membrane is the site of:
a. The enzymes of cell wall biosynthesis.
b. The carrier lipids on which the subunits
of the cell wall are assembled.

5. Reproduction:
❖ A specific protein in the membrane attaches to the DNA and separates the duplicated
chromosomes from each other.
❖ A septum forms by the cytoplasmic membrane to separate the cytoplasm of the two
daughter cells.

6. Chemotactic system:
❖ Attractants and repellants bind to specific receptors in the cytoplasmic membrane
and send signals to the cell's interior.
❖ The cell then responds to the surface message.

Cell Wall
❖ The bacterial cell wall is the structure that immediately surrounds the cytoplasmic
membrane.
❖ It is 10-25 nm thick strong and relatively rigid, though having some elasticity

Structure of the cell wall

 The cell wall of bacteria is a complex structure.

 Its impressive strength is primarily due to peptidoglycan (murein or mucopeptide).
 Peptidoglycan: a complex polymer consisting of N-acetylglucosamine (NAG) and N-
acetylmuramic acid (NAM) unique to bacteria.
 A set of identical tetrapeptide side chains are attached to NAM.

Page | 8
Gram-positive cell wall:
1. Peptidoglycan:
 There are as many as 40 sheets of peptidoglycan.
 comprising up to 50% of the cell wall material.
 Despite the thickness of peptidoglycan, chemicals can readily pass through.

2. Teichoic acids:
 They are the polymer of ribitol or glycerol phosphate.
 They are found in the cell wall of most Gram-positive bacteria.
 Teichoic acids and cell wall associated proteins are the major surface antigens
of the Gram-positive bacteria.

Gram Negative bacteria

Gram positive bacteria

Gram-negative cell wall:

1. Peptidoglycan:
 It is much thinner.
 composed of only one or two sheets.
 comprising 5-10% of the cell wall material.

2. Outer membrane:
 It is phospholipid protein bilayer present external to the peptidoglycan layer.
 The outer surface of the lipid bilayer is composed of molecules of
lipopolysaccharide (LPS) which consists of a complex lipid called lipid A
chemically linked to polysaccharides.
 Lipid A of the LPS forms the endotoxin of the Gram-negative bacteria, while
polysaccharides are the outermost molecules of the cell wall and are major
surface antigens of the Gram-negative bacterial cell (somatic or O antigen).

3. Periplasmic space:
 It is the space between the cytoplasmic and outer membranes.
 It contains the peptidoglycan layer and a gel-like solution of proteins.

Page | 9
Functions of the cell wall
1) It maintains the characteristic shape of the bacterium.
2) It supports the weak cytoplasmic membrane against the high internal osmotic
pressure of the protoplasm (5-25 atm.).
3) It plays an important role in cell division.
4) It is responsible for the staining affinity of the organism.

Cell Wall deficient Bacteria

Mycoplasma:
❖ It is the only group of bacteria that exists naturally without cell wall.
❖ Mycoplasmas do not assume a defined recognizable shape, because they lack a rigid
cell wall.
❖ These organisms are naturally resistant to cell wall inhibitors, such as penicillin and
cephalosporins.

L. Forms:

❖ They are wall defective or wall deficient bacteria.

❖ "L" stands for Lister Institute in London, where they were first discovered.
❖ L- Forms may develop from cells that normally possess cell wall, when they are
exposed to hydrolysis by lysozyme or by blocking peptidoglycan biosynthesis with
antibiotics, such as penicillin, provided that they are present in an isotonic medium.
❖ Some L. forms resynthesize their walls once the inducing stimulus is removed.
Others → permanently lose the capacity to produce a cell wall.
❖ L. forms may survive antibiotic therapy.
❖ Their reversion to the walled state can produce relapses of the overt infection.

L-Forms

Mycoplasma

Page | 10
 Capsule and Related Structures
 Many bacteria synthesize large amount of extracellular polymer that collects
outside the cell wall to form an additional surface layer.
 This layer is formed only inside the host (in-vivo).
 All capsules are Made of polysaccharides except Bacillus anthracis (polypeptide).

1) Capsule: It is such a layer that adheres to the surface of the cell and forms a well-
defined halo when differentially stained, to be resolved with the light microscope.
2) Slime layer: It is a surface layer that is loosely distributed around the cell.
3) Glycocalyx: It is a loose meshwork of polysaccharide fibrils extending outwards
from the cell.

Functions:
1. It protects the cell wall against various kinds of antibacterial agents
Examples: bacteriophages, colicins, complement and lysozymes.
2. It protects the bacterial cell from phagocytosis.
the capsule is considered an important virulence factor.
3. Some bacteria attach to the target surface by using their capsules or glycocalyx in
order to establish infection.
Streptococcus mutans form glycocalyx with which the bacteria stick to the tooth
enamel.

Page | 11
 Appendages
 Several Structures project through the cell wall of bacteria to form surface
appendages.
 The most commonly observed are flagella and Pilli.

Flagella
Many genera of bacteria move by means of flagella.

 Flagella are only 20 nm in diameter.

too small to be detected by Light microscope.
They can be demonstrated clearly with the electron microscope.

 The location and number of flagella on a cell vary according to bacterial species.

1) Monotrichous (single polar flagellum)

2) lophotrichous (multiple polar flagella)

3) peritrichous (flagella distributed over

the entire cell)

 Flagella consist of a single type of protein called flagellin which differs in different
bacterial species.
 The flagellins are highly antigenic (H antigen).
 Motile bacteria tend to migrate towards regions where there Is a higher concentration
of nutrients and solutes (chemotaxis) and away from disinfecting substances (negative
chemotaxis).

Axial filaments
❖ composed of two groups of fibers that originate within the opposite ends of the cell and
overlap in the middle.
❖ Structurally and chemically, the fibers of the axial filaments are similar to flagella and
they are sometimes called "endoflagella".
❖ Spirochaetes move by means of these axial filaments.
❖ When the cell moves → It rotates around Its longitudinal axis and flexes and bends along
Its length.

Page | 12
 Pilli (Fimbriae)
singular: pilus

❖ Definition: are protein tubes that extend from the cells.

❖ They are shorter and thinner than flagella.
❖ can be observed only by the electron microscope.
❖ They are composed of structural protein subunits termed pillins.

Functions:

1. Adherence: It is the function of the short pill (fimbria) that occur in great numbers
around the cell.
They enable bacteria to attach to the surfaces,
contributing to the establishment of
Infection → virulence factor.

Examples → N. gonorrhoeae withstands the

flushing action of urine by adhering to the
urethral mucosa.

2. Conjugation: A special long pilus called the sex pilus (F pilus) Is Involved In the transfer
of DNA between bacteria, a process known as conjugation

Page | 13
 Bacterial Spores (Endospores)
❖ Some bacteria (Bacillus and Clostridium) develop a highly resistant resting phase or
endospore that does not grow or reproduce, and exhibits absolute dormancy.
❖ A single vegetative bacterium forms a single spore by a process called sporulation.
❖ A single vegetative bacterium emerges from a spore during germination.

Sporulation
 Sporulation is triggered by the onset of unfavorable environmental conditions:
1) depletion of nutrients.
2) accumulation of metabolites.
3) changes in the growth requirements (moisture, temperature, pH, or oxygen
tension).

 The cytoplasmic membrane invaginates enclosing a section of the cytoplasm that

contains:
1) The bacterial chromosome.
2) Some ribosomes.
3) other cytoplasmic materials that will be needed for germination.
 It acquires a thick cortex and a thin but tough outer spore coat.

Viability and resistance

Spores are much more resistant to:

1) Disinfectants
2) drying
3) heating.

Moist heat at 121°C for 10-20 minutes is needed to kill spores while 60°C suffices to kill
vegetative forms.

The marked resistance of the spores has been attributed to several factors:
1. Thermal resistance is provided by their high content of Ca2+ and dipicolinic acid
(a compound unique to endospores).
2. The impermeability of their cortex and outer coat.
3. Their low content of water.
4. Their very low metabolic and enzymatic activity.

Page | 14
Germination
 Endospores respond quickly to environmental changes returning to the vegetative
state within 15 min.
 In the process of germination, the spores absorb water and swell, the protective
coat disintegrates and a single vegetative cell emerges.

Morphology
1- Staining:
❖ Using Gram's stain
❖ the spore remains uncolored and can be seen as a clear area within the
stained cell.
❖ The spores can be stained using special procedures.
2- The position:
❖ In relation to the body of the bacillus,
the spore may be central, terminal
or subterminal.
3- The shape:
❖ The spores may be oval or rounded.

The position and shape of spores are characteristic of the species and may help in the
microscopic identification of the bacterium

MCQs
1- The following are functions of the cytoplasmic membrane EXCEPT:
a- Respiration
b- Cell wall biosynthesis
c- Reproduction
d- Staining affinity
e- Selective transport

2- Lipid A is a cell wall component of:

a- Gram positive bacteria
b- Gram negative bacteria
c- Fungi
d- Algae
e- Viruses

Page | 15
3- One of the following is a function of the cell wall:
a- Maintaining the characteristic shape of the bacterial cell
b- Selective transport
c- Respiration, since respiratory enzymes are located in it
d- Protein synthesis
e- Excretion of extracellular enzymes

4- All the following are characters of L-forms of bacteria EXCEPT:

a- They are naturally occurring bacteria without cell wall.
b- They are resistant to antibiotics which inhibit cell wall synthesis.
c- They develop only in isotonic media.
d- They can produce relapses of overt infections.
e- They may resynthesize the cell wall.

5- Bacteria are protected from phagocytosis by:

a- The capsule
b- Lipoprotein
c- The mesosome
d- The outer membrane
e- Peptidoglycan

6- All of the following are true concerning pili EXCEPT:

a- They mediate bacterial adherence.
b- They may be involved in bacterial conjugation.
c- Their antigen is called H antigen.
d- They are important virulence factors.
e- They are protein in nature.

7- The marked resistance of the spores can be attributed to all the

following factors EXCEPT:
a- The impermeability of their cortex and outer coat
b- Their ability to resist phagocytosis
c- Their low content of water
c- Their very low metabolic and enzymatic activity
d- Their high content of Ca and dipicolinic acid

Page | 16
 Bacterial Growth and Physiology
Growth involves an increase in the size and number of organisms.

In the laboratory, bacterial growth can be seen in one of two main forms:
1. Development of colonies, which are the macroscopic products of 20-30 cell
divisions of a single bacterium on solid media.
2. Transformation of a clear fluid medium to a turbid suspension.

Bacterial Reproduction

Bacterial multiplication takes place by simple binary fission:

1) The cell grows in size, usually elongates.
2) The bacterial chromosome acts as a template for the replication of another copy.
3) Each copy becomes attached to a mesosome on the cytoplasmic membrane.
4) The protoplasm becomes divided into two equal parts by the growth of a
transverse septum from the cytoplasmic membrane and cell wall.

In some species, this septum splits the parent cell completely into two separate
daughter cells.
In others, the cell walls of the daughter cells remain continuous for some time after
division giving the characteristic arrangement → pairs, clusters or chains.

Generation time (doubling time):

❖ is the time between two successive divisions.
❖ It may be as short as 13 min in Vibrio cholerae
may reach 24 h. in Mycobacterium tuberculosis.

Page | 17
 Growth Requirements
bacteria need the following growth requirements:

1-Nutrients:
According to the means by which a particular organism obtains energy and raw
material to sustain its growth, bacteria are classified into:

Autotrophs Heterotrophs
They can utilize simple inorganic materials require organic source of carbon
(CO2) as a source of carbon and
ammonium salts as a source of nitrogen.

They can synthesize complex organic cannot synthesize organic complex

substances from the simple inorganic substances
materials.
The energy required for their metabolism
is predominantly derived from light or
simple chemical reactions.

Autotrophs are of no or little medical most bacteria of medical

importance importance are heterotrophs

2- Oxygen (02) :
According to 02 requirements, bacteria are classified into:

Type Definition Examples

Strict (obligate) Require oxygen for growth Pseudomonas aeruginosa
aerobes
Strict (obligate) Require complete absence of oxygen Bacteroides fragilis
anaerobes
Facultative grow better in presence of oxygen but Staphylococci, E. coli
anaerobes still are able to grow in its absence (Most medically
important bacteria)
Micro-aerophilic Require reduced oxygen level Campylobacter and
organisms Helicobacter
Aerotolerant have an anaerobic pattern of metabolism Clostridium perfringens
anaerobes but can tolerate the presence of oxygen
because they possess superoxide
dismutase

Page | 18
Respiration and energy production:
❖ The cellular respiration is another
name of glucose catabolism.
❖ When it takes place in presence of oxygen,
it is called aerobic cellular respiration.
❖ When it takes place in absence of oxygen,
it is called anaerobic cellular respiration.

aerobic cellular respiration anaerobic cellular respiration

The glucose catabolism under aerobic occurs in the absence of oxygen
conditions
The final electron acceptor is molecular The final electron acceptor is an inorganic
O2 molecule such as → nitrate (NO3-), sulfate
(SO4-2), or CO2.
Results in the production of energy in The net yield of ATP molecules is less than it
the form of 38 ATP molecules is with aerobic cellular respiration because
nitrate, sulfate, and CO2 are not as good at
accepting electrons as oxygen.
During this type of respiration,
superoxide (O2-) and hydrogen peroxide
(H2O2) are formed.
These molecules are highly toxic.
To cope with this, aerobic organisms Compared to aerobes → obligate anaerobes
have developed two enzymes → lack superoxide dismutase and catalase and
superoxide dismutase and catalase, so they cannot grow in presence of O2.
which detoxify these molecules.

Fermentation: It is an anaerobic process, because it takes place in the absence of

oxygen.
It is used by facultative anaerobes when they exist in an environment that does not
contain a suitable inorganic final electron acceptor (NO3-, SO4-2 or CO2).
This is the least efficient method of generating energy.

3 . Carbon dioxide (C02):

❖ The minute amount of CO2 present in air is sufficient for most bacteria.
❖ certain species require higher concentrations (5-10%) of CO2 for growth
(capnophilic) → Neisseria spp. and Brucella abortus.

Page | 19
4. Temperature:
A. Mesophiles
 are organisms able to grow within a temperature
range of 20-40°C.
 Pathogens which replicate on or in human body
are able to grow within this range, with an optimum
temperature of 37°C which is the normal body temperature.
B. Psychrophiles (cold-loving)
 are capable of growth at refrigeration temperature (0-80C)
 Example: Flavobacterium spp.·
C. Thermophiles (Heat-loving)
 grow best at high temperature (>60°C)
 Example: Bacillus stearothermophilus.

5 . Hydrogen ion concentration (pH):

❖ Most microorganisms of clinical significance grow best in media whose pH is close to
that of human body (pH 7.2).

❖ some microorganisms grow better at:

1- an alkaline pH (8-9) → V. cholerae.
2- acidic pH (4 or less) → Lactobacilli.

Growth Phases (Bacterial Growth Curve)

If a small number of an organism is placed in a suitable fluid nutrient medium under

appropriate physical and chemical conditions, then the number of viable cells per
milliliter is determined periodically, and plotted, a characteristic growth curve with
four phases is obtained.

1. Lag phase:
❖ The initial number of bacterial cells remains constant.
❖ During this period, the cells adapt to their new environment.
❖ Enzymes and intermediates are formed to permit growth.

2. Exponential (logarithmic) phase:

❖ There is marked increase in cell number and its rate is accelerated exponentially with
time giving a characteristic linear plot on a logarithmic scale.
❖ In this phase, the organism shows typical morphology.

Page | 20
3. Stationary phase:
❖ Exhaustion of nutrients and accumulation of toxic products cause growth to
decrease.
❖ There is slow loss of cells through death which is just balanced by formation of new
cells through growth and division.
❖ The number of viable bacteria remains constant.

4. Decline phase:
❖ At the end of the stationary phase, the death rate increases and exceeds the
multiplication rate due to nutrient exhaustion and accumulation of toxic metabolic
end products.
❖ So, the number of viable bacteria decreases.

Page | 21
 MCQs
1. What types of bacteria synthesize organic compounds from Inorganic
compounds?
a- Heterotrophs
b- Obligate anaerobes
c- Aerobes
d- Facultative anaerobes
e- Autotrophs

2· Which of the following terms best describes bacteria that lack catalase
but not superoxide dismutase?
a- Obligate aerobe
b- Obligate anaerobe
c- Facultative anaerobe
d- Aerotolerant anaerobe
e- Microaerophilic

3. Capnophilic bacteria require:

a- Low concentration of O2
b- High concentration of O2
c- High concentration of CO2
d- Alkaline pH
e- High temperature

4. What type of bacterium is most likely to cause spoilage of refrigerated

foods?
a- Mesophilic
b- Thermophilic
c- Psychrophilic
d- Capnophilic
e- Microaerophilic

5- Bacterial cell death is balanced by the formation of new cells in:

a- Lag phase
b- Exponential phase
c- Stationary phase
d- Decline phase
e- Log phase

Page | 22
 Bacterial Viruses
(BACTERIOPHAGES)

Definition:
Bacteriophages (or phages) are viruses that parasitize bacteria
→ the bacterial cell serves as a host for the virus.

Morphology of the Bacteriophage:

1. A head: containing the nucleic acid core (usually DNA, rarely RNA) surrounded by a
protein coat (capsid).

2. A tail: consists of a hollow core surrounded by a contractile sheath which ends in a

base plate to which tail fibers are attached.

Replication of Bacteriophages

Two cycles for phage replication are known:

A- Lytic (vegetative) cycle:

It is so-called because it ends in lysis of the bacterial host cell and release of the newly
formed phages.

The stages of this cycle are:

1. Adsorption:
 The phage attaches, by its tail, to specific receptors on bacterial cell.
 The specificity of this process determines the susceptibility of bacteria to different
phages.
2. Penetration:
 The tail sheath contracts and the nucleic acid is injected into the cell.
 The empty head and the tail are left outside the cell.
3. Eclipse phase:
 in which no phage components are detected inside the cell.
 It takes a short time (minutes to hours) during which viral nucleic acid directs the
host cell metabolism to synthesize the enzymes and proteins required for phage
synthesis.

Page | 23
4. Intracellular synthesis of phage nucleic acids, capsids and tails.
 Several hundreds of phage components are synthesized.
5. Assembly:
 The phage components aggregate to form complete phage particles which mature
into typical infectious phages.
6. Release:
 The bacterial cell bursts liberating a large number of phage particles to infect new
cells.

During the lytic phage cycle, fragments of the bacterial DNA may be incorporated into
the phage head. The phage can then transfer the incorporated bacterial DNA into
another bacterial host "generalized transduction"

B - Temperate (lysogenic) cycle

In this cycle, the phage (temperate phage does not replicate and lyse the bacteria but the
phage DNA becomes integrated with the bacterial chromosome and divides with it to pass
into daughter cells.
The integrated phage genome is called "prophage" and the bacteria carrying it are called
"lysogenic" bacteria

The presence of the prophage in the bacterium renders it:

1. Immune to infection by another phage.
2. Lysogenic: the bacterium acquires new properties → diphtheria bacilli can produce
toxin only when lysogenized.
Acquisition of a new character coded for by a prophage DNA is called "lysogenic
conversion", or "phage conversion".
When the phage is lost from the bacterium, this new characteristic is lost.

Page | 24
Outcome of the Temperate cycle
1. The prophage may be carried inside the bacterial cell indefinitely passing to daughter
cells.
2. The prophage may be induced to detach from the bacterial chromosome and start a
Lytic cycle. Induction may be spontaneous or achieved by an inducer as U.V. light.

During the process of induction, the prophage may carry with it few genes of the
bacterial chromosome. When it infects another bacterium, it passes this fragment
to it giving it new characters. This is known as "specialized transduction"

Practical Uses of Bacteriophages

1. Phages are used as cloning vectors in recombinant DNA technology. They carry and
introduce foreign DNA fragments into a host cell.
2. Phage typing:
❖ Since bacteria differs in their sensitivity to different phages, phages are used to
identify and type strains of bacteria that are biochemically and antigenically
indistinguishable.
❖ This phage typing is important in epidemiologic studies → to trace the source of
infection in outbreaks of post-operative wound sepsis caused by Staphylococcus
aureus.
3. Phages are used as research elements in some biological and genetic studies.

MCQs
1- In lytic cycle of bacteriophages all the following occur EXCEPT:
a- Lysis of the bacterial host cell & release of newly formed phages.
b- The tail sheath contracts & nucleic acid is injected into the cell.
c- The phage attaches by its tail to a specific receptor.
d- The prophage is carried inside the bacterial cell indefinitely passing to daughter
cells.
e- The phage components aggregate to form complete phage particles.

2- The lysogenic bacterial cell ls the cell containing:

a- Lysosomes
b- Lysozymes
c- Bacteriocins
d- Prophage
e- Endospores

Page | 25
Page | 26
General
 BACTERIAL GENETICS
❖ Genetics is the science which defines and analyzes heredity.
❖ The unit of heredity is the gene.
❖ The Gene: a segment of DNA that carries information for a
specific biochemical or physiologic property.

The bacterial genome: the total set of genes present inside the bacterial cell.
It comprises:
1. The bacterial chromosome: that can encode up to 4000 separate genes necessary for
bacterial growth and propagation.

2. Plasmids

3. Transposable genetic elements

4. Bacteriophage DNA (prophage).

1. The Bacterial Chromosome:

❖ Being a prokaryote →the bacterial cell lacks a nuclear membrane.

❖ The DNA is concentrated m the cytoplasm as a nucleoid.
❖ The nucleoid consists of a single chromosome, which is a circular, supercoiled, double-
stranded DNA molecule, associated at one point with a mesosome.
❖ This attachment plays a role in the separation of the two sister chromosomes following
chromosomal replication.

❖ The bacterial chromosome has the general chemical structure of DNA molecules:
 Each strand is formed of regularly alternating phosphate and sugar (deoxyribose)
groups.
 A nitrogenous base (A, G, C, or T) is attached to the sugar group and is projecting
inwards towards the other strand.
 The two strands are held together by hydrogen bonds between complementary
bases (A-T) or (C-G) present at the same level.
 The average length of the bacterial chromosome is 4000-5000 Kbps.

Page | 1
 The bacterial chromosome replicates by the semi-conservative method of DNA
replication →
❖ The two strands are separated.
❖ Each strand acts as a template to synthesize a complementary strand through
the action of the polymerase enzyme.
❖ The bacterial chromosome follows the same rules of gene expression and
protein synthesis (transcription and translation) as higher organisms.

2. Plasmids

❖ Plasmids are → extra-chromosomal, circular, double-stranded DNA molecules dispersed

in the cytoplasm.

❖ They are much smaller than the bacterial chromosome (from several to 100 Kbps).
❖ Plasmids are capable of replicating independently of the bacterial chromosome.
❖ Multiple copies of the same plasmid may exist in the same cell (plasmid copy number).

According to the copy number, plasmids can be categorized into 2 groups:

1. Relaxed replicating plasmids:
 They can replicate in the absence of protein synthesis.
 They are usually present in 30-50 copies/cell, and are relatively small in size.

2. Stringent plasmids:
 They require protein synthesis.
 They are usually large and present in a few copies (1-5) per cell.

Page | 2
Plasmids are generally dispensable →

❖ This indicates that most plasmids encode properties that are not essential for growth,
replication or survival of the host bacterium.

❖ This is evidenced by:

a- The spontaneous loss of plasmids during cell division.
b- Plasmid curing: The experimental kicking off of the plasmids using physical agents
(heat) or chemical agents (antibiotics).

Functions (traits) exhibited by plasmids:

1. Sex pilus formation:

 Some plasmids carry fertility (F) factors that code for the formation of a sex pilus which
mediates the process of conjugation.
 such plasmids are also known as conjugative plasmids.

Conjugative Non-conjugative plasmids

plasmids
Size Large small
Copy number 1-2 (stringent) >30 (relaxed)
F factors Present Absent
Sex pilus formation Yes No
Transfer By conjugation With the help of conjugative plasmid
Common in
Host bacteria Common in Gram +ve cocci
Gram -ve bacilli

Page | 3
 2. Antibiotic resistance:
 Some plasmids carry genes for resistance (R-factors) to one or several antimicrobial
drugs.
 They often control the formation of enzymes capable of destroying the antimicrobial
drugs.
 Example: ꞵ-lactamase which determines resistance to penicillin and cephalosporins.
 R-factors are usually conjugative plasmids that can be transferred among bacteria by
conjugation.
 This results in the rapid spread of drug-resistance among bacterial populations and the
development of multiple drug-resistant bacterial strains.

3. Virulence plasmids:
 may code for:
• exotoxins.
• Adhesins.
• invasion factors.

4. Bacteriocin production:

 Bacteriocins: bactericidal substances produced by certain bacterial strains and are

active against other strains of the same or closely related species.

 Example → colicin E1 produced by E.coli.

5. Other functions:
a- Nitrogen fixation.
b- Sugar fermentation.
c- Antibiotic production.
d- H2S Production.
e- Resistance to heavy metals.
f- Degradation of aromatic compounds.

3. Transposable Genetic Elements

 Definition: non-replicating DNA segments that are capable of inserting themselves

into other DNA molecules.
They are also capable of mediating their own transfer from one location to another on
the same chromosome or between chromosomes and plasmids.

Page | 4
  Transposition occurs infrequently (once every 105-107 generations) often in a
random pattern.
 The insertion of a transposable element into a gene usually leads to inactivation of
that gene.

 Classes:
a- Transposons → which encode specific genes (such as antibiotic resistance).
b- Pathogenicity islands (PAI) → which give the bacterium a variety of virulence
characters → such as the ability to adhere to or invade host cells.

3. Bacteriophage DNA
The DNA of the temperate bacteriophage that is integrated in the chromosome of a
lysogenic bacterial cell (the prophage) is considered as a part of the genome of such
bacteria.

MCQs
1- Bacterial genetic information is carried on the following EXCEPT:
a. Ribosomes
b. Chromosome
c. Transposons
d. Plasmids
e. Bacteriophage
Page | 5
 2- Plasmids:
a) Are single-stranded DNA molecules.
b) Carry optional genes (are dispensable).
c) Carry genes essential for growth
d) Are always found in linear form
e) Are always present as one copy/cell

3- Plasmids differ from transposable genetic elements, as plasmids:

a) Become inserted into chromosomes
b) Are self-replicating outside the chromosome
c) Move from chromosome to chromosome
d) Carry genes for virulence (exotoxin production)
e) Carry genes for antibiotic resistance

4- Plasmids may code for any of the following EXCEPT:

a) Sex pilus formation
b) Bacteriocin production
c) Growth
d) Antibiotic resistance
e) Virulence

5- Conjugative plasmids:
a) Are usually small in size
b) Carry fertility (F) factor
c) Are relaxed plasmids
d) Have a large copy number
e) Are common in Gram positive cocci

Page | 6
 BACTERIAL VARIATION
 Bacterial variations are changes in the bacterial characters.
 They may be phenotypic or genotypic.

Phenotypic variation Genotypic variation

It occurs in response to changes in the It occurs as a result of a change in the
environmental conditions without changes underlying genetic constitution
in the genetic constitution
Reversible (transient) Irreversible (permanent)
Not heritable Heritable
Examples: Examples:
1- L-Forms. 1- Mutation
2- Loss of flagella upon 2- Gene transfer:
exposure to phenol. a- Transformation
b- Transduction
c- Conjugation

Mutation

It results from a change in the nucleotide sequence of DNA that may occur :
a) Spontaneously as a replication error (rate of once every 106-107 cells).
b) induced by radiation or chemical agents (higher rate of once every
103-104 cells).

Mutation can be classified into:

1. Single-base (point) mutations:

involve the replacement (substitution) of a single nucleotide in the coding sequence.
This may result in:
a- Same sense (silent) mutations: occur when the resulting base triplet (codon) codes for
the same amino acid as the original triplet.
b- Missense mutations:
 occur when the mutant base changes the coding sequence so that a different amino
acid is produced.
Page | 7
  The resulting protein may be functioning or not, depending on the importance of
the area affected by the mutation.

2. Frame-shift mutations: occur when a nucleotide is inserted into, or deleted from the
coding sequence, resulting in a shift of the reading frame → insertion of a transposable
element.

Induced mutations may be used to manipulate viral genomes for vaccine production
and gene therapy.

Page | 8
 Gene Transfer
There are 3 methods for gene transfer among bacteria

1. Transformation
❖ Dying bacteria release DNA which can be taken up by other bacteria.
❖ Such DNA may be chromosomal or plasmid in origin, and may carry genes that
"transform" the Recipient bacterium.
❖ The transforming DNA may become integrated with the bacterial chromosome or re-
established extra-chromosomally in the recipient cell.
❖ Transformation depends on competence, which is the ability of the recipient bacterial
cell to take up DNA.
❖ Competence depends on the presence of proteins in the cell membrane that have a
special affinity to bind DNA and transport it into the cytoplasm.
❖ Artificial competence can be induced during recombinant DNA techniques by treating
the recipient bacteria with calcium chloride, which alters cell membrane permeability,
enabling the uptake of DNA.

2. Transduction

It is the transfer of DNA from one cell to another by means of a bacteriophage.

Types of Transduction:

1) Generalized transduction:
❖ During the lytic phage cycle, the bacterial DNA is fragmented and any fragment of
DNA (whether chromosomal or plasmid) may be incorporated into the phage head.
❖ The phage particle can then transfer the incorporated bacterial DNA into another
bacterial host.
Page | 9
2) Specialized transduction:

❖ It takes place when a prophage contained in a lysogenized bacterial cell is induced to

detach.
❖ Such prophage may carry with it the adjacent piece of the chromosomal DNA and
transfer it to another bacterial cell.

Page | 10
3. Conjugation:

❖ It is the most frequently observed mechanism of DNA transfer.

❖ It involves 2 cell types:

1. donors (F+) which possess the fertility (F) factor
2. Recipients (F) which lack the F factor.

❖ The F factor carries the genes for the synthesis of the sex pilus which acts as a
conjugation tube between the donor and recipient bacterial cells.
❖ The 2 DNA strands of the F factor are then separated, and one strand is transferred from
the donor to the recipient cell.
❖ Each strand forms a complementary strand.
❖ Result: the recipient cell acquires a copy of the F plasmid and becomes an F+ cell.

Page | 11
 MCQs
1- Transformation in bacteria depends on:
a. F factors
b. R factors
c. Bacteriophages
d. Cosmids
e. Competence of bacteria

2- One of the following requires cell to cell contact:

a- Transformation
b- Conjugation
c- Transduction
d- Transcription
e- Transposition

3- Which of the following is mediated by a bacteriophage that carries host cell

DNA:
a) Transformation
b) Conjugation
c) Transduction
d) Translation
e) Transcription

4- Regarding generalized transduction:

a) It occurs during lytic cycle of bacteriophage.
b) It occurs during lysogenic cycle of prophage.
c) A specific piece of bacterial DNA is transferred from one cell to another.
d) Sex pilus is necessary.
e) It results in phenotypic variation of bacterial character

Page | 12
 ANTIMICROBIAL CHEMOTHERAPY

Antimicrobial chemotherapeutic agents:

❖ are chemically synthesized substances that are used to treat infectious diseases by killing
or inhibiting the growth (or multiplication) of microorganisms.

Antibiotics:
❖ are low-molecular weight antimicrobial substances that are produced as secondary
metabolites by certain groups of microorganisms → Streptomyces, Bacillus, and a few
molds (Penicillium and Cephalosporium).
❖ Although their original source was a microorganism → some antibiotics are currently
made synthetically (synthetic antibiotics).
❖ Chemical modification of certain antibiotics, to achieve the desired properties, has been
a prominent method of new drug development (semisynthetic antibiotics).

Bacteriostatic agent:
❖ is an antimicrobial agent that is capable of inhibiting bacterial multiplication.
❖ Multiplication resumes upon removal of the agent.

Bactericidal agent:
❖ is an antimicrobial agent that is capable of killing bacteria.
❖ Multiplication cannot be resumed.

Page | 13
 Selective toxicity:
❖ is the ability of an antimicrobial agent to harm a pathogen without harming the host.
❖ It may be a function of a specific receptor (or target) for the drug found in the microbe
but not in the human body (peptidoglycan), or it may depend on the inhibition of a
biochemical event essential for the organism but not for the host.

Spectrum of activity:
❖ the range of microorganisms that are affected by certain antibiotics is expressed as its
spectrum of action.
❖ Antibiotics which kill or inhibit the growth of a wide range of Gram-positive and Gram-
negative bacteria are said to be broad spectrum.
❖ If effective mainly against either Gram-positive or Gram-negative bacteria, they are
narrow spectrum.
❖ If effective against a single organism or disease, they are referred to as limited
spectrum.

Mechanisms of Action of Antimicrobial Agents

1. Inhibition of bacterial cell wall synthesis

1. ꞵ-lactam antibiotics → penicillin, cephalosporins.

2. Glycopeptides → vancomycin, teicoplanin.
3. Cycloserine and bacitracin.

❖ These antibiotics are bactericidal with minimal tissue toxicity.

❖ The ꞵ-lactam drugs inhibit the last steps of peptidoglycan synthesis.

This inhibition is initiated by binding of the drug to certain cell receptors known as
penicillin-binding proteins (PBPs).
❖ glycopeptides & cycloserine inhibit early steps in the biosynthesis of peptidoglycan,
which occur inside the cytoplasmic membrane.

❖ The mechanism of resistance to ꞵ-lactam antibiotics is different from that for the other
groups.

❖ vancomycin could be used successfully in infections caused by ꞵ-lactam resistant

staphylococci.
Page | 14
2. Interference with the cell membrane function

Some agents disrupt the cytoplasmic membrane and interfere with its function.

a- Antibacterial agents: polymyxin and colistin.

b- Antifungal agents: Amphotericin B, nystatin and imidazoles.
❖ These agents are Microbicidal.
❖ They are highly toxic as they have narrow margin of selective toxicity.

3. Inhibition of bacterial protein synthesis

❖ Bacteria have 70S ribosomes (with 30S and 50S subunits) whereas mammalian cells
have 80S ribosomes (40S and 60S subunits).
❖ This difference makes bacterial ribosomes a selective target for antimicrobials

1. Agents acting on 30S ribosomal subunit:

tetracycline and aminoglycosides
(gentamicin, amikacin, streptomycin).

2. Agents acting on the 50S ribosomal subunit:

macrolides (erythromycin,azithromycin),
lincomycins (clindamycin), streptogramins,
linezolid, chloramphenicol and fusidic acid.

4. Inhibition of bacterial nucleic acid synthesis:

1. Inhibition of RNA synthesis through the strong binding to

DNA-dependent RNA polymerase: rifampin.
2. Inhibition of DNA synthesis through blocking DNA gyrase: quinolones and novobiocin.
3. Inhibition of dihydrofolic acid reductase leading to inhibition of folic acid synthesis.
The latter is important for purine synthesis → nucleic acid formation.
Examples → trimethoprim and pyrimethamine.
4. Inhibition of folic acid synthesis by competitive antagonism → sulphonamides.
For many organisms → para-amino benzoic acid (PABA) is essential for the synthesis of
folic acid.
Sulphonamides are structural analogues of PABA.
They compete with PABA for the active center of the enzyme involved in folic acid synthesis.
As a result, nonfunctional analogues of folic acid are formed and nucleic acid synthesis is
inhibited.
Page | 15
 Choice of an Antimicrobial
Agent for Therapy

The following are guidelines that can be followed

for proper antibiotic use:

1. Select an antibiotic that is able to penetrate to the site of infection and achieve effective
concentration → certain drugs are able to pass the blood-brain barrier, others are highly
concentrated in urine.
2. Identify the nature of the infection whether bacterial, viral, fungal, or parasitic.
A common mistake is to give an antibacterial agent for a viral infection.
3. Choose as narrow an antibiotic spectrum as you can.
When you get the results of culture and susceptibility, revise your treatment to narrow-
down the spectrum as far as possible.
The use of broad-spectrum antibiotics is likely to faster induce resistance to antibiotics and
may be complicated by superinfection.

4. Give the appropriate dose of the antibiotic for the proper duration.
Inadequate dosage or undue prolonged therapy may result in drug toxicity and antibiotic
resistance.

Page | 16
5. Know the potential of the drug to produce toxicity: Some drugs known to be of low toxicity
will exert high toxicity if they accumulate in the blood due to liver or kidney dysfunction.
Use antibiotics that are only safe for the pregnant and lactating women and for infants and
children.
6. Choose bactericidal rather than bacteriostatic antibiotics.

Microbial Susceptibilities to Antimicrobial Agents

❖ Microorganisms vary in their susceptibility to different chemotherapeutic agents.

❖ The appropriate antibiotic to treat any infection should be determined in vitro before
any antibiotic is given.
❖ The in vivo activity of an antimicrobial agent is not always the same as its in vitro
susceptibility because it involves many host factors that are not tested in vitro.
❖ The activity of an antimicrobial agent against an organism is dependent on its
concentration.
❖ Some idea of the effectiveness of a chemotherapeutic agent can be obtained from
determining the minimal inhibitory concentration (MIC).
❖ The MIC is defined as the lowest concentration of a drug that prevents growth of the
test organism.
❖ The MIC forms the basis for susceptibility and determining breakpoints.
❖ The breakpoint of an antimicrobial agent is the concentration that can be achieved in
the serum with optimal dose.
❖ Organisms with MICs at or below the breakpoint are considered susceptible.
❖ On the other hand, organisms with MICs above the breakpoint are considered resistant.

Routine in vitro susceptibility testing can be done by one of the following methods:
1. Disc diffusion method.
2. Dilution method such as tube broth dilution.
3. Gradient diffusion (E test) method.
Page | 17
 Empiric Therapy

 The empiric therapy is a "best guess" procedure based upon a provisional diagnosis made
by the physician that a patient has a bacterial infection which requires treatment.
 Depending on the type of infection, there will be a short list of bacteria most likely to be
causing that infection.
 Depending on the type of bacteria, there will be an antibiotic most likely to successfully
treat that infection.
 "Best guess" treatment is not always successful or appropriate as many bacteria have
unpredictable susceptibilities to antimicrobial agents.

Indications:
1. In seriously-ill patients empiric therapy should be
started without delay but after collecting specimens
for culture.
2. In closed lesions, where there is no available sample.

Page | 18
 Combined Therapy

❖ The ideal rule in antimicrobial therapy is mono-therapy which means choosing one drug
effective against a particular organism.
❖ There are conditions which necessitate the use of more than one antibiotic in order to
achieve a successful clinical response.

Possible indications:
1- Severe ill patients suspected of having serious infections:
a- Bacterial meningitis
b- Sepsis in immunocompromised patients caused by pseudomonas aeruginosa,
klebsiella, Enterobacter, staphylococcus aureus.
2- Febrile neutropenia.
3- To delay the emergence of drug-resistant mutants → treatment of TB.
4- To achieve bactericidal action through synergistic effect → in enterococcal
endocarditis.
5- Mixed infections → infection following massive trauma.

Effects of combined therapy

1. Synergistic effect (1+1= >2):

❖ The combined action is significantly greater than the sum of both effects.
❖ Examples:
1. Vancomycin + gentamicin in treatment of methicillin-resistant staphylococci.
2. Sulfamethoxazole + trimethoprim (cotrimoxazole) in treatment of
shigellosis.

2. Antagonistic effect (1 +1 =<1):

❖ The combined action is less than that of the more
effective agent when used alone.
❖ Example:
Penicillin + chloramphenicol in treatment of
meningitis.

3. Indifference (1 +1 =1):
❖ The combined action is no greater than that of the more effective agent when used
alone.
❖ Example:
Cefepime + vancomycin …. clindamycin + vancomycin.
Page | 19
 4. Addition (1 +1 =2):
❖ The combined action is equivalent to the sum of the actions of each drug when
used alone.

Complications of Chemotherapy

1) Toxicity: may be dose-dependent or independent.

Examples:
a- Tetracycline may cause staining of teeth in infants.
b- Streptomycin may affect the 8th cranial nerve leading
to vestibular dysfunction.
c- Aminoglycosides may cause nephrotoxicity.
d- Chloramphenicol can cause bone marrow depression.

2) Allergy (hypersensitivity): usually not dose-dependent.

Examples:
a- Penicillin may cause urticaria, anaphylactic shock
or serum sickness.
b- Local application of sulphonamides may result in
contact dermatitis.

3) Emergence of resistant strains:

 The abuse of antibiotics (low dosage, interrupted
course, no real indication, and improper choice)
encourages the emergence of resistant mutants.
 These mutants will overgrow and replace the originally
susceptible bacteria.
 It is recommended that in vitro susceptibility testing
should be performed to guide the selection of
antibacterial drugs.
Page | 20
4) Superinfection:
It occurs as a result of outgrowth of resistant members of normal flora when the sensitive
ones are eradicated during antibiotic therapy.
Examples:
a- Pseudomembranous colitis caused by outgrowth of Clostridium difficile.
b- Oral thrush caused by overgrowth of the yeast Candida

Resistance to Antimicrobial Agents

 Antibiotic resistance is a global problem faced today in the treatment of infectious

diseases.
 Resistance to antibiotics is more prevalent in hospitals especially intensive care units due
to the higher antibiotic use.
 Resistance to antimicrobial agents is of two categories either intrinsic or acquired.

Intrinsic (inherent or natural) resistance

 This type of resistance refers to bacteria that are insensitive, in their natural state, to an
antibiotic without the acquisition of resistance factors.
 It is consistent and can be expected once the organism is known.
 Intrinsic resistance occurs in the following situations:
1. Streptomycetes are protected from the antibiotics they produce.
2. Gram-negative cell membrane has pores too small to allow large antibiotic
molecules, → nafcillin, to penetrate.
3. An organism lacks the target or receptor for the antibiotic as in the case of resistance
of Enterococcus species to cephalosporins.

Acquired resistance
 It results from altered bacterial physiology and structure due to changes in the genome
of the organism.
 It is inconsistent and unpredictable.

Page | 21
  The unpredictable nature of this resistance is the 1ry reason why laboratory methods
to detect resistance are necessary.

Acquired resistance mechanisms are driven by two genetic processes in bacteria:

(1) Mutation and selection (sometimes referred to as vertical evolution): Exposure
of an organism to an antibiotic exerts a selective pressure on the organism and leads to
mutation.
The more frequent the exposure to the antibiotic the greater the potential resistance.
(2) Exchange of genes between strains and species (sometimes called horizontal
evolution).
Resistance genes can be encoded on plasmids, phages and transposable genetic
elements.

Mechanisms of acquired resistance

Bacteria have the ability to use one or more of the following mechanisms:

A) Reduction of the intracellular concentration of the antibiotic by:

a) Decrease in influx of antibiotic through:

 Reduction of permeability of the outer membrane by modification or
 Loss of porin (a hollow membrane protein) required for entry of the antibiotic
molecules.

b) Efflux pumps:
The antibiotic is pumped out across the cytoplasmic membrane faster than it
can diffuse in, so the concentration of antibiotic remains too low to be effective.
Page | 22
B) Inactivation of the antibiotic:
 Production of ꞵ-lactamases leads to hydrolysis of the ꞵ-lactam ring → inactivating
penicillin and cephalosporins.
 Production of acetyl transferase results in chloramphenicol resistance.
 Production of aminoglycosides-modifying enzymes

C) Target modification:
Modification of the target site for the antibiotic results in a reduced affinity for its receptor:

 Modification of the penicillin-binding proteins (PBPs) is a primary mode of

resistance to ꞵ-lactam antibiotics in methicillin-resistant S. aureus (MRSA).
 alteration of the 50S ribosomal subunit reduces the affinity of macrolides linezolid
and streptogramins for the ribosome.
 Alteration of the 30S ribosomal subunit reduces the affinity of aminoglycosides for
the ribosome.

D) Target elimination by developing new metabolic pathways:

These bacteria have the ability to create new metabolic pathways that bypass the
original target → resistance to trimethoprim.

E) Target overproduction: This may be the mechanism used by S. aureus strains with
intermediate susceptibility to vancomycin (VISA).

Antimicrobial Chemoprophylaxis

Chemoprophylaxis: the administration of an effective antimicrobial

agent to prevent rather than to treat infection with a certain
microbe, thus preventing development of a disease.

Examples:

1) Long-acting penicillin (or erythromycin): is given to rheumatic patients to prevent

reinfection with S. pyogenes.
2) Rifampicin: is given to close contacts of meningococcal meningitis for 2 days to
prevent meningitis.
3) Penicillin or erythromycin: is given to individuals with abnormal heart valves prior to
dental procedures to prevent endocarditis.
4) Preoperative in some surgical operations.
Page | 23
 MCQs
1) Selective toxicity of an antibiotic:
a) Depends on presence of a receptor for the drug in hosts not in organisms
b) Is the ability of the drug to inhibit growth of a wide range of bacteria
c) Depends on inhibition of a biochemical event essential for the host
d) Is the ability of the drug to harm the organism without harming the host
e) Is one of the complications of antibiotic therapy

2) Which of the following antimicrobial agents is most toxic to humans?

a) Bacitracin
b) Cephalosporin
c) Amphotericin B
d) Penicillin
e) Vancomycin

3) One of the following antimicrobial drugs is not among the group acting through
inhibition of the bacterial cell wall:
a) Penicillin
b) Vancomycin
c) Cephalosporins
d) Bacitracin
e) Novobiocin
Page | 24
4) Which of the following antibiotics inhibits bacterial protein synthesis by acting on
the 30S ribosomal subunit?
a) Vancomycin
b) Macrolides
c) Polymyxin
d) Aminoglycosides
e) Chloramphenicol

5) The following are mechanisms of acquired resistance to antimicrobial agents

EXCEPT:
a) Decreasing the influx of the antibiotic
b) Modification of the receptor (target) site
c) Target elimination by developing new metabolic pathways
d) Target overproduction
e) Absence of cell wall

6) The MIC is the:

a) Highest concentration of a drug required to inhibit bacterial growth
b) Standard dose of a drug required to inhibit bacterial growth
c) Lowest concentration of a drug required to inhibit bacterial growth
d) Lowest dilution of the drug required to inhibit bacterial growth
e) Maximum dose of a drug required to inhibit bacterial growth

7) combined antibiotic therapy is indicated in the following conditions EXCEPT:

a) Mixed infections
b) T.B.
c) Viral meningitis
d) Endocarditis
e) Febrile neutropenia

8) Regarding the effect of combined therapy with antimicrobial drugs, the expression,
"1 + 1 = >2" means:
a) Antagonistic effect
b) Synergistic effect
c) Indifference
d) Addition
e) Ineffectiveness

Page | 25
 DISINFECTION AND STERILIZATION

Sterilization:

❖ Validated process used to render a product free

of all forms of viable microorganisms including all
bacterial spores.

❖ Methods:
1. Steam under pressure.
2. hydrogen peroxide gas plasma.
3. ethylene oxide gas
4. dry heat.

These are the main validated sterilization processes for use in the healthcare facilities.

❖ Sterilization is essential for culture media, and critical items intended to enter the
vascular system and sterile tissues such as vascular catheters and surgical instruments.

Disinfection:

❖ It is a process that eliminates most pathogenic microorganisms except spores.

❖ unlike sterilization, disinfection is not sporicidal.

❖ Disinfection is required for devices or equipment that do not penetrate tissues but used
in contact with the skin (stethoscope diaphragm swabbed with 70% alcohol) or mucous
membranes (immersion of endoscope in 2% ortho-phthalaldehyde (OPA) disinfectant for
12 minutes).

Page | 26
Disinfectant:

❖ Usually a chemical agent (but sometimes a physical agent) that achieves disinfection.
❖ It refers to substances applied to inanimate objects.

Disinfectants may be categorized into 3 levels:

1. High level disinfectant:

Germicide that kills all microbial pathogens except large numbers spores.
Examples:
 OPA for endoscopes.
 hydrogen peroxide for contact lens.
 chlorine for blood spills.

2. Intermediate level disinfectant:

Germicide that kills all microbial pathogens
except bacterial spores.
Examples:
 isopropyl alcohol.
 iodophors.

3. Low level disinfectant:

Germicide that kills most vegetative bacteria (except tubercle bacilli) and lipid-enveloped
and medium-sized viruses such as human immunodeficiency virus and hepatitis B virus.
Examples:
 quaternary ammonium compounds for disinfection of floors and food preparation
areas.

Antiseptic:

❖ A chemical disinfectant which can be safely applied to skin and mucous membranes but
not suitable for systemic administration.
❖ The term is used especially for preparations applied topically to living tissue.
❖ Examples:
 70% isopropyl alcohol to prepare skin for injection.
 preoperative skin preparation with alcohol-based iodine compound in surgical
operations.

Page | 27
Germicide:

❖ Agent that destroys microorganisms.

❖ may be → virucide, bactericide, fungicide, sporicide and tuberculocide.
❖ The term germicide includes both antiseptics and disinfectants.
❖ Antiseptics are germicides applied to living tissue and skin; disinfectants applied only to
inanimate objects.

Sterilant:
Chemical germicide that achieves sterilization

Cleaning (or precleaning):

❖ Removal of foreign material (organic or inorganic contaminants) from medical devices

as part of decontamination process.
❖ It is usually done with water and soap, detergents or enzymatic products.
❖ Cleaning must always precede disinfection and sterilization.

Decontamination:

❖ Reduction of pathogenic microorganisms to a level at which items are safe to handle.

❖ Decontamination includes sterilization and all disinfection levels.

Main Methods of Disinfection

1. Chemical disinfectants.

2. Boiling water:
❖ Boiling (100°C) for 20 minutes achieves high disinfection.
❖ It can be useful in emergencies if sterilizer is not available.

3. Pasteurization:
❖ Pasteurization of milk by heating at 63°C for 30 min.
or at 72°C for 20 sec → followed by rapid cooling.

Page | 28
 ❖ destroys important pathogens:
1) Mycobacterium tuberculosis
2) Brucella
3) Salmonella
4) Coxiella burnetti.

4. Thermal disinfection by hot water:

❖ can be performed in special washing machines or linen in hospital laundry, dishes and
devices which cannot withstand higher temperature.

5. Ultraviolet radiation (UV):

❖ UV can be artificially produced by mercury lamps.
❖ UV rays have weak penetration power and is used only for air and surface disinfection,
→ laboratory safety cabinets.

Methods Of Sterilization

A.Steam sterilization:

❖ It is the most safe and commonly used sterilization method.

❖ It is accomplished in an autoclave and uses moist heat in the form of saturated (dry)
steam under pressure for a specified exposure time and at a specified temperature, as
the sterilizing agent.
❖ There are four parameters of steam sterilization:
1. Steam
2. Pressure
3. Temperature
4. time.
Page | 29
 ❖ The ideal steam for sterilization is saturated steam.
❖ It is essential to make steam saturated which means free of air because air acts as an
insulator and hinders penetration.

❖ Pressure serves as a means to obtain the high temperatures necessary to quickly kill
microorganisms.

❖ The two common steam-sterilizing temperatures are 121°C (maintained for a minimal
exposure time 30 minutes) and 132°C (maintained for 4 minutes).

❖ As regard mode of action, moist heat destroys microorganisms by coagulation and

denaturation of enzymes and structural proteins.

❖ Steam sterilization is nontoxic, inexpensive and rapidly heats and penetrates fabrics.

❖ It is the most widely used and the most reliable

Monitoring of steam sterilizers (autoclaves):

1. Mechanical indicators:
Using a printout or graph that monitors the time, temperature and pressure of the
sterilization cycle.

2. Chemical indicators or integrators:

Chemically impregnated paper strips that must be
used with each sterilization cycle to monitor the
temperature or time and temperature.
Visible color changes occur at specified temperature and time.

3. Biological indicators:
Paper strips impregnated with the spores of Geobacillus stearothermophilus.
The biological indicators are placed at the coldest point of the chamber.
After finishing the cycle of sterilization, spore strips are incubated in a fluid medium at
37°C for 48h.
Absence of bacterial growth indicates an efficient sterilization cycle.

Page | 30
B.Low temperature sterilization methods:

1. Hydrogen peroxide gas plasma

❖ Gas plasmas have been referred to as the fourth state of matter (liquids, solids, gases,
and gas plasmas).

❖ Gas plasmas are generated in an enclosed chamber under deep vacuum using radio
frequency or microwave energy to excite the gas molecules and produce charged
particles, many of which are in the form of free radicals.
❖ The free radicals interact with essential cell components (enzymes, nucleic acids) and
thereby disrupt the metabolism of microorganisms, in addition to the direct inactivation
by hydrogen peroxide.

❖ Total time of sterilization cycle is about 50 minutes.

❖ Medical materials and devices that cannot tolerate high temperatures and humidity,
such as some plastics, electrical devices, and corrosion-susceptible metal alloys, can be
sterilized by this method.

❖ G. stearothermophilus (formerly Bacillus stearothermophilus) spores are used as a

biological indicator to monitor efficiency of the sterilization process.

Page | 31
 2. Ethylene oxide gas sterilization
❖ Exposure time is long and varies from 3 to 6 hours.
❖ The method is expensive with probable toxicity.
❖ It can be used for instruments that cannot be subjected to steam.
❖ Bacillus atrophaeus (formerly B subtilis) spores are used as a biological indicator.

3. Peracetic acid sterilization

❖ It is used to sterilize medical, surgical, and dental instruments
(endoscopes, arthroscopes).
❖ Peracetic acid denatures proteins, disrupts cell wall, and oxidizes
proteins and enzymes of microbes.

C.Dry heat sterilization:

includes the following forms:

1. Incineration:
 is particularly applicable for dead animal bodies, infectious hospital waste such as
used surgical dressings, needles.
2. Red heat:
 Inoculating wires, loops and points of forceps are sterilized by holding them in the
flame until they are red hot.
3. Dry Heat Sterilizers or hot air ovens
 The method employs dry hot air as the sterilizing agent.
 The most common time-temperature relationships are 170°C for 60 minutes, 160°C
for 120 minutes, and 150°C for 150 minutes.
Page | 32
  Bacillus atrophaeus spores should be used as a biological indicator.
 Mode of action → killing is due to oxidation of the microbial cell constituents
 This method is used for materials that might be damaged by moist heat (powders,
petroleum products, sharp instruments).

 The advantages for dry heat:

1. nontoxic
2. relatively inexpensive
3. noncorrosive for metal and sharp
instruments.

 The disadvantages:
1. the slow rate of heat penetration
2. time-consuming and the high temperatures
are not suitable for most materials.

D.Other sterilization methods

1. Ionizing radiation:
 Sterilization by ionizing radiation can be obtained by cobalt 60 gamma rays or electron
accelerators (ꞵ-rays).
 Ionizing radiation has a high penetrating power → used for sterilization of prepacked
heat-sensitive items such as bone grafts, surgical sutures, disposable plastic syringes,
gloves, catheters and plastic Petri dishes.
 Bacillus pumilus spores are used as a biological indicator to monitor efficiency of
radiation sterilization.

2. Filtration:
 used to remove bacteria from thermolabile pharmaceutical fluids (antibiotic solutions,
hormones, vitamins) that cannot be purified by any other means.
 Fluids can be rendered free of bacteria by passage through bacterial membrane filters
with pore size as small as 0.22 µm.
 Filters can also be used to remove microorganisms from air supplied to critical areas such
as operating rooms, drug factories and laboratory biosafety cabinets. Such filters are
known as high efficiency particulate air (HEPA) filters which can provide sterile air at the
filter face.
 The endopigment producing Serratia marcescens may be used to test the efficiency of
bacterial membrane filters.
 spores of the fungus Aspergillus may be used to test the efficiency of HEPA filters.
Page | 33
 3. Ozone:
 Ozone (03) consists of 02 with a loosely bonded third oxygen atom that makes ozone a
powerful oxidant that destroys microorganisms.
 Ozone has been used for years as a drinking water disinfectant.

4. Formaldehyde Steam:
 Low-temperature sterilization method that involves use of formalin, which is
vaporized into formaldehyde gas.
 The method may be used in healthcare facilities to sterilize heat-sensitive medical
equipment such as the mechanical ventilator and incubators for neonates.
 Unfortunately→ formaldehyde is a mutagen and a potential human carcinogen,
therefore must be regulated and fully contained to guarantee the permissible
exposure limit of healthcare workers for formaldehyde.

5. Infrared radiation

MCQs
1) One of the following statements is CORRECT:
a) Sterilization is complete removal or inactivation of all forms of microbial life.
b) Disinfection is elimination of all pathogenic organisms including spores.
c) Low level disinfection is effective against Mycobacterium tuberculosis.
d) Antiseptics are chemical disinfectants applied to surfaces and floors.
e) High level disinfection is enough for surgical instruments and needles.
Page | 34
2) Pasteurization:
a) Is generally performed at 87°C for 30 minutes.
b) Can destroy important pathogenic organisms.
c) Is a method of sterilization.
d) Is done by hot water at temperatures higher than 100°c
e) Cannot destroy Mycobacterium tuberculosis.

3) Regarding hot air oven:

a) It is used to sterilize powders and petroleum products.
b) The sterilizing agent is moist heat.
c) It has a corroding effect.
d) It doesn't necessitate prolonged exposure.
e) It is characterized by rapid and even penetration of heat into the materials to be
sterilized.

4) Regarding biological indicators for monitoring autoclaves:

a) They are placed at the hottest part of the chamber.
b) They change their color at 121°C
c) They are paper strips containing the spores of G. stearothermophilus.
d) Presence of bacterial growth indicates an efficient sterilization cycle.
e) They are checked for color change at the end of each sterilization cycle

Page | 35
 BACTERIAL PATHOGENESIS

Infection: a process by which the organism enters into a relationship with the host.
 Although microbial infections occur frequently, most infections end without
occurrence of pathological changes and thus are not manifested as clinical disease.
 These infections are termed:
1) Subclinical
2) silent
3) abortive infections.

The outcome of bacterial infections depends on the mutual relationship between bacteria and
host.

Bacteria could be classified into:

1. Saprophytic bacteria:
 are those which live freely in nature, on decaying organic matter, in soil or water.
 They do not require a living host.

2. Parasitic bacteria:
 are those which live on or in a living host.
 They are classified according to their relation to the host into:
a) Pathogenic: Bacteria capable of causing disease.
b) Non-pathogenic (commensals): Bacteria that do not cause disease, and are
part of the normal flora.
c) Opportunistic pathogens: These are potentially pathogenic bacteria that do
not cause disease under normal conditions but can cause disease in
immunocompromised patients, or when they find their way to another site
other than their normal habitat.
Many of these opportunistic pathogens are originally commensals.

Page | 36
Stages of the Infectious Process

1) Source of infection which may be man (case or carrier), animal or soil.

2) Mode of transmission → droplet inhalation, ingestion, injection, insects, contact and
transplacental.
3) Portal of entry → respiratory tract, gastrointestinal tract, skin.
The organism then starts to multiply within the host causing tissue damage (disease).
4) Portal of exit → urine, stools, blood, respiratory or genital discharge, from which the
organism is transmitted to a new host.

Koch's postulates.
❖ These are criteria that were proposed by Koch in order to determine if the organism

❖ isolated from the patient actually caused the disease.

❖ these criteria must be satisfied to confirm the causal role of an organism.

❖ These criteria are as follows:

1. The organism must be Isolated from every patient with the disease.
2. The organism must be Isolated free from all other organisms and grown in pure
culture in vitro.
3. The pure organism must cause the disease in a healthy, susceptible animal.
4. The organism must be recovered from the inoculated animal.

Page | 37
The outcome of infection depends on the interaction between microbial factors (virulence)
and host resistance factors (Immunity).

Microbial Virulence

Pathogenicity: a qualitative description of a species of bacteria denoting ability to produce

disease.
Virulence: a quantitative character (degree of pathogenicity) of a strain belonging to a
pathogenic species.

Virulence Is genetically determined by genes carried on plasmids, phages, pathogenicity Islands

and chromosomes.

Page | 38
 Virulence Factors of Bacteria

A virulence factor is either a structure (capsule)

or a product (toxins) that enables the organism to
cause disease.

A - Adherence factors
They enable bacteria to attach to the host surfaces, thus contributing to the establishment of the
infection.
example:
1. The fimbriae of Neisseria gonorrhoeae and E. coli help the attachment of these
organisms to the urinary tract epithelium.
2. The glycocalyx of Staphylococcus epidermidis and certain viridans streptococci
allows the organisms to adhere strongly to the heart valves.
Mutants that lack these factors are often avirulent.

B - Invasion factors
Invasion of tissue followed by inflammation is one of the main mechanisms by which bacteria
can cause disease.

This invasion is helped by:

A. Enzymes
1) Collagenase and hyaluronidase which degrade collagen and hyaluronic acid and allow
the bacteria to spread through subcutaneous tissues.
2) immunoglobulin A protease which degrades lgA.
3) Leukocidin which can destroy both polymorphonuclear leucocytes and macrophages.
4) Deoxyribonuclease that breaks down DNA.
5) Lecithinase that breaks down lecithin of cell membrane

Page | 39
B. Antiphagocytic factors

1) Capsule: The capsule prevents the phagocytes from attachment to the bacteria →
Strept. pneumoniae.

2) Cell wall proteins of Gram-positive cocci, such as the M protein of Strept. pyogenes
and protein A of Staph. aureus.

3) Coagulase: It accelerates the formation of a fibrin clot from fibrinogen. This clot can
protect bacteria from phagocytosis → Staph. aureus.

C. Toxin production
Toxin production is another mechanism by which bacteria can produce disease.

Bacterial toxins are either exotoxins or endotoxins.

Exotoxins Endotoxins
Source Secreted by both gram Part of cell wall of gram-negative
positive and gram negative bacteria.
Liberated upon cell disintegration.
Coding genes Encoded by chromosomes, Encoded by genes on the
plasmids, bacteriophages or chromosome.
PAIs.
Examples C. diphtheria (phage) E. coli
Cl. Tetani (plasmid) Meningococci
B. pertussis (chromosome)
H. pylori (PAI)
Nature protein Lipopolysaccharide (Lipid A)
Antigenicity Highly antigenic Poorly antigenic
Heat stability Unstable to temperature Stable to temperature above 60 C
above 60 C for several hours.
Detoxification Can be converted into Cannot
Toxoids.
Specificity Every toxin has specific action General effect (septic shock)
Toxicity High Low

Page | 40
 Treatment of exotoxin with formalin removes its toxicity and retains its antigenicity converting
it into toxoid, that can be used for immunization.

MCQs
1. Opportunistic pathogens:
a) Are never the cause of a clinical infection
b) Are usually highly pathogenic
c) Are rarely part of the normal flora
d) Cause disease mainly in immunocompromised individuals
e) Are resistant to killing by steam sterilization

2. Exotoxins have the following characters, EXCEPT:

a) They may be encoded by genes on the chromosome.
b) They can be converted to toxoids.
c) They have specific action.
d) They are polypeptides.
e) They are heat stable.

3. Endotoxins:
a) Are secreted mainly by Gram-positive bacteria
b) Are highly antigenic
c) Are stable at temperatures above 60°C
d) Can be converted into toxoid
e) Have specific action

Page | 41
General
 General Virology

 Viruses are one of the smallest infectious agents.

 They are obligatory intracellular parasites because they have no metabolic activity.
 Viruses can infect all organisms in nature:
1. Bacteriophages: are bacterial viruses.
2. Plant viruses: include complete viruses and viroids.
3. Animal viruses: infect insects or vertebrates including man.

Viruses differ from bacteria in the following:

1. Viruses are very small in size, ranging from 20-300 nm.
Therefore: They can only be seen under the electron microscope (except poxviruses).
They can pass through bacterial filters.
They need ultracentrifugation for sedimentation.
2. Viruses contain only one type of nucleic acid (DNA or RNA), never both.
3. They are obligatory intracellular parasites (can only replicate inside living cells) and
do not divide by binary fission.
4. They cannot be cultivated in the laboratory on artificial culture media → they can be
grown on tissue culture.
5. They are not susceptible to antibacterial antibiotics.

Structure and Composition of Viruses

 The typical complete virus particle, called virion, consists of a genome of either DNA or
RNA, surrounded by a capsid (protein coat).
 The nucleic acid and the protein coat are called nucleocapsid.
 Some viruses, called enveloped viruses, have an outer Lipid containing envelope whereas
others are non-enveloped (naked).
Page | 1
Viral nucleic acid (genome)
❖ It is the genetic material of a virus, which may be either RNA or DNA.
❖ Most DNA viruses are double-stranded (ds) while most RNA viruses are single stranded
(ss).
❖ The viral ssRNA may be positive sense strand (+sense) or negative sense strand (-sense).
❖ It is responsible for virulence → it is the infectious part of the virus.

Viral capsid
Viral capsid is composed of many small protein subunits called capsomers.
Functions:
1. It protects the nucleic acid (genome) against harmful environmental factors.
2. It mediates attachment to host cell (in non-enveloped viruses}.
3. It is responsible for the viral symmetry (or morphology} which may be:
a) Icosahedral (many sided) symmetry: Icosahedral or isomeric or cubic viruses
resemble a crystal with 20 triangular facets and 12 comers.
This includes all DNA viruses, except poxviruses (brick shaped), and some RNA
viruses.
b) Helical (coiled tubes) symmetry: The viral nucleic acid is closely associated with
the protein capsid forming a coil-shaped helical nucleocapsid.
This includes many of RNA viruses → rabies virus.
c) Complex symmetry: Examples include the brick-shaped poxviruses or
bacteriophages.

Viral envelope
 It is a lipoprotein membrane composed of lipids,
derived from host cell membrane during release
by budding, and protein that is virus-specific.
 the envelope may have glycoprotein spikes which
are the organ of attachment of the enveloped virus
to host cell receptors.
 Therefore, dissolving the envelope inhibits attachment and the virus loses its infectivity.
 Enveloped viruses are less stable → more easily inactivated than naked viruses.
 They are more sensitive to heat, drying, detergents and lipid solvents.
 enveloped viruses, being unable to survive in the environment, are transmitted
essentially by direct contact via blood and body fluids.

The surface proteins of the virus, whether they are the capsid proteins (in naked
viruses) or the glycoproteins (in enveloped viruses) are responsible for attachment to
host cell receptors
Page | 2
the principal antigens against which the host elicits its immune response to viruses.
Classification of Viruses

a) Classification by symptomatology It is the old classification based on diseases that viruses

produce → tropism → neurotropic viruses, enteroviruses.

b) The hierarchical virus classification

The scheme classifying viruses into orders, families and subfamilies is
based on:
1. Nature of the nucleic acid: RNA or DNA genome.
2. Virus replication strategy
3. Symmetry of the capsid
4. Presence or absence of an envelope Further classification is based on additional
properties → antigenicity, host range and nucleic acid sequence.

c) The Baltimore classification:

 It is based on virus genome replication strategy.
 The central idea is that all viruses must generate positive strand mRNAs from their
genomes, in order to produce proteins and replicate themselves.
 The precise mechanisms whereby this is achieved differ for each virus family.

Page | 3
Virus Replication
 Viruses are unable to replicate on their own because they lack the genes and enzymes
necessary for energy production.
 replication depends on living host cells and is directed by the viral genome to produce the
virus components.

Viral replication occurs in the following steps.

1. Attachment or adsorption:
 Adsorption of the virus occurs to specific receptor sites on the surface of the susceptible
host cell.
 These interactions determine viral host range (human viruses and plant viruses) and
tissue specificity or tropism (hepatotropic viruses and neurotropic viruses).
2. Penetration:
The viruses may enter the host cells by either:
a- endocytosis in case of non-enveloped viruses.
b- fusion of viral envelope with host cell membrane in case of enveloped viruses.
3. Uncoating:
The nucleic acid is released from the capsid by the action of cellular enzymes and becomes
available for replication.

Page | 4
4. Synthesis of viral components

A) Synthesis of viral proteins:

Transcription:

❖ Viruses must first synthesize virus-specific messenger RNA (mRNA) to synthesize virus
specific proteins.

❖ Transcription of mRNA varies according to the type of viral nucleic acid whether DNA or
RNA, ds or ss, positive or negative sense strand, as follows:

a) DNA viruses: mRNA can be transcribed from the negative sense strand using the
host's DNA-dependent RNA polymerase.

b) RNA viruses: There is no host cell RNA polymerase that can use the viral RNA as a
template for synthesis of mRNA.
RNA viruses fall into 4 groups according to the strategy for synthesizing mRNA→

In dsRNA viruses, the negative sense strand is transcribed by viral RNAdependent RNA
polymerase into mRNA.

In ssRNA viruses there are 3 distinct routes to the formation of mRNA:

i. The strand with positive sense acts directly as mRNA.

ii. The strand with negative sense must first be transcribed, using viral RNA-
dependent RNA polymerase, into positive sense strand which can then act as
mRNA.

iii. In retroviruses, the positive ssRNA is first made into a negative sense ssDNA
using the viral reverse transcriptase.
Then dsDNA is formed by the host DNA-dependent DNA polymerase.

This dsDNA enters the nucleus and is either:

a) transcribed by host's DNA-dependent RNA polymerase into mRNA or
b) integrated in host cell genome causing transformation.

Page | 5
Translation:
Once the viral mRNA is transcribed, it is translated using host ribosomes to synthesize viral
proteins.

B) Synthesis of viral nucleic acid:

Replication of the viral genome requires the synthesis of a strand with a complementary
base sequence, which serves as the template for the synthesis of several copies of the
original viral genome.

5. Assembly:
❖ The newly synthesized protein coats enclose the replicated nucleic acids to form mature
viruses (virions).
❖ This occurs either in the nucleus of the host cell → herpes viruses
or in the cytoplasm → polioviruses.

6. Release: The new viruses are released either by:

a) lysis of host cell in case of non-enveloped viruses → poliovirus
b) budding through the cell membrane in case of enveloped viruses →HIV.

Eclipse is the time from uncoating until assembly of mature viruses.

During this phase, no infectious viruses can be detected in the host cell.
Some viruses do not initiate synthesis and remain latent within the host cell for
variable periods

Page | 6
Pathogenesis of Viral Diseases

Entry of viruses
❖ Viruses enter the body either by inhalation (respiratory tract), ingestion (GIT), contact
(urogenital system) or through skin (injections, blood transfusion, insect and animal bites).
❖ Viral infection may be:
a) Local infection: where the virus produces disease at the portal of entry.
b) systemic or deep viral infections: where the virus spreads to distant organs either
via the blood (viraemia), or by other means (along nerves).

Local infections Systemic infections

Example Common cold Measles
Site of pathology Portal of entry Distant sites
Incubation period Short Long
Viremia Absent Present
Duration of immunity Short Life long
Immunoglobulins IgA IgM - IgG

Fate of viral infections

1. inapparent or subclinical viral infections:

Viral infection without overt signs and symptoms.
2. Apparent infections (disease):
Local or systemic viral infections with the
appearance of clinical signs and symptoms.
3. Persistent viral infections (chronic):
the virus is continuously detected with mild
or no clinical symptoms, → chronic hepatitis B.
4. Latent viral infections:
The virus persists in a dormant form and may
flare up intermittently to produce disease → herpes viruses.
5. Slow virus infections:
Virus infections with long incubation periods (months or years).
They are caused by two types of infectious agents:
1. Conventional viruses →
a variant of measles virus which causes subacute sclerosing panencephalitis
(SSPE).
2. Unconventional agents (prions).
Page | 7
Laboratory Diagnosis of Viral Infections
The laboratory diagnosis of viral infection involves 2 main diagnostic
methods:

A- Direct methods: which depend either

on the detection of viruses and/or their
components in the patient's specimens,
or on isolation of viruses.

B- Indirect methods: which depend mainly on the detection of antibodies against the
suspected virus in the patient's serum, or on skin tests.

Treatment of Viral Infections Viruses

 cannot be treated with antibiotics because they lack the structural targets on which
antibiotics can act.
 Viruses are obligate intracellular parasites, so antiviral drugs must selectively inhibit viral
replication without causing damage to host cells.
 The number of antiviral drugs is little compared to antibacterial drugs.

Mechanisms of antiviral drugs:

1- Fusion inhibitors → block virus entry.
2- Uncoating inhibitors → inhibit virus uncoating.
3- Neuraminidase inhibitor → interfere with viral release from infected cells.
4- Nucleoside analogues → inhibit DNA polymerase → inhibit DNA synthesis
5- Inhibitors of mRNA Synthesis
6- Reverse transcriptase inhibitors.
7- Protease inhibitors.
8- Inhibitors of viral protein synthesis.

Page | 8
 MCQs
1- Viruses differ from bacteria in the following EXCEPT:
a- They are very small in size.
b- They contain two types of nucleic acid.
c- They are obligatory intracellular parasites.
d- They need ultra-centrifugation for their sedimentation.
e- They can be seen only by the electron microscope.

2- All of the following is true concerning viral capsid EXCEPT:

a- It is formed of capsomers.
b- It is protein in nature.
c- It is responsible for viral symmetry.
d- It is the infectious part of the virus.
e- It protects the nucleic acid.

3- Local viral infections are characterized by:

a- Long incubation period
b- Short duration of immunity
c- Insignificant role of lgA
d- Important role of lgM and lgG
e- A stage of viraemia

Page | 9
 General mycology

Mycology is the study of fungi.

Fungi Bacteria
Size Larger Smaller
Nucleus Eukaryote Prokaryote
Mitochondria Present Absent
Ergosterol in cytoplasmic Present Absent
membrane
Cell wall Chitin Peptidoglycan
Spores For reproduction For survival
Metabolism Heterotrophic Hetero and autotrophic
No obligate anaerobe Many obligate anaerobes

Mycoplasma is the only bacteria that contains cholesterol in the cytoplasmic

membrane
Reproduction may be by both sexual (meiotic) or asexual (mitotic) spores

Page | 10
Morphological Forms:

1- Molds:
They consist of long filaments (hyphae) which may be:
a) Septate (with cross walls)
b) Non-septate (without cross walls).
They grow by branching and tip elongation forming a mass called mycelium on culture media
Examples → Aspergillus, Penicillum and the dermatophytes.

2- Yeasts:
 They grow as single cells (round or oval).
 They reproduce by budding and may form pseudo-hyphae (hyphae with constrictions →
sausage-like chain)
 Examples → Candida and Cryptococcus.

3- Dimorphic fungi
those that can switch between the previous two forms depending on the temperature:
a) At room temperature: they grow as molds (hyphae).
b) At body temperature: they grow as yeasts.
Example → Histoplasma
Page | 11
Clinical Classification:

A- Mycotic infections

1. Superficial mycoses: affecting the keratinized layer of the skin → Pityriasis versicolor.

2. Cutaneous mycoses: affecting the deep layers of the skin → candida and dermatophytes.

3. Subcutaneous mycoses: in which fungi present in the soil are implanted in the
subcutaneous tissue by trauma, → mycetoma.

4. Deep (systemic) mycoses: affecting internal organs.

These fungi fall in two groups:

a) "True pathogens" infecting normal healthy individuals → Histoplasma and

Blastomyces.

b) "Opportunistic pathogens" infecting immunocompromised individuals →

Pneumocystis, Cryptococcus and Candida.

B-Mycotoxicosis:

It is produced by consumption of food containing fungal toxins

Examples →

a) Mushroom poisoning causes damage to liver, kidney and bone marrow.

b) Aflatoxin of Aspergillus flavus may cause chronic liver damage and cancer.

C- Allergic disorders: Spores of free-living fungi as Aspergillus may be the allergen in some
cases of atopy (asthma, hay fever, urticaria).

Pathogenesis
 Infection with certain systemic fungi (Histoplasma) elicits a granulomatous host defense
response (composed of macrophages and helper T cells).
 infection with other fungi (Aspergillus) elicits a pyogenic response (composed of
neutrophils).
Page | 12
Diagnosis of fungal infections
The laboratory diagnosis of fungal infection involves 2 main diagnostic
methods:
A- Direct methods: which depend either on the detection of fungi and/or their antigens
in the patient's specimens, or on isolation of fungi.
B- Indirect methods: which depend mainly on the detection of serum antibodies against
the suspected fungus in systemic mycosis or, less frequently, on skin tests

Antifungal Drugs:

 Because fungi are eukaryotes, the range of non-toxic

systemically active antifungal drugs is still limited.

 The selective toxicity of antifungal drugs is based on

the presence of ergosterol in fungal cell membranes,
in contrast to the cholesterol found in human cell
membranes and the absence of sterols in bacterial
cell membranes.

 The most commonly used drugs are →

1. amphotericin B
2. nystatin
3. azole drugs (fluconazole, ketoconazole and itraconazole).

MCQs

1- Fungi have the following characters EXCEPT:

a- They replicate sexually and asexually.
b- They are eukaryotic.
c- They have ergosterol in the cell membrane.
d- They are heterotrophic.
e- They are susceptible to antibacterial agents.
Page | 13