INTRODUCTION TO

CLINICAL MICROBIOLOGY
 DEFINITION
 Microorganisms are minute living entities that
are usually unable to be viewed with naked eyes
 (bacteria, Fungi, protozoans, algea, viruses)

 Clinical/medical microbiology is the study of

microbes involved in human diseases, their
epidemiology, control and treatment.

 Also Diagnosis + Defining treatment of the

disease (selection of antibiotic, antifungal or
antiviral)
 Brief history of medical
microbiology

Agostino Bassi
(1835) Louis Pasteur (1865)
Silk worm disease Silkworm disease by
by fungus protozoan

Joseph Lister Robert Koch

(1860) (1910)
Chemical Pioneer medical
disinfectant to microbiologist
clean surgical Cholera, anthrax,
instruments tuberculosis

Alexander
Fleming (1929)
Discovered
penicillin
KOCH’S POSTULATES
Common human disease causing microbes
IMPORTANT TERMS USED
IN MEDICAL MICROBIOLOGY
 TYPES OF HOST-MICROBE
RELATIONSHIPS

Saprophytes These microorganisms are nonpathogenic; their

natural habitat is dead organic matter
Commensals Normal inhabitants of skin and mucosa; the normal
flora is thus the total commensal population
Parasites Unicellular or metazoan organism living in or on an
organism of another species (host) on the expense of
the host
Primary Cause disease in host regardless of the host’s resident
Pathogen microbiota or immune system

Opportunisti Can cause disease in immunocompromised individuals

c pathogens given an “opportune” situation; these are frequently
germs of the normal flora or occasionally from the
surrounding environment, animals, or other germ
carriers
Synergism Sometimes, two (or more) microorganism may work
together “team up” to produce a disease that neither
could cause by itself
 Microbial activity
Pathogenicity Capacity of a pathogen to cause disease
Virulence Sum of the disease-causing properties of a
pathogenic strain
Incubation period The time elapse between the entry of pathogen
and appearance of disease
Minimum infective Smallest number of pathogens sufficient to cause
dose an infection

Virulence of a pathogen can be quantified using controlled

experiment in alaboratry animals

ID50= number of pathogen cells or virions required to cause

active infection in 50% of inoculated animals

LD50= number of pathogens cells or virions or toxins conc.

required to kill 50% of the infected animals
 What is infection?
1. Infection Invasion of a host organism by microorganisms,
proliferation of the invading organisms, and host
reaction
1A. Endogenous Infection arising from the colonizing flora
infection
1B. Exogenous infection Infection arising from invasion of host by
microorganisms from sources external to it
1C. Nosocomial Infection acquired during hospitalization (urinary
infection tract infections,
infections of the respiratory organs, wound infection,
sepsis)
1D. Local infection Infection that remains restricted to the portal of entry
and surrounding area
1E Generalized Lymphogenous and/or hematogenous spread of
infection invading
pathogen starting from the portal of entry; infection of
organs to which pathogen shows a specific affinity
(organotropism);
three stages: incubation, generalization, organ
Manifestation
1F. Sepsis Systemic disease caused by microorganisms and/or
their
toxic products; there is often a localized focus of
infection
from which pathogens or toxic products enter the
bloodstream continuously or in intermittent phase
1G. Transitory Brief presence of microorganisms in the bloodstream
bacteremia/
viremia/parasitemia
1H. Superinfection Occurrence of a second infection in the course of a first
infection
Relapses Series of infections by the same pathogenic strain

Reinfection Series of infections by different pathogenic strain

NORMAL MICROBIAL FLORA
 Definition
Normal flora is the mixtureof microorganisms (bacteria
and fungi) that are regularly found at any anatomical
site of human body like
 Skin
 Eyes (i.e. Conjunctiva)
 Nose (i.e. Respiratory tract)
 Mouth (i.e. Human Oral Cavity)
 Ears
 Urogenital tract
 GIT tract

 Gnotobiotic refers to a microbiologically monitored environment or

animal that is germfree (axenic) or in which the identities of all microbiota
are known
TRANSIENT NORMAL FLORA
 Normal flora that are temporarily living on and within
humans.
 The transient microbes living in the external
environment are attracted to moist, warm body areas.
1. washed from external areas.

2. not able to compete with resident normal flora.

3. may be killed by substances produced by the

resident normal flora.
4. may not survive in the acidic or alkaline pH of the
site.
5. may be flushed away by bodily secretions like tears,
sweat, oil, urine, feces,..).
NORMAL FLORA OF SKIN
 The adult human covered with approximately 2 square
meters of skin  1012bacteria
 can acquire any transient bacteria from the
environment
 either get washed off or die because the skin
is
 dry,
 has acidic pH,

 produce sweat and oil.

 Resident bacteria of the skin can be in any

layer of the skin.
-SKIN
 Aerobic Bacteria:
- Present in the outer layer of skin.
- Staphylococcus epidermidis (accounts 90%) +
Staphylococcus aureus.
 Anaerobic Bacteria: (More than Aerobic bacteria)
- Present in the deeper skin layers, hair follicles, and
sweat & sebaceous glands.
- Propionibacterium acnes.

Skin normal flora are generally

harmless but it might cause
bloodstream infections if skin
was penetrated.
 EYES FLORA
 The conjunctiva of the eye has
primarily S. epidermidis, followed
by S. aureus, C. diphtheroids, and
S. pneumoniae.

 Some skin normal flora are also present but at fewer amounts.

 Tears (Lysozyme enzyme), mucus, and oil will protect the

conjunctiva of the eye from colonization by more bacteria.
 EARS FLORA
 The middle ear and inner
ear: are usually sterile.

 The outer ear and the

auditory canal: contain the
same normal flora of the skin.

 When the person coughs,

sneezes, or blows his nose,
these microbes may move into
the middle ear where they
cause infection.
 RESPIRATORY TRACT
 Upper Respiratory Tract:
- Nose and throat
Have many microorganisms.
Some are normal flora, some are opportunistic, and others are
transient (C. diphtheroids) .
- Nasopharynx: Streptococcus pneumoniae
In immune compromised or elderly it might cause acute
bacterial pneumonia.

 Lower Respiratory Tract:

Is usually sterile because the mucous membranes of the lungs
remove any microbes.
ORAL CAVITY (MOUTH)

 resist mechanical removal by adhering to surfaces

(glycocalyx etc. ) like the gums and teeth
 very comfortable environment due to the availability of
water and nutrients, the suitability of pH and temperature,
and the presence of many other growth factors
 Colonize within hours after a human is born
 Initially aerobes and facultative anaerobes (Streptoccocus,
Lactobacillus, )
 onset of 1st teeth the anaerobes (Porphyromonas,
Prevotella, and Fusobacterium) become dominant
 Potential in causing dental plaque, gingivitus etc.
 Entry of pathogen in blood stream  endocarditis.
 GASTROINTESTINAL TRACT
 Stomach:
Only few bacteria are present in the
stomach due to gastric enzymes and
acidic pH.

 Small intestine:
Only few normal flora are present in
the upper part of small intestine because
bile kills them. Lower parts have more no.
of normal flora.
LARGE INTESTINE
 The large intestine or colon has the largest microbial community .in
the body.
 Microscopic counts of feces 1012 / gram wet weight.

 Over 400 different species

 Colon viewed as a large fermentation vessel,

 consist primarily of anaerobic, spore/ non-spore forming gram + and –

ive bacteria
 Ratio of anaerobic to facultative is 300 to 1

 Few protozoa and yeast spp. also found

 an adult eliminates about 3 x10 13 microorganisms daily

 Disruptive factors include

1. stress,

2. altitude changes,

3. starvation,

4. parasitic organisms,

5. Diarrhea

6. use of antibiotics or probiotics

INITIAL FLORA IN LARGE INTESTINE
 In breast-fed  In bottle-fed infants
 Bifidobacteria are not
1. Bifidobacteria
account for more predominant. When
than 90% of the total breast-fed infants are
switched to a diet of
intestinal bacteria. cow's milk or solid
2. food, bifidobacteria are
Enterobacteriaceae progressively joined by:
3. Enterococci 1. Enterics
4. Bacteroides 2. Bacteroides
5. Staphylococci 3. Enterococci
4. Lactobacilli
6. Lactobacilli
5. Clostridia
7. Clostridia
 UROGENITAL TRACT
Urinary Tract
 Kidneys, Ureters and Urinary Bladder: are sterile.
 Lower Urethra and external opening: bacteria, yeast, and
viruses. Has the same bacteria present on the skin.

Genital Organs
 Male and female genitals: are sterile except vagina.
 Vagina: Lactobacillus spp. keeps the pH acidic to protect the
vagina from opportunistic infections e.g. fungal vaginitis
(Candida albicans) or bacterial vaginosis (Bacteroides spp.,
Gardnerella vaginalis).
 IMPORTANCE
 Advantages
 constitute a protective host defense mechanism by occupying
ecological niches
 produce vitamin B and vitamin K

 contribute to immunity by inducing low levels of circulating

and secretory antibodies (cross react with pathogens).
 antagonism against nonindigenous species by production of
inhibitory fatty acids, peroxides, bacteriocins, etc.

 Disadvantages
 Can act as opportunistic pathogen :
 a) When individuals become immunocompromised or
debilitated.
 b) When they change their usual anatomic location.
 FACTS ABOUT NORMAL FLORA
 A fetus is sterile when born (No Normal Flora), then
newborn start having the normal flora from its mother,
air, food and the environment.

 Our internal organs are sterile like the spleen, liver,

pancreas, bladder, CSF, and blood unless during
infection.

 Normal flora differ from one human to another

depending on age, diet, genetics and geographic habitat.

 When the number of resident normal flora is greatly

reduced, opportunistic microbes can easily cause
infections in these areas e.g. Candida albicans that
cause candidiasis.
THANK U