29-Feb-20

INTRODUCTION TO
MICROBIOLOGY
Dr. Amira Mokhtar
Professor of Clinical Pathology
Ain – Shams University

Intended Learning Outcomes

(ILOs)
By the end of the course the candidate will be able to :

a1-Know different types of microorganisms , classification of bacteria,

bacterial structure & different methods of lab. diagnosis.

b1-Identify & differentiate between microorganisms to detect their clinical

significance & virulence .

c1-Apply this knowledge when dealing with the microorganisms.

d1- Solve problems & do case discussion.

e1-Communicate & work in groups.

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Classification of microorganisms
1) Bacteria ( cocci, bacilli, coccobacilli, spirochaetes).

2) Chlamydia ( resemble viruses in being obligate

intracellular , differ as it possess both DNA & RNA ,
susceptible to antibacterial drugs).

3) Viruses ( DNA & RNA)

4) Fungi (Yeast,..)
5) protozoa

Bacterial shape

Bacteria come in a wide variety of shapes:

A. Rod-shape
B. Round or spherical
C. Round in clusters
D. Round in twos
E. Spiral
F. Comma-shape.

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Bacterial structure
A) Cell envelop :
- Cell membrane ( Phospholipid).
- Cell wall ( peptidoglycan + teichoic acid or
lipopolysaccharide), preserve shape.
- Capsule , usually polysaccharide ( protect from
phagocytosis, virulence factor).

B) Appendages:
- Flagella ( originate from cytoplasm , long contractile
protein for motility)
- Pili ( fimbriae) promote adhesion to surfaces.

C) Cytoplasmic structures e.g. Ribosomes, DNA

A-Monotrichous; B-Lophotrichous;
C-Amphitrichous; D-Peritrichous;

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Cell wall deficient bacteria (CWD)

(L - form)
- No cell wall ( coccoid bodies or spheres).
- Antibiotics that inhibit cell wall synthesis e.g. penicillin
may produce L – form
- L – form no longer killed by many commonly used
antibiotics.
- Mycoplasma has no cell wall but not L – form as it is not
originally derived from bacteria have cell wall , it has no
definit shape.
- Cell wall detect bact. morphology & shape so, L – form has
morphology differ from bacteria which they are derived
- L - form bacteria always Gram –ve due to lack cell wall.

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cell wall difference between

Gram +ve & Gram -ve bacteria
- Cell wall in Gram +ve bacteria consists of 90%
peptidoglycan complexed with teichoic acid , so
more acidic & has affinity to basic dye

- Gram –ve cell wall consists of 5-20% peptidoglycan

which is not the outermost layer as in Gram +ve
but lies between plasma membrane & outer
membrane.

- Outer memb. Is lipopolysaccharide & is harmful

(endotoxin)

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Outer membrane

This lipid bilayer is found in Gram negative

bacteria and is the source of lipopolysaccharide
(LPS) in these bacteria. LPS is toxic and turns
on the immune system ( activate) , but not
present in Gram positive bacteria.

The pathogenic capability of Gram-negative

bacteria is often associated with the LPS
( endotoxin) …….. ENDOTOXAEMIA.

Classification of bacteria
According to:
1) Shape:
Cocci , bacilli, coccobacilli, vibrio, curved,
S-shaped, coils, fusiform
2) Staining :
Gram +ve ,-ve , acid fast , Neisser stain, Geimsa
stain, iodine, ……..
3) Aerotolerance:
Strict aerobe , strict anaerobe, facultative
anaerobe, microaerophilic.

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Classification of bacteria
4) Spores:
Spore forming organisms ( clostridia, bacillus
group), terminal or subterminal, rounded or oval
spores , Spore stain.
5) Motility :
Motile ( E.coli) , non motile ( Klebsiella), type of
motility.
6) Fermentation :
Glucose F. , Lactose F. , Sucrose F.

Classification of bacteria
7) Biochemical reactions :
Oxidase , Catalase, Coagulase,……,…..
8) Intracellular organisms:
Obligate I.C : Viruses, Rickettsia, Chlamydia ,
Coxiella , Bartonella.
Facultative I.C. : T.B. , Brucella, Legionella ,
Listeria, Histoplasma

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Classification of bacteria
9) Type of hemolysis on blood agar :
α ,β ,у hemolysis
10) Toxins:
- Endotoxin ( in cell wall of Gram –ve bact.)
- Exotoxin ( secreted by Gram +ve & -ve).
11) Pigments:
- Endopigment ( S.aureus).
- Exopigment ( pseudomonas ).
12) Pathogenicity:
Saprophytic, pathogenic , Opportunistic pathogen

Virulence factors

Factors that enable microorganisms to

establish itself on or within a host and
enhance disease (pathogenic virulent
organisms).

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Virulence factors

1-Toxins ( exotoxins & endotoxins) e.g. Staph., Diphtheria,

clostridia,…..,GNB ( LPS endotoxins)
2-Enzymes (lipase,hyalurinidase,coagulase,…)
3-Pili (adhere to cell receptors)
4-Capsules (prevent phagocytosis)
5-Surface proteins (promote binding to mucosal cells) e.g.
protein A in S.aureus

Infections
- Community acquired , hospital acquired
- Clinical infection, subclinical infection
- Latent infection ….. Reactivation ….. Recurrence
- Carrier (typhoid, diphtheria, meningococcal)
- Epidemic: a wide spread infection affecting many
individuals in an area at the same time
- Pandemic : has worldwide distribution
- Endemic: Infection constantly present at low
level.
- Outbreak: occurrence of disease (infection)
greater than expected in a particular time and
place.

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Laboratory diagnosis
- Clinical specimens + request reach the lab. for
culture & sensitivity ( 48 h.) , Ag detection or
antibody detection serologically.

- All specimens should be collected before the

start of antibiotic & transported rapidly to
the laborarory.

Laboratory diagnosis
Specimens:
* Urine (MSU, suprapubic aspiration , catheter, morning, 24 h.)
* Sputum, TTA, bronchial lavage, gastric wash (T.B.)
* Swabs (Throat, nasal, nasopharyngeal, per nasal, ear, eye, wound,
vaginal, endocervical, rectal)
* Stool (dry clean containers)
* Blood
* Body fluids (CSF, pleural effusion, ascitic fluid, synovial fluid)
* Prostatic fluid
* Semen (abstinence 3 days, transport within 2 hour, write time of
collection, pass urine before collection)
* Pus (aspiration by sterile syringe)
* Urethral discharge, morning drop (gonococci)
* Prosthetic valve, vegetation (infective endocarditis)

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Laboratory diagnosis

Request :
Essential clinical informations:
Age, sex, main clinical condition, date of onset
of the illness, antibiotic intake, antibiotic
allergy, history of recent travel abroad,
occupation. For serological tests the dates of
past immunization or suspected contact with
a source of infection.

Laboratory diagnosis
1) Direct methods :
- Naked eye examination : rice water stool (cholera),

anchovy sauce sputum (lung amoebiasis), sulphur granules

(actinomycosis), blood and mucus in stool (dysentery),

purulent sputum & turbid CSF , urine ,ascitic or pleural

fluid (infection), salivary sample (discard)

- Direct microscopy (Light: Wet, Gram, Z. N., Giemsa, dark

ground e.g. treponema pallidum , electron e.g. Rota virus)

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Laboratory diagnosis
- Isolation of the pathogen (artificial culture media,
tissue culture)

- Identification (Conventional B.R., API, automated)

• Antigen detection (Slide agglutination test : Latex

& coagglutination, ELISA, DFA)

• Nucleic acid detection by PCR & Gen probe

Laboratory diagnosis

II) Indirect methods :

Serum antibody detection (10 – 15 days later)

III) Antibiotic sensitivity tests :

- Conventional (Disk diffusion, MIC , E - test)
- Automated methods (Microscan)

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Contents of the lecture

- Different types of microorganisms
( bacteria, viruses, Chlamydia, Fungi, Protozoa)
- Bacterial structure ( cell wall , capsule,flagella.pili,….)
- Difference between Gram +ve & Gram -ve cell wall
- Classification of bacteria
- Different types of infection (clinical ,
subclinical,latent,hospital acquired, community
acquired, Carrier)
- Definition of epidemic, outbreak, pandemic, & endemic
disease
- Methods of Laboratory diagnosis
- specimens + request
- Different types of specimens
- Informations required in the request.

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