Definition of Microbiology: it is the study of the micro-organisms.

Microbiology in relation to medicine: is concerned mainly with the isolation and identification of the mecro-organisms that cause disease.

The microbial world is a realm of life made up of microorganisms and viruses.

Group of micro-organisms:

1.  Algae (singular: Alga):

Simple plants, some of which are unicellular. It contains chlorophyll, it lives in, or beside the water.

2.  Bacteria (sing. Bacterium):

A group of micro-organisms. Their cells may be spherical, rod-like, comma-shaped ect… it lives in soil, water, or air; or as parasites of man, animals, and plants. Some parasitic bacteria are pathogenic.

3.  Fungi (sing. Fungus):

A simple organism (formerly regarded as a plant) that lacks the green pigment (chlorophyll). It includes the yeasts, rusts, moulds, and mushrooms. Some species infect and cause disease in man. Some yeasts are a good source of vitamins, also many antibiotics as penicillin are obtained from moulds.

4.  Protozoa (sing. Protozoan)

A group of microscopic unicellular organisms. Most of which are free living but some, such as plasmodium, leishmania and amoeba, are important disease-causing parasites of man.

5.  Rickettsiae (sing. Rickettsia):

A group of very small non motile spherical of rod-like parasitic organisms. They cause such illnesses as rickettsiae pox, rocky mountain spotted fever, and typhus. It infects anthropoids ( ticks, mites, ect…) through which they can be transmitted to mammals (including man).

6.Viruses (sing. Virus)

A particle that is capable of replication but only within living cell. Viruses are too small to be visible with a light microscope, but only by the electron one. They infect animals, planets, man and micro-organisms. It cause many diseases, including the common cold, chickenpox, herpes, influenza, mumps, polio, AIDS, rabies etc.. Antiviral drugs are effective against some of them. And many viral diseases are controlled by means of vaccines.


-Medical microbiology.

- Food microbiology.

- Soil microbiology.

- Industrial microbiology.

- Dairy microbiology.


An instrument for producing a greatly magnified image of an object, which many be so small as to invisible to the naked eye. There are many types of microscopes as:

-  The light microscope.

-  The electcron microscope.

-  The surgical microscope.

Projector lens (eye piece)


Objective lenses

Stage (specimen)

Condenser lens.


(illumination source)

The main parts of a light microscope.

Electron gun

(illumination source)


Condenser lens


Specimen holder

Objective lenses

Projector lens

Control panel

Fluorescent screen

The main parts of the transmission electron microscope.



It is the study of the bacteria.

Bacteria: is a group of micro-organisms with prokaryotic nucleus.

Bacterial cell structures:


Cell wall

Cytoplasmic membrane




1. Capsule:

- Present in some and not all bacterial species.

- it is a jelly like substance (polysaccharide) surround the cell wall.

- the capsule protects the bacterial cell from phagocytoisis and viral invasion, it also helps the pathogenic becteria to invade the host.

2. The cell wall:

- Envelopes the cell to protect it.

- Give the cell its special shape.

- Differentiates between gram positive(g+ve) and gram negative (g-ve) becteria.

3- Cytoplasmic membrane:

- Very thin membrane composed of phospholipids and proteins.

- It has the characteristic of selective permeability to give the cell its demands.

4- The nucleus:

- It is the Liquid portion present inside the cytoplasmic Membrane.

- It contains ribosomal granles which are the centers for proteins and enzymes synthesis.

5- the nucleus:

It is primitive (prokaryotic) in bacteria, consists of single chromosome. It has an important role in cell division.

6. Appendages:

a) Flagella (flagellum).

-  thread like appendages, composed of proteins.

-  It is the organ of Iocomotion.

b) pili (sing. Pilus):

- they are shorter and finder than flagellae, present in the pathogenic becteria especially g-ve. It helps it to be adherent the host.

7- Spores:

- Under unfavorable conditions, members of several types of bacterial genera, are capable of forming endospores, in order to resist these conditions and become active again with favor table conditions.

- the endospores may be:

- Terminal - Sub terminal - Central.


Because the bacteria are colorless, so it is difficult to be microscopically studied without staining.

1- Simple stains:

Methylene blue and crystal violet.

2- Compound stains:

(Gram stain) – gram negative cells, appear red in color.

-  gram positive cells, appear blue in color.

Bacterial morphological characteristics

1-  shape:

1- Spherical = cocci (coccus).

2- Cylindrical rod = bacilli (bacillus).

3- Comma shaped

4- Spiral = spirilla (spirillum)

2- Arrangement:

- Cocci : 1- Monococcus.

2- Diplococci. (pairs)

3- Tetracocci.

4- Streptococci. (chain)

5- Staphylococci (grape)

_ Bacilli: 1- Monobacillus.

i. Diplobacilli.

ii.  Streptobacilli

3- Size: 0.5 1 um. × 2-5 um.

4- Gram stain:

According to their response to gram stain:

1- Gram positive becteria. – responding, - blue color.

2- Gram negative becteria. – not responding, - red color

5- Motility:

1- Motile (has flagellae) 2- Non motile(has no flagellae)

Host parasite relationship

-  The parasite:

It is an organism that resides on or within another living organism (host), in order to find the environments and nutrients it requires for growth and reproduction.

Most successful parasites achieve a balance with the host.

Some parasites are harmful to the host.

Some parasites are useful to the host.

-  The host:

-  Aman, an animal or a plant in, or upon, which a parasite lives, grows and reproduces.

The infection:

Is the process whereby the parasite enters into a relation-ship with the host. It passes by two steps:

1-  Entrance of the parasite into the host.

2-  Establishment and multiplication of the parasite within the host.

Bacterial morphological characteristics

1- Shape:-

1- Spherical = cocci (coccus)

2- Cylindrical rod = bacilli (bacillus)

3- Comma shaped =

4- Spiral = spirilla (spirillum)

2- Arrangement:-

-Cocci: - 1- Monococcus. (Pairs)

2- Diplococci.

3- Tetracocci.

4- Streptococci. (Chain)

5- Staphylococci (Grape)

-Bacilli: - 1 - Monobacillus

2 - Diplobacilli.

3 - Streptobacilli.

3- Size:-

0.5 – 1 nm. X 2 – 5 nm.

4- Gram stain :-

According to their response to gram stain:-

1- Gram positive bacteria: - responding –blue color.

2- Gram negative bacteria -not responding, -red color.

5- Motility:-

1- Motile (has flagellae). 2- Non motile (has no flagellae).

Host parasite relationship

The parasite:-

It is an organism that resides on or within another living organism (host), in order to find the environments and nutrients it requires for growth and reproduction.

Most successful parasites achieve a balance with the host.

Some parasites are useful to the host.

The host:-

A man, an animal or a plant in, or upon, which a parasite lives, grows and reproduces.

The infection:-

Is the process whereby the parasite enters into relation-ship with the host? It passes by two steps:-

1- Entrance of the parasite info the host.

2- Establishment and multiplication of the parasite within the host.


Is the ability of microorganism to cause a disease?


Are poisons produced by a living organism (especially bacteria). It may be:-

1- Exotoxins: Excreted by living g.+ve bacterial cells.

2- Endotoxins: Integral parts of microbial cell walls of g-ve organisms liberated upon their disintegration.

Pathogenic bacteria

These are the bacteria that causing diseases. They include:-

(1) Pyogenic cocco:-

1- The staphylococci :-

_ g.+ve, spherical cells, usually arranged in irregular clusters.

_ Non motile and non spore forming.

_ Diseases: - focal suppuration (furuncle and abscess), wound infection. Otitis and UTI.

The streptococci:-

_ g.+ve spherical cells arranged in chains.

_ Non motile and nonspore forming.

_ Diseases: - Erysipelas, puerperal sepsis, wound infection, tonsillitis and infective endocarditis.

_ Post streptococcal diseases :-( due to hypersensitivity response to the organism) e.g. acute glomerulonephritis and rheumatic fever.

3-The pneumococci:-

_ g.+ve diplococci arranged in chains.

_ Possessing a capsule.

_ Pathology: pneumococcal pneumonia.


_ Are a group of g-ve diplococci arranged in pairs.

_ Nonmotile and nonspore forming.

_ e.g.:- N. meningitides (meningococcal meningitis).

N. gonorrhea (gonococcus gonorrhea).

(2)Gram-positive bacilli:-

1- Aerobic spore – forming bacilli:-

_ e.g.:- Anthrax.

_ g.+ve: - Bacilli.

_ arranged in chains.

_ Pathology: - -Anthrax.

2- Anaerobic spore-forming bacilli:-

_ e.g.:- Clostridia.

_ g.+ve :- Bacilli.

_ e.g.:- clostridium botulism and clostridium tetani.

(3) corynebacteria:-

_ g.+ve bacilli (rods).

_ Non motile, _Non spore-forming, _Club like.

_ Disease: - Diphtheria.


_ Are rod shaped, non spore forming, aerobic bacteria (bacilli).

_ Don't stain readily but, once stained, resist decolorization by acid or alcohol and are therefore called (acid-fast) bacilli.

_ e.g.:- Mycobacterium tuberculosis:-Dis. Tuberculosis.

- Mycobacterium leprae: -Dis. Leprosy.

(5)Enteric g-ve micro-organisms:-

_ bacilli.

_ Non spore-forming.

_ Motile (peritrichous flagella).

_ Its natural habitar is the intestinal tract.

_ Endo-toxin and exo-toxin producing bacteria.

e.g. (1) The Salmonellae:-

1- S. Typhi.

2- S. Paratyphi A.

3- S. Paratyphi B.

4- S. Typhimumrium.

5- S. Enter.

- Diseases:-

_ Enteric fever. (Typhoid f.)

_ Bacteremia with focal lesions.

_ Entero-colitis (gastro enteritis).

(2) The shigellae:-

_ As salmonella except:- non motile.

_ Diseases: - Bacillary dysentery.

(3) The vibrios:-

_curved comma shaped, possessing a single polar flagellum.

_ E.g. Vibrio cholera.

_ Diseases: - cholera.

(4) Escherichia coli:-

_ e.g. E.coli.

_ Diseases: - _Enteritis. _ UTI.

(5) Pseudomonas:-

e.g. ps. Aeruginosa.

_ Diseases:-

- Enteritis, - UTI, - Otitis media, -Wound infection (with characteristic green colored pus)

(6) Small g-ve Rods:-

E.g. Brucellae:-

_ Small, aerobic, g-ve, nonmotile, non spore-forming cocco-bacilli.

_ Diseases: - Brucellosis due to drinking infected milk.

(Undulant fever or Malta fever)


Viruses that infect the bacterial cells are known as bacterophages.



It is the study of the viruses.

Size and shape

Viruses range in size form 20 to 300 nm in diameter, many of which have typical shapes that aid for its identification.


- Viruses are obligatory, intra cellular parasites and thus can only replicate in living cells.

- Viruses are subcellulais particles that cannot metabolize on their own, so it can not be consider as truly living organisms.

- It is so small that to be visible by the light microscope, but can be visible only by the electron microscope.

- Viruses can infect man, animals, plants and micro organisms, causing a lot of diseases as: AIDS, Virus hepatitis, Measles, Mumps……..etc.

- Anti viral drugs are effective only against some viruses and some having no treatment up till now, but many viruses can be controlled by vaccines.

Virus structure


Viruses contain either DNA or RNA. Nucleic acids represent the main component of the virus core and are associated with core proteins.


A protein coat enclosing the genome and core protein.


Lipid bilayer membrane surrounding the Capsid of some viruses. Many viruses have no envelope.

Virus replication

1- Attachment to cell surface molecules (receptors).

2- Penetration of the viruses into the host cell by endocytosis.

3- Replication of viral protein of nucleic acid and attached core protein, in order to direct the host cell ribosome to produce viral proteins.

4- Assembly and maturation to form viral particles

5- Release of the virus.

During latent infections the virus does not undergo replication.

Virus classification

Viruses can be classified according to:-

1- Diseases: as : Measles and Mumps viruses; or organ system involved: as : Hepatitis virus.

2- Nucleic acid type / virus structure DNA viruses or RNA viruses.

Detection of virus infections

1- Direct detection of virus particles or nucleic acid by: electron microscope; particle agglutination; immunoflourecence; PCR (Polymerase Chain Reaction).

2- Indirect detection of virus (specific host response) by serological tests as complement fixation test, ELISA

Common Viral Infection



The influenza viruses are a common cause of Respiratory tract infection.

Virus: Enveloped RNA virus of 100 nm diameter; there are three types A, Band C,. Spread by droplets ; infection of upper respiratory tract causing ; incubation period of 1-4 days followed by virus replication in upper respiratory tract;

Epidemics occurs in types A,B,C but pandemic occurs mostly in type A .

Treatment. Amantadine or rimantadine, for prophylaxis only.

Prevention. Inactivated vaccines (whole virus or subunit given intramuscularly)

have an efficacy of 60-80% provided vaccine components and current wild-type

viruses are sufficiently similar.


Transmission is by droplet spread or contact with saliva. It occurs in children 5-15 years .old . Interfamily infections are common. It is RNA viruses, 150-300nm in diameter.

The incubation period is 18-21 days. There is a short prodromal phase (48h) of malaise and fever, followed by parotid gland enlargement. Complications : -

• Meningitis, often mild in <5% of cases.

• Epididymo-orchitis in about 25% of adult males infected with the virus. It is an occasional cause of sterility.

• Pancreatitis, myocarditis, arthritis (rare), oophoritis. Prevention. Attenuated live virus vaccine is normally given in combination with measles and rubella vaccines (MMR) in childhood immunization schemes: There has been a sharp decrease after 20 years of mumps vaccination.


Measles RNA virus. Transmission is by droplet spread. It is highly infectious. The incubation period is 9-10 days. There is a prodromal phase (48h) of fever, cough, rhinitis and conjunctivitis, followed by the appearance of a maculopapular rash starting on the face and trunk, and spreading peripherally; lesions also present on the mucosa, particularly in the mouth (Koplik spots).


• Pneumonia

• Encephalitis

• Otitis media (bacterial superinfection, e.g. Staphylococci, Streptococci)

Prevention. Attenuated live virus vaccine is normally given in combination with rubella and mumps vaccines (MMR).


RNA virus of 60nm diameter.

The incubation perio4 is 14 days, with primary replication in the cervical lymph nodes, followed by rash. Lifelong immunity follows natural infection.