MICROBIOLOGY

Definition of Microbiology
Study of very small living organisms by means of microscope.
It includes Immunology , Bacteriology , Mycology , Virology , Parasitology &
Applied Microbiology . It deals with the aetiology , transmission , pathogenesis
,laboratory diagnosis , anti- microbial therapy , prevention & control of infectious diseases.
It also includes study of the immune responses of the host to foreign substances with
resulting either immunity or hypersensitivity .

Definition of Fungi
Fungi are non-photosynthetic, relatively large eukaryotic mocroorganisms, posses rigid
cell walls. It may be mould or unicellular (yeasts).

Definition of Bacteria
Bacteria are small microorganisms with a prokaryotic cell structure, posses a rigid cell
wall and a system of genetic transfer.

Definition of Viruses
Viruses are the smallest infectious agents with either DNA or RNA, reproduces inside the
living cells and transfer viral genome to others cells.

Definition of parasites
Parasites are infectious agents which take up nourishment and shelter on or within their
host.

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 INFECTION
Infection is a process where by microorganisms gain entrance into a host and multiply in
tissues with consequent damage . A wide varety of infectious microorganisms can be grouped
according to their habitat or disease producing capabilities.

Saprophytes : Microorganisms which feed on deep organic matter .

Parasites : microorganisms which reside on or within another living organisms in order
to find the nutrients and environment for growth and reproduction . Oblijate parasites are those
that have absolute requirement for the host and can not survive or propagate without it e.g ,
viruses .
Pathogens: Microorganisms which can cause disease .
Commensals: Generally harmless microorganisms which live and multiply on the body surfaces
(Skin and mucous membrane ) .
Opportunistic pathogens: are potential pathogens which are non - pathogenic in their
normal habitat but become a pathogenic at site where the defenses of the body are insufficient .

Periodicity of disease occurance

There are terms used to express the relaive prevalence of infectious diseases .
Epidemic: an illness in community clearly in excess of normal expectation e.g , cholera ,
viral hepatitis .
Endemic : when prevalent in a geographic area continuously at a relatively low level
e.g leprosy .
Sporadic: occasional and infrequent occrrence of cases ; few , separated in space and time
No connection with each other e.g. Polionyelitis , diphtheria .
Pandemic: when it spreads from one country to another in a short time or occurs at the same
time in different countries e.g. SARS , A vian inflenza .

Zoonotic infections
Infections that are naturally transmitted from vertebrate animals to man e.g. , plague ,
rabies, leptospirosis .

Types of infection
Clinical: Infection with recognized cliniclal manifestation .
Subclinical : Infection without recognizable signs and symptoms .
Latent : A persistand inapparent infection . It may flare up under certain conditions e.g.
herpes .
Relapse : Recurrence after its apparent recovery .
Toxic: Signs & symptoms of a particular disease e.g. tetanus due to its specific toxin .
Super: Sudden growth of a type of microorganism different from the original offender
during anti -microvial therapy e.g. intestinal candidiasis , pseudomembranous
colitis.

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 SIX LINKS OF INFECTION

1. Causal agent : etiological agent (microorganism )

2. Source or reservoir
Sources - places from which an infectious agent passes immediately to a susceptible host;
exogenous / endogenous
Endogenous source: From within the patient’s own body e.g., colon , skin , anterior
nares, nasopharynx
May be due to commensals acting as opporrrtunistic pathogens e.g. viridans streptococci ;
a commensal of the mouth & throat may cause subacute bacterial endocarditis.
Exogenous source : From outside e.g. Human (patient , carrier ), animal , inanimate
object.
Reservoir - Places where an infectious agent lives & multiplies.

3. Portal exit

4. Mode of transmission : The mechanism by which an infectious agent is transported from

the source of infection to a susceptiible host .
(a) Contact transmission - direct , indirect ,sexual
(b) Air-bone tranamission - droplet infectiuon ,infectious dust
(c) vehicle transmission - water -bone , food - bone ,milk-bone, hand,
transfusion , transplantation
(d) Vector- bone transmission - mechanical , biological
(e) Vertical transmission - from mother to foetus
(f) Auto-infection - an endogenous infection (Self Infection)

5. Portal of entry

6. Susceptible host (Non-immune person)

Microbial Pathogenicity

It is the capacity of the microorganism to cause disease .

Attributes of microorganisms which unable then to caues disease are
Transmissibility : communicability from source to a new host, it depends on the links in the
process of infection
Infectivity : The ability to break through the defenses of the new host . It depens on
-Dosage of pathogen
-Phase of growth of the pathogen
-Virulence of the microorganism ( toxigenicity , invasiveness , genetic
variation)

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Sterilization & Disinfection
Sterilization : Freeing of an article from all forms of living microorganisms including spores .
Disinfection : Freeing of an article from pathogenic microorganisms excluding spores .
Methods
1. PHYSICAL METHODS
1.1 Heat
Dry heat: kills microorganisms probably by destructive oxidation of cell constituents
Flaming- Use only for metal articles (forcepss , scalpels ) Place the articles in a metal
tray . Add 10 drops of ethanol , tilting during flaming
Red heat- Vaccinating needles or lancets for taking capillary blood samples should be
heated in the flame of a spirit lamp until they are red hot .
Hot-air oven - Set the thermometer at 175 C & switch on the oven .When the
temperature reaches 175 C , continue heating for a further 1 hr . Switch off
the heat . Wait until the temperature falls to 40 C . Open the oven door .
The wrapping paper used should have turned brown . If turns pale yellow , the oven is
not hot enough ; if it is blackened , the oven is too hot .
Moist heat : kills microorganisms by coagulation of structural proteins & denature
the enzymes .
Temperature below 100 C-Pasteurization of milk (63 C _ 30 min , 72 C _ 20 sec )
Water bath for sera , vaccine ( 56 - 60 C _1 hr )
Temperature at 100 C- Boiling / tyndallization
Temperature above 100 C-Steam under pressure 15 lb per sq in > 760 mmHg , 121
C_15-20min. (Autoclave )

1.2 Radiation
1. Non-ionizing radiation (Ultra violet radiation)
2. Ionizing radiation ( Gamma rays, X’ray).
1.3 Filtration
1. Filter for liquids
2. Filter for air.

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2 CHEMICAL METHODS
It includes chemical agents which are used mainly as disinfectants.
Chemical agents used for Sterilization and Disinfection
1. Soaps and Detergents
2. Volatile solvents (Ethyl alcohol, Isopropyl alcohol, Methylated spirit)
3. Phenol and Phenolic compounds (Expensive, not only damage but also denature
proteins).
4. Gaseous chemicals (Formaldehyde- Fumigation and sterilization of OT / Ethylene
oxide- surgical instruments and plastics)
5. Liquid sporicidal chemicals ( Glutaraldehyde- 10 times more effective than
formaldehyde and is less toxic )

Disposal of specimens and infected material

(a) Incineration
Use an old metal drum . Fix a strong metal grating firmly about one third of the way up
the drum . Cut a wide openning below the level of the grating . Find a removable lid for the drum
Place all the infected material to be discarded on the grating of the incinerator . Fill the
botton with paper , sticks etc . Light the fire and keep it burning until all the infected material has
become ashes .

(b) Burial
Dig a pit 4 -5 meters deep and 1 -2 meters wide . Make a lid that fits tightly over the pit .
The upper rin of the pit should be strengthened by linning it with brick stones . Throw the
infected materials into the pit & replace the lid immediately . Once a week , cover the disposal
with 10 cm thick dried leaves or quick line .

Sterilization & cleaning of non-disposibale containers

A. Stool containers
Fill with a 5% phenol solution . Leave it for 24 hrs .Enpty into the lavatory (don’t do if
lavatory is connected to a septic tank ) . Clean the Jar with detergent and water .

B. Sputum pots , tubes of pus & CSF (several possible methods )

Use autoclave , 120 C _30’ or boiling in washing powder _30’ or use 10ml undiluted
formaldehyde solution , 5 ml of 5% phenol . Leave it for 24 hrs .

C. Urine bottles
Empty the bottles into the lavatory . Fill them with a 10 % solution of commercial bleach
or a 2% solution of phenol . Leave it for 24 hrs .

D. Tubes of blood

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 Tubes of fresh blood collected the same day should be rinsed in cold water . Soak in a
detergent solution . Tubes of old blood kept for several days at room temperature should be
filled with a 10% solution of commercial bleach . Left for 12 hrs and then rinsed and cleaned .

IMMUNE RESPONSES

An immune response is a response of the immune system to the invasion of a foreign

material (antigen) and may be non-specific, or specific,and humoral (antibody mediated) or
cellular (cell-mediated).

Components of the Immune System

Primary / central lymphoid organ-

Bone marrow (production of stem cell & maturation of B lymphocytes)
Thymus (in which maturation of T lymphocytes occur)

Secondary lymphoid tissue-

Spleen, lymph nodes, mucosal associted lymphoid tissue (MALT) of the respiratory
tract, the gastrointestinal tract(GALT) and the genitourinary tract.
This is the enviroment in which lymphocytes can interact with each other and with antigen.

Cell involved in immune system

Cells of the mononuclear phagocyte system(monocyte, macrophage)
Stem cells -->myeloid seties-->T luymphocytes-->mature in thymus
3 main function- phagocytosis, antigen presentation, cytokine production

Lymphocytes ( T & B, natural killer cells)

Stem cells -->lymphoid series --> T lymphocytes--> mature in thymus
4 subsets -- (1). Helper T (TH)cells
They produce cytokines that can regulate the activities of T, B moncytes / marcrophage
& other cells of the immune system.Augment cell-mediated & humoral
immune response.
(2). cytoxic T (TC)cells
They play an important role in defense aganst viral ,intracellular parasite infections and
Graft by lysis of the antigen bearing cells . They can also lyse cancer cells that express
tumor specific antigens .
(3). Suppressor T (TS)cells .
They appear to terminate or supress immune responses .
(4). T delayed - type hypersensitivity (TDTH)cells
They play and inportant role in cell mediated hypersensitivity .
Stem cells --> B lymphocytes --> Activated B cells --> plasma cells -->produce antibody
They play and important role in humoral immunity .

Granulocytes (Neutrophils , Eosinophils , Basophils )

Humoral factors involved in immune system -
Antibodies , Complement , Cytokine , Other chemical mediators

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Functions of the immune system

1. Defense -against microorganisms (Infectious agents )

2. Homeostasis -maintain the physiological balance of cells population in the body by
removing aging , dead , damaged and self reactive cells .
3. Surveillance -For killing abnormal mutant cells and tumor cells

Antigen

An antigen is a substance which when introduced into the tissues of a living animal will
provoke , after a latent period , an immune response directed specifically at the inducing
substance .
Antigenicity ( Immunogenicity )-Capacity to induce a detectable immune response depends on
(a) foreigness / non-self
(b) molecular size
(c) chemical & structural complexity
(d) antigenic determinant
(e) dosage , route & timing of antigen administration

Antibody / Immunoglobulin

Antibodies are glycoproteins that bind specifically to the antigen that induced their formation .
5 distinct classes ; IgG,IgA,IgM,IgD,IgE.

IgG: Major immunoglobulin of serum .Major antibody of the secondary response

found in both serum & tissue fluids . Pass through the placenta .
IgA: Found in both serum & secretion (saliva , colostrum , respiratory ,
gastrointestinal, genitourilary) . Local immunity .
IgM: Main antibody in primary response . Produce by a foetus with an infection
IgD: <1% of the circulating antibody present on B cell surface .
IgE: Found on basophil & mast cell surface . Usually low level , large amount and
allergy / type I hypersensitivity . Play an important role in defense against
helminth infection .

Antigen - Antibody Reactions

When molecules of antigen & antibody are brought together in solution , they interact
each other by formation of a link between and antigen - binding site on the Fab fragment of the
immunognobulin molecule & the antigenic determinant of the antigen molecule . The reaction
is generally specific . The union is firm but often reversible .

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Outcome of Immune response

o Unresponsiveness - Tolerance
o Hyporesponse - Immunodeficiency
o Optimal response - Immunity ( protective)
o Hyper - response - Hypersensitivity(harmful)
o Escape of tolerance(control) - Autoimmunity ( harmful)

Different types of Defense Mechanism & Immunity

There are two fundamentally different types of responses to invading microbes . Innate
(natural) responses occur to the same extent however many times the infectious agent is
encountered , whereas acquired ( adaptive ) responses improve on repeated exposure to a given
infection . Both uses to defense mechanisns ; humoral or cellular.
Innate has short term effect of immunity, no memory, non-specific defense system and
appear since born whereas adaptive immune system has long term immunity, memory to
recognize , specific and appear later than innate.

§ Innate or natural / non- adaptive immunity

Natural immunity is resistance this is not acquired throught contact with an antigen . It is
not antigen specific and ability of the host to eliminate a wide range of potentially infectious
agents in the environment since birth . It is largely genetically determined .

Individual resistance is related to : Age , Sex ,Hormonal influences , and nutritional factors .
External / physiologic defense mechanism.
a. Mechanical barrier : The skin and mucous membranes .
b. Chemical barrier : Free fatty acids in sebaceous secretions and sweat -by virtue of
their acid pH . Mucus and tears contain lysozyme and other substances with antimicrobial
properties.IgA antibodies on surface epithelial cell prevent attachment of adhesive bacterial
surface proteins (e.g.the pili of gonococci and Escherichia coli ).
c. Biological barrier :Constant normal microbial flora , 1012 bacterial on the skin and
1014 in the gut that itself opposes establishment of pathogenic microorgsnisms ( “ bacterial
interference’’)

Internal defense mechanism

i. Humoral arm - Non-adaptive Humoral immunity
Complement , acute phase proteins , and cytokines ( interferon)
ii. Cellular arm- Non-adaptive cell mediated immunity
Phagocytic cells ( neutrophils , monocytes , and macrophages ) , cells
that release inflammatory mediators ( basophils , mast cells and eosinophils
)and natural killer cells .
Phagocytosis: Chemotasis , attachment , internalization , digestion ; Oxygen dependent,
Oxygen independent mechanisms.

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 § Acquired or adaptive immunity

a. Internal antigen-specific defense mechanism-

2 i. Humoral arm - Adaptive Humoral immunity
Activation of B cell -> plasma cells -> Abs
ii. Cellular arm - Adaptive Cell mediated immunity (Activation of Cytotoxic T
cells).

Classification & Categorization of Acquired Immunity

Naturally Acquired Active Immunity

The protection provided by previous exposure pathogenic microorganism or

antigenically related organism . It is acquired through overt clinical infection or repeated
subclinical infections . E.g whooping cough , measles , mumps ----long lasting immunity
Sore throat , influenza ---short duration of immunity

Artificially Acquired Active Immunity

The protection develops as a result of the deliberate administration of appropriate
antigenic material (active immunization ) in the form of vaccine or toxoids .

Naturally Acquried Passive Immunity

The prodection develops as a result of transfer of IgG antibodies across the placenda and
natural transfer of specific antibodies ( IgA ) to baby through the colostrum and milk from
mother to child . Natural passive immunity wanes after 4 -6 months of life .

Artificially Acquired Passive Immunity

The production develops as a result of transfer of immunoglobulins and immune sera

from an immune individual to a non- immune , susceptible recipient .

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 Hypersensitivity

A condition in which an immune response results in exaggerated or inappropriate

reactions that is harmful to the host .

Classification ( Modified from Gell and Coombs )

1. Type I: Anaphylactic ( immediate) Hypersensitivity
2. Type II: Cytoxic Hypersensitivity .
3. Type III: Immune complex Hypersensitivity
4. Type IV: Cell - mediated ( delayed ) Hypersensitivity
Type I , II , III are antibody - mediated .
Type IV is cell - mediated .

Type I Hypersensitivity
Tissue reactions occur within minutes after the antigen combines with the specific
antibody after second contact with same antigen . An antigen ( allergen ) induces the fromation
of IgE antibody which binds firrmly by its Fc portion to a receptor (Fc R ) on the surface of
e
basophils and mast cells . Some weeks later , a second contact of the individual with the same
antigen results in the binding of the antigen to the cell -bound IgE . Cross - linking of the cell -
bound IgE antibodies by antigen is followed by mast cell or basophil degranulation , wth
release of pharmacologically active mediators within minutes .

Some examples of allergens are :

1. Plant pollens and mold spores
2. Faecal pellets of the house dust mite
3. Animal hair , dander and feathers
4. Foods (milk , peanus ,eggs , fish , nuts , chocolate )
5. Foreign serum and hormones ( anti - tetanus serum , anti diphtheretic serum )
6. Insect venoms (Bee, scorpion )
7. Drugs and chemicals ( antibiotics , antiseptics , vitamins , anaesthetics ) .

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Clinical Conditions
1. Anaphylactic shock ( systemic form or anaphylaxis )if allergen is injected
parenterally as in the case of a drug such as penicillin , and by the bite or sting of
insect .
2. Hay fever , bronchial asthma if antigen comes in contact with the respiratory mucous
membrane . E.g.,pollen , animal dander , faecal pellets, house dust mite .
3. Gastrointestinal allergy . Food allergen comes in contact with intestinal mucous
membrane.
4. Atopic dermatitis ( skin rashes , urticaria ) .
Prevention and Treatment
1. Avoid allergens if possible
2. Desensitization
(a) Acute desensitization :administration of small amounts of antigen at 15 minute
intervals antigen IgE complexes form on a small scale and not enough
mediator is released to prduce a major reaction .
(b) Chronic desensitization : long term weekly administration of antigen to which the
person is hypersensitive . This stimulates the production of IgG –
blocking
antibodies in the serum , which can prevent subsequent antigen from reaching IgE
on mast cells , thus preventing a reaction .
3. Drug treatment : Epinephrine , antihistamines , corticosteroids , isotrenaline and theophyl
line .
4. Maintenace of airway , support respiratory and circulatory function .
Examples of Type II Hypersensitivity
1. RBC lysis : in mismatched blood transfusion and Rh incompatibility , Haemolytic
disease of newborn , autoimmune haemolytic anaemia.
2. WBC lysis : in SLE , granulocytopenia .
3. Platelet lysis : in ITP

Eamples of Type III Hypersensitivity

1. post - strettococcal glomerunonephritis .

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2. Autoimmune diseases - SLE , Rhematoid arthritis ,

Type IV hypersensitivity (Delayed hypersensitivity reaction)

It is a function of immunologically commited (sensitized) T cells. It starts hours or
days after contact with the antigen and often lasts for days.
(a) provides resistance to
(1) Chronic imtracellular bacterial infections (TB, lepreosy ,brucellosis ,
listeriosis )
(2) Fungal inections ( histoplasmosis,blastomycosis)
(3) Viral infection ( Herpes and mumps )
(4) Protozoal infecrions ( leishmaniasis)
(5) Helminthic infections ( as schistosomiasis )
(b) Play a role in rejection of graft tissue and organs

Immunization
Is the process of creation of immunity by the administration of immunizing agents .
Objectives of Immunization
To produce a degree of resistance as greater as or greater than which follows a clinical
atrtack of natural infection without harm to the recipient .
Type of Immunization
1. Active Immunization
2. Passive Immunization
3. Combined Immunization

Active immunization -is a process of creation of active immunity by the administration of

immunizing agent in the form of toxoid and vaccine .

Immunizing Agent for Active Immunization

Toxoid : The exotoxins of some bacteria are converted in the laboratory to a non-
toxigenic form by treatment with formalin or other E.g tetanus toxoid , diphtheria toxoid .

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whole - cell killed vaccines: Suspension of inactivated intact microorganisms produce serious
side effects E.g Whooping cough (pertussis) vaccine , typhoid (TAB)vaccine .
Attenuated vaccines : Vaccines consist of living micro-organisms that through
laboratory processing have lost their virulence or has been greatly reduced . The genetically
stable attenuated micro organisms can still multiply in the host but lack the ability to cause
disease . It induces a higher and long -lasting level of immunity .It lessens the need for booster
doses E.g. oral polio vaccine , mumps vaccine, measles vaccine , rubella vaccine .
Purified antigens , subunit vaccines: a subunit vaccine is composed of a part of the
whole microorganism that is known to contain the antigenic molecules that stimulate immunity
E.g. vaccine containing purified capsular polysaccharide against strains of Strep .pneumaniae ,
Neisseria meningitidis , Haemophilus inlenzae .
Recombinant vaccine : If the protective antigen of microorganism is known ,large
quantities of purified antigen can be produced by inserting segments of nucleic acid that code
for the antigen into bacteria , yeasts or animal cells.

Passive immunization is the process of creation of passive immunity by administration of

passive immunizing agents.
Immunizing agents for passive immunization
Immune sera : It is usually prepared by immunizing horse with toxoids and then
obtaining sera containing antitoxins from these animals E.g. Anti- tetanus serum (ATS) , Anti-
gas-gangrene serum (AGGS) ,Anti-diphtheria serum (ADS) , Anti-rabies serum .
Immune serum globulin (ISG): Prepared from large pool of normal human adult plasma.
Employed in the certain viral diseases ; Hepatitis A &B, Measles , Rubella either to prevent
infection or to modify the course of illness .
Specific immune serum globulin: These preparations are obtained from the blood of
individuals immunized with a given antigen and they contain higher concentrarion of
specific antibody E.g. tetanus immune globulin , Human rabies immune globulin , Vaccinia
immune globulin , Zoster immune globulin , Hepatitis B immune globin .
Immunocompetent cells : Passive administration of viable T Lymphocyte from reactive
person to non-reactive person can create cell- mediated immunity.
Combined Immunization : Active and passive immunization given at the same but at
different sites.

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Hazards of Immunization
1. Transfer of infection (HIV ,HBV )
2. Sepsis
3. Local irritant action due to adjuvant
4. Febrile convulsion
5. Hypersensitivity reactions , serum sickness.
6. Encephalopathy
7. Prenatal infection in immunocompromised host if live vaccine given

Universal Childhood Immunization (UCI)

Immunizing agents Age
BCG, Hep B (Hospital birth)........................................... Since birth
OPV - DPT (I), Hep B-> Penta 1, OPV 1 ............................ 2 months
OPV - DPT(II), Hep B-> Penta 2, OPV 2 .......................... 4 months
OPV - DPT(III), Hep B-> Penta 3, OPV 3......................... 6 months
Measles ....................................... 9 & 18 months

BCG ( Bacille Calmette - Guerin ): Live attenuated vaccine , given

intradermally , immunity last for 7 yrs.
Oral polo vaccine (Sabin vaccine ): Live attenuated poliovirus type 1-3 , given orally
,immunity life -long .
Diptheria toxid - Pertussis vaccine - Tetanus toxoid : 3 I/M doses given one month interval
immunity 1yrs
Measles vaccine : Live attenuated measles virus , single dose , 0.5 ml, I/M immunity -14yrs
HBV Vaccines
Plasma derived vaccine (heat inactivated or chemically inactivated subviral particles derived
from plasma collected from HBs Ag chronic carriers ) E.g. DMR HB plasma derived vaccine in
Myanmar.
Recombinant vaccine ( HBs Ag particles expressed from recombinant DNA in the yeats
Sacchromyces cerevisiae or Hanseunalle polymorphi )
Schedule
Infant or adult - 0 ,1 , 6 months

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For rapid immunization - 0 , 1 , 2 months Booster at 6 months
Dose:>10 yrs 20 ug , < 10yr 10 ug
Route and site : adult & children (I/M in deltoid muscle ) , Neonate & infant (I/M, antero-
lateral thigh)

Importance of antimicrobial drugs

Antimicrobial drugs: Chemotherapeutic substances that kill or inhibit the growth of

microorganisms already established in the tissues of the body . It exerts a selective toxicity on
the causal organisms of a given infection without being toxic to the tissue of the host .
Antibiotics: Specific diffusible soluble metabolic products of some living microorganisms
that kill or inhibit the growth of other microorganisms e.g. Penicillin is produced from
filamentous fungui ; Penicillium species .
Chemotherapy: Treatment by Chemotherapeutic agents .
Chemoprophylaxis: Prevention by chemotherapeutic agents .

Mechanism of action of anti-microbial drugs

1. Effect on cell wall e.g. , penicilin , cephalosporin , ketoconazole
2. Effect on protein synthesis e.g.,tetracycline , chloramphenicol
3. Effect on metabolic pathway e.g., sulfonamides , isoniazid
4. Effect on DNA e.g. , quinolone , erythromycin
5. uncertain site of action e.g. , metronidazole

Dangers of indiscriminate use of anti-microbial drugs

1. Hypersensitivity
2. Super-infection
3. Masking of serious infection
4. Direct drug toxicity
5. Drug resistance

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 Anatomy of Bacteria

Essential structure Additonal structure

1. Cell wall 1. Plasmid
2. Cytoplasmic membrane 2. Inclusion granules
3. Cytoplasm 3. Capsules , micro-capsule
4. Ribosomes 4. Flagella
5. Nuclear body 5. Fimbriae
6. Bacterial spores
maximum tolerated dose
chemothesapaite Index =---------------------------------------------------
minimum curative dose

Physiology of Bacteria

Oxygen & carbon - dioxide requirements

1. Strict aerobes : grow only in oxygen
2. facultative aerobes: grow in reduced oxygen concentration
3. Strict anaerobes: grow only in absence of oxygen

Temperature requirements
1. Optimum : 37°C
2. Mesophilic : 25 -40 C
3. Psychrophilic : <20 C
4. Thermophilic : 55 - 80 C

Moisture & Drying

Water is an essential ingredient of bateria & effect varies with different species
e.g. ,Treponema pallidum is highly sensitive whereas spores are resistant .

pH
Majority : 7.2 - 7.6 ,

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 lactobacilli : acidic pH

Light
Except phototrophic species , bacteria grow well in the dark. They are sensitive to UV
light & other radiations . Exposure to light may influence pigment production e.g.,
photochromogenic mycobacteria species .

Osmotic effect
Sudden exposure to hypertonic solution may cause plasmolysis .

Mechanical & Sonic stress

Bacteria cell wall may be ruptured by vigorous shaking or ultrasonic vibration .

Systematic classification
Based on morphology & gram stain reaction , bacteria are classified as;
Gram positive cocci
Staphylococcus aureus Abscess, food poisoning , toxic shock syndrome ,meningitis
Staphylococcus albus Endocarditis, nosocomial infections( hospital )
Staphylococcus saprophyticus Urinary tract infection
Streptococcus pyogenes Celllitis, tonsillitis, rheumatic fever, pos-strep glomerulonephritis
Streptococcus viridans Dental caries , endocarditis
Streptococcus pneumoniae Pneumonia, meningitis , endocarditis
Streptococcus agalactiae Neonatal sepsis, meningitis
Streptococcus faecalis Abdominal abscess, urinary tract infection , endocarditis

Gram positive bacilli

Corynebacterium diphtheriae Diphtheria
Bacillus anthracis Anthrax
Bacillus cereus Food poisoning
Clostridium tetani tetanus
Clostridium botulinum Botulism

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Clostridium perfringens Food poisoning,gas-gangrene

Gram negative cocci

Neisseria gonorrhoeae Gonorrhoea
Neisseria meningitidis Meningitis

Gram negative bacilli

Escherichia coli Urinary tract infection , diarrhoea / dysentery syndrome
Salmonella typhi & paratyphi Enteric fever
Shigella species Bacillary dysentery
Proteus species Urinary tract infection ,pneumonia , bacteraemia
Pseudomonas species Urinary tract infection, wound sepsis , pneumonia, corneal ulcer
Klebsiella species Nosocomial infection ,pneumonia , urinary tract infection
Bordetella pertussis Whooping cough
Yersinia pestis Plague
Bacteroides species Wound infections, Post partum sepsis.

Gram negative comma bacilli

Vibrio cholerae Cholera
Helicobacter pylori Gastritis , gastric ulcer, adenocarcinoma stomach

Acid fast bacilli

Mycobacterium tuberculosis Tuberculosis
Mycobacterium leprae Leprosy
Atpical mycobacteria Atypical tuberculosis

Spirochetes
Treponema pallidum Syphilis
Leptospira interrogans Leptospirosis

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Obligate intracellulai parasites
Chlamydia trachomatis Trachoma , conjunctivitis, genital infection , reapiratory
infections
Chlamydia pneumoniae Acute respiratory infection
Rickettsia tsutsugamushi Scrub typhus
Coxiella burneti Q fever

Wall - less bacteria

Mycoplasma pneumoniae Pneumonia, tracheobronchitis, pharyngitis
Mycoplasma hominis Pyelonephritis , pelvic inflammatory disease (PID) ,postpartum
sepsis
Ureaplasma urealyticum Non-gonococcal urethritis

Common bacterial Infactions

Staphylococcal Infections
Infectious agents: Staphylococcus species, Gram positive cocci in irregular clusters .
Diseases: 2 forms ; invasive and toxigenic
Invasive diseases are charaterized by abscess formation ,generally in cutaneous tissue in
healthy individuals . Patients who are debilitated , immunosuppressed , and who
have been extensively operated upon may develop deep abscesses in any organ system.
Toxigenic diseases are food poisoning , toxic epidermal necrolysis ,scalded baby
Syndrome, Toxic shock syndrome .
Reservoir : Humans
Mode of transmission: the major site of colonization is the anterior nares . Transmission
may be direct contact with patients or carriers , or indirect via articles soiled with discharges
from lesions of infected people . Autoinfection is responsible for one-third of infections .
Hands are the most important vehicle for transmitting infecton .
Diagnosis : Clinial and bacteriological comfirmation .
Prevention: Hand washing reduces spread.

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Treatment : Appropriate antibiotics(Penicillin groups).

Streptococcal Diseases
Infections agent: Streptococcus species, Gram positive cocci in chain .
Reservor: Humans
Mode of transmission: large respiratory droplets or direct contact with patients or nasal
carriers. Contamination of milk or egg products by humans appears to be the important source
of food-bone episodes .
Incubation period: Short , usually 1-3 days
Period of communicability: In untreated cases with purulent discharge , weeks or months,
whereas with adequate penicillin therapy ,24 hrs .
Diagnosis: Clinical & bacteriological confirmation
Prevention : Adequate penicillin treatment of Streptococcal pharyngitis within 10 days
of onset will prevent rheumatic fever . Long acting penicillin perparation is used to prevent
recurrences of rheumatic fever. Patients with history of rheumatic fever or rheumatic heart
disease must receive prophylaxis before undergoing procedure e.g.dental extraction which can
cause transient bacteremia.

Gonorrhoea
Infection agent: Neisseria gonorrhoeae , Gram negative kindney shaped diplococci.
Reservoir: Humans
Mode of transmission :Sexual, contact with the infected birth canal (ophthalmia neonatorum)
Incubation period : Usually 2-7 days
Diagnosis : Clinical and bacteriological confrimation . In males , a purulent discharge
from the anterior urethra with dysuria appears 2-7 days after an exposure. Infection may be self-
limited , or result in chronic carrier state. In females , a few day after exposure , an initial
urethritis or cervicitis occurs . About 20% develop endometritis, salpingitis or pelvic peritonitis ,
and subsequent risk of infertility and ectopic pregnancy.
Prevention : Appropriate condom used
Avoid Sexual contact with carriers
Treatment: Appropriate antibiotics (Cephalosporin group, Gentamycin).

20
Diphtheria
An acute bacterial disease caused toxigenic strain of Corynebacterium diphteriae.
Primarily involue tonsils , pharynx, larynx,nose, skin & sometime the conjunctivae of genitalia.
The characteristic lesion is patches of an adherent grayish membrane with a surrounding
inflammation.
Inapparent infection outnumber clinical cases .
Nasal diphtheria - mild, often chronic , one sided nasal discharge , excoriation
Pharyngotonsillar diphtheria- sore throat with enlarged , tender cervical lymph node
Laryngeal Diphtheria - serious in infant & young children
Cutaneous diphtheria - indistinguishable to impetigo
Late effects of absorption of toxin appear after 2-6 week include cranial , peripheral nerves
palsies & myocarditis.
Case fatality -5-10%
Reservior - humans
Mode of transmission- contact with patients or carriers soiled with discharge from lesions of
infected people . Raw milk has served as a vehicle .
Incubation period - Usually 2-5 days
Period of communicability- Variable (usually 2 week or less)
Diagnosis- Clinical and bacteriological confirmation

Differential diagnosis- Streptococcal & viral pharymgitis, vincent’s angina, infectious

mononucleosis oral syphilis , candidiasis
Pervention- DPT vaccination
Treatment- Antibiotic and anti-toxin

Anthrax
Infectious agent: Bacillus anthracis , gram positive , encapsulated spore - forming
aerobic bacilli
reservior: Herbivorous animals
Mode of tranamission: Contact with tissue of animal (Cutaneous), inhalation of spores
(pulmonary) and ingestion of contaminated meat (Gastrointestinal)
Incubation period: A few hours to 7 days

21
Period of communicability: Man to man transmision ;rare .Spore contaminated artical & soil ;
infective for decade
Diagnosis: Clinical and bacteriological confrimation
Prevention: Cell free vaccine to high risk personel .Dispose animal faeces by burning
or by deep burial in lime pit . Decontaminate animal products; gas sterilized commercial
wool ,hair & hides in endemic area, wear proective clothing or gloves when handling potentially
infected material . Active immunization of domestic animals.
Treatment: Antibiotic

Tetanus
Infection agent: Clostridium tetani , gram positive spore -bearing anaerobic bacilli
Reservior: Instestine of horse & other animals, including humans (a harmless normal
inhibitant)
mode of transmission: Tetanus spores introduced into the body usually through a puncture wound
contaminated with soil , street dust or animal or human feces ;through lacerations , burns.
Incubation period: Usually 3-21 days ( 1day to several month )
Diagnosis: Clinical and bacteriological confirmation . It is characterized by painful
muscular contractions (masseter “ risus sardonicus ’’and neck muscles “lock jaw’’, trunk
muscles opisthotonus ). Abdominal rigidity is a common first sign suggestive of tetanus in older
children & adults.
Prevention: UCI with tetanus toxoid (DPT , DT , TT )
Treatment: Surgical wound debridement , Antibiotics,Tetanus immune globulin

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 Gram Positive Spore-Forming Bacilli (C. Tetani)
Leptospirosis
Infection agent: Leptospira interrogans; tightly coiled , thin flexible spirochetes , one end
is often bent forming a hook.
Reservoir & Source: Animal (Rodents). Patients after first week of illness
Mode of transmission: Inoculative method ;penetration of mucous membrane or breaks in
skin.
Incubation period: 1-2 weeks
Diagnosis: Clinical (fever,intense headache, jaundice ,haemorrhage ,nephritis ) and
bacteriobiological comfrimation (Dark ground microscopic examinition of blood and urine,
serology )
Prevention: Avoid exposure to potentially contaminated water, Control rodents. Give
chemoprophylaxis during heavy exposure . Vaccinate farm & pet animal.
Treatment: Antibiotics

Cholera
Infectious agent: Vibrio cholerae ; gram negative coma shape bacilli with a single polar
flagellum . They are actively motile, falcultative anaerobes..
Reservoir: Humans . Vibrios survive in water for up to 3 weeks
Mode of transmission: Person to person contact, by water ,food ,and flies.
Incubation period: 1-3 days
Period of communicability: variable (usually 2 weeks or less)
Diagnosis: Clinical (abrupt onset of watery diarrhoea due to enterotoxin which
causes hypersecretion of fluid & eletrolyte in small intestine ) and bacteriological confrimation
Prevetion: Health education ; Active immunization with cholera vaccine .
Treatment: Prompt fluid & eletrolytes replacement

23
 Gram Negative Comma Bacilli
Enteric fever
Infectious agent: Salmonella typhi, Salmonella paratyphi A,B,C: gram negative
bacilli,motile by peritrichous flagella.
Reservior: Humans ; patients & carriers
Mode of tranamission:Vehicle -borne indirect contact with articles soiled with dischages from
lesions of infected people
Incubation period : 10-14 days
Diagnosis: Clinical (An acute severs illness, containous fever,step-ladder pattern
,bradycardia , headache, apathy , prostration , splenomegaly ,maculopapular rash (rose-sport)
,leucopenia ,constipation followed by “ peasoup’’ diarrhoea ,abdominal
distention),bacteriological (1week blood culture,2,3 week stool & urine culture) and
serological(Widal test)confirmation.
Prevention: Health education , TAB vaccination
Treatment: Appropriate antibiotics

Whopping cough
Infectious agent: Bordetella pertussis , small gram negative bacilli with capsule.
Mode of transmission: Via reapiratory droplets.
Incubation period: 1-2 weeks
Diagnosis: Clinical (disintegration of organisms libreate toxin that irritate respiratory
epithelial cells , catarrhal , paroxysmal , convalescent stages)and bacteriological confrimation
Prevention: DPT , DT vaccination
Treatment: Antibiotics and Hyperimmune globulin

Plague

24
Infectious agent: Yersinia pestis: a gram negative bacilli, bipolar staining (safety pin appear
ance) .
Reservoir: Wild rodents
Mode of transmission: Zoonosis . By rat flea Xenopsylla cheopis ) bite or contact
Incubation period: 2-7 days
Diagnosis: Clinical (high fever , painful lymphadenopathy; bubonic plague , cough
,blood- stained sputum ; pneumonic plague , haemorrhage;septicamic plague)and bacteriological
confirmation.
Prevention: Anti-rodent , anti- flea measures, vaccination
Treatment: Antibiotics

Tuberculosis
Infectious agent: Mycobacterium tuberculosis , Mycobacterium bovic & other atypical
mycobacteria ; acid fast bacilli.
Mode of transmission: Via droplets produced by coughing . Raw milk has served as a
vehicle .
Diagnosis: Clinical (pulumonary tuberculosis ; cough more than 3week , fever ,
weight loss, extrapulumonary tuberculosis , miliary tuberculosis )and bacteriological (sputum
smear microscopy with Ziehl Neelsen stain , LJ media )confirmation.
Prevention: BCG vaccination , socio -economic development , health education
Treatment: DOTS (anti-TB drugs).

Leprosy
Infectious agent: Mycobacterium leprae; acid fast bacilli arranged in cigar bundles shapes.
Reservior: Humans
Mode of transmission: Contact with patients. Bacilli remain viable for at least 7 days in
dried nasal secretion .
Incubation period: 9 month to 20 years
Diagnosis:Clinical (affect cooler parts of the body ; skin, peripheral nerve ,Types; lepromatous
(nodular skin lesions) , Tuberculoid ( macular skin lesions with severe asymmetric nerve
involvement), Borderline (Indeterminate )and bacteriological confirmation
Treatment: Rifampicin , depsone , clofazimine .

25
 Viruses in general
. Obligate intracellular parasites
. Smallest infectious agents.
. Consist of either DNA or RNA but not both with protein capsid.
. Some have extra-lipoprotein covering derived from host cell membrane.
. Certain viruses have Haemagglutinin & Neuraminidase spikes .
. Can only grow in living cells(developing chick empryo,tissue culture ,intact
animal)
Classification

Medically important DNA viruses

Pox virus
Variola major & minor smallpox
Cowpox Localized ulcerating lesion
Vaccinia Localized lesion , used for smallpox vaccine
Monkeypox Small-pox like illness
Mollussum contagiosum Benign skin nodule
Parvovirus Aplastic crisis (B 19 infection )
Papovavirus
Human Papilloma virus warts , laryngeal papilloma , laryngeal carcinoma
Adenovirus Respiratory tract infection , conjunctivitis, gastroenteritis,
urinary tract infection ( acute haemorrhagic cystitis)

Herpesviruses
HHV 1(herpes simplex 1) Oro-pharyngeal disease, kerato-conjunctivitis,skin infections , en-
cephalitis
HHV 2(herpes simplex 2) Genital herpes , neonatal herpes
HHV 3(Varicella zoster ) Varicella (chickenpox), Zoster (Shingles)
HHV 4(Epstein Barr ) Infectious mononucleosis, oral hairy leukoplakia, tumors
HHV 5(Cytomegalovirus) Infectious mononucleosis ,congenital & perinatal infections
HHV 6 Exanthema subitum ( roseola unfantum, or 6 disease),
hepatitis, pneumonia

26
HHV 7 ?
HHV 8 Kaposi’s sarcoma , primary effusion, lymphoma

Medically important RNA viruses

Retroviruses
Human immunodeficiency virus (Acquired immunodeficiency syndrome).
Myxoviruses
Influenza viruses Uncomplicated influenza, pneumonia, Reye’s syndrome
Parainfluenza virus Common cold , laryngotracheobronchitis , bronchiolitis pneumonia
Mumps virus Parotitis , aseptic memingoencephalitis , orchitis ,thyroiditis,
aqueductal stenosis, hydrocephalus, polyarthritis ,pancreatitis , nephritis.
Measles virus Measles , acute encephalitis,SSPE,giant cell pneumonia
Respiratory syncytial virus Bronchiolitis , pneumonia
Rubella virus German measles , post natal rubella, congenital rubella syndrome.
Picornaviruses
Enterovirus
-Polioviruses type 1-3 Poliomyelitis
-Coxsackie A type 1-24(no23)Vesicular pharyngitis, hand-food-mouth disease,haemorjagic
conjunctivitis
-Coxsackie B type 1-6 Pleurodynia ,aseptic meningitis comon colds,diarrhoea, hepatitis
-ECHO types 1-33(no10,28) aseptic meningitis ,infantile diarrhoea, common colds
-Entroviruses type 68-71 Respiratory tract infections, haemorrhagic conjunctivitis,
meningitis
-Rhinovirus Common colds
Corona virus
SARS corona virus Severe Acute Respiratory syndrome(atypical pneumonia)

Arboviruses
Dengue virus Dengue fever ,dengue haemorrhagic fever, dengue shock
syndrome
Japanese B Encephalitis virus Japanese B Encephalitis
Rhabdovirus
Rabies virus Rabies

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Hepatitis Viruses

Virus Hepatitis A Hepatitis B Hepatitis C Hepatitis D Hepatitis E

Genome ssRNA ssDNA ssRNA ssRNA ssRNA
Envelope Nil Yes Yes Yes(HBsFg) Nil
Stability Heat/acid Acid sensitive Ether sensitive Acid sensitive Heat
Transmission Fecal-oral Parenteral Parenteral Parenteral Fecal-oral
Prevalence High High Moderate Low
Regional
Fulminant disease Rare Rare Rare Frequent In pregnant
Chronicity Never Often Often Often Never
Oncogenicity No Yes Yes ? No

Viral hepatis B
Infectious agents: Hepatitis B virus; DNA virus , Envelope (+)
Source: Patients and carriers
Mode of transmission: Sexual, parenteral , vertical
Incubation period: 6 weeks to 6 months
Clinical outcome: Inapparent , anicteric , icteric,fulminant hepatitis
Carrier-->Adult 15%, children 85%,neonate 90%
Chronic hepatitis , cirrhosis ,hepatocellular carcinoma
Diagnosis Serological markers
1. HBs Ag-surface antigen , present during incubation period , acute stage , convalescence,
chronic carrier
2. HBe Ag-persent during incubation period ,acute stage, convalescence, indicates
infectivity
3. HBc Ag-core antigen in liver cell
4. HBV DNA-present during incubation period , acute stage, increase infectivity
5. HBc Ab(anti-HBc 1gM)-present in acute stage
6. HBe Ab(anti-HBe)-present in later acute stage ,convalescence, decrease infectivity
7. HBs Ab(anti-HBs)-present in convalescence, after vaccination ,indicate immunity

Hepatitis Serology
1. HBs Ag + IgM anti HBc = Acute infection

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 2. IgM anti HBc > 6 mths = Chronic infection
3. HBe Ag = Acute or chronic infection
4. Anti HBe Ag = Benign outcome
5. Anti HBc = Current or Previous infection
6. Anti HBs = Recovery or Immune after vaccine

Prevention & Control

1. General measues
i. Screening of donors (Blood, organ, etc )
ii. Use blood & blood products only if necessary
iii. Disinfection -0.5 - 5% NaHOCL(sodium hydrochloride) solution
iv. Use of glove , masks, goggles , protective clothing , disposable needles
v. Health education ; community ,carrier contant
2. Specific measures
i. Hepatitis B vaccine
ii. Hepatitis B Immune Globulin
iii. Interferon
iv. Antiviral

Acquied Immunodeficiency Syndrome

Causal Organisms - Human Immunodeficiency Virus ( HIV-1 and HIV-2 ).

AIDS is a severe disease syndrome representing the late stage of human
immunodeficiency virus infection . 70% of cases are symptomatic , manifests erythematous
maculopatular rash on the trank associated with fever and systemic effects ; retro-orbital pain ,
lymphadenopathy .Virus mainly affects immune system and suppress all functions .

loss of defense ( opportunistic infections )

Protozoa : Toxoplasmosis , cryptosporidiosis
Fungi: Candidiasis , cryptococcosis , histoplasmosis, pneumocystis carinii
pneumonia(PCP).
Bacteria: Tuberculosis , E-Coli infections , Bacterial Skin Infections.

29
Virus : Cytomegalovirus , herpes virus , hepatitis B virus , human papilloma virus
infections
Loss of surveillance ( malignancy)
Kaposi’s sarcoma, Burkitt’s lymphoma, anogenital cancer
Reservoir- Humans
Mode of transmission- Blood borne , sexual,vertical
Incubation period - variale ( 10 - 20 yrs)
Period of communicability- unknown ; presumed to begin early after onset of HIV infection
and extend throughout life .
Diagnosis- Clinical and HIV antibody testing (screening )
Prevention - General measures ( same as Hepatitis B infection )
Treatment- Anti-retroviral therapy + symptomatic treatment of opportunistic infection

Myxoviral Infections :
Influenza
Infectious agent: Influenza virus type A,B,C ; single stranded RNA virus (8 segments )
Envelope (+) , contains haemagglutinin & neuraminidase protein spikes .
Tissue tropism: Epithelial cells of respiratory tract
Source : Patients ( 1-2 days before and after onset)
Reservior : All mammalian influenza viruses derive from avian influenza reservior
(H5N1)
Mode of transmission: Person to person by air - borne spread , by contact with
contaminated hands or surface
Incubation period; 1-4 days
Diagnosis : Clinical ( abrupt onset of high fever , chills , myalgia , malaise , headache,
dry cough . Secondary bacterial invasion --> pneumonia , original antigenic phenomenon make
influenza epidemic or pandemic forms ) and laboratory diagnosis make by serology & viral
isolation from nasal washing / throat swabs ( taken within 3 days )
Prevention : Active immunization (influenza vaccine for high - risk group )

Mumps
Infectious agents : Mumps virus ,RNA virus , envelope (+), contains haemagglutinin &
fusion, protein spike.
Tissue tropism: Salivary glands , testes , ovary, pancreas , thyroid, central nervous system
Source: Humans are only natural host

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Mode of transmission: Person to person by direct contact air - bone spread, through
fomites con taminated with saliva or urine
Incubation period : 1-3 weeks
Diagnosis : Clinical ( low grade fever , malaise, anorexia , enlargement of parotid
glands as well as other salivary glands . Oophritis, orchitis-->infertility)and laboratory diagnosis
made by serology & viral isolation from saliva, CSF ,urine (taken within 2 wks ) .
Pervention : Active immunization (live attenuated mumps virus vaccine ).

Measles
Infectious agents : Measles virus ; RNA virus ,Envelope (+), contains haemagglutinin &
fusion, protein spkie .
Tissue tropism: Epithelial cell of respiratory tract , skin , conjunctiva
Source : Human are only natural host
Mode of transmission Person to person by air-borne spread

Incubation period : 9- 11 days

Diagnosis : fever , sneezing , coughing , redness of eye , koplik’s spot in the mouth ,
maculopapular rash --> 4 days fever , begin on face , neck and shoulders --> post measles stains
. Secondary bacterial invasion most often with beta haemolytic strpetococci --> giant cell
pneumonia , otitis media , encephalitis , post - measles GE,subacute sclerosing panencephlitis
( after 5- 15 yrs )and laboratory diagnosis made by serology & viral isolotion from
nasopharyngeal swab , blood ( taken 2-3 days before the onset of symptom up to 1 day
after the appearance of rash ).
Pervention : Active immunization ( attenuated live vaccine , UCI -9 months of age )
Passive immunization ( immunoglobulin from pooled normal adult sera)

Rubella ( German measles )

Infectious agents : Rubella virus , RNA virus
Tissue tropism: Epithelial cells of respiratory tract , cervical lymph node
Reservoir: Humans
Mode of transmission: Person to person by direct contact or air- borne spread , vertical
Incubation period : 2-3 weeks
diagnosis: Clinical ( Acute febrile illness , rash starts on the face , extends over the
trunk & extremities , posterior auricular and suboccipital lymphadenopathy, in women;
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transient arthralgia and arthritis , thrombocytopenic purpura and encephalitis ) and laboratory
diagnosis made by serology & viral isolation . Congenital rubella syndrome occurs in up to
90% of infants born to mother acquired rubella infection during the 1st trimester of pregnancy ;
deafness , cataract , microcephaly, mental retardation , congenital heart disease )
Prevention: Active immunization ( attenuated live rubella vaccine )

Severe acute reaspiratory syndrome ( SARS)

Infectious agent: SARS corona virus ( SARS coV); New type of corona virus . RNA virus .
It mutate easily and emergence of new mutants trigger epidemic .
Incubation period : 2-10 days
Clinical findings :
1. Asymptomatic or mild respiratory illness
2. Moderate : Temperature >100.4 F + one or more of clinical respiratory illness
3. Severe : Signs & symptoms of 2+ X-ray evidence of pneumonia , respiratory distress
syndrome
Mode of transmission : Droplets spread , indirect contact though formites ( contaminated with
respira
tory secretion & body fluids ), faecal -oral route, contaminated blood .
Diagnosis:
1. Specimens , respiratory tract specimens, blood, stool , post- mortem tissue specimen .
2. Laboratory test; Detection of antibody ( ELISA, IFA), RNA of SARS CoV(PCR), cell
culture.
Poliomyelitis
Infectious agents : Polivo virus type 1,2,3. Small RNA virus , Envelope (-)
Tissue tropism : Nervous system
Source: Partient & people with inapparent infections
Mode of transmission: Ingestion of contaminated food & drinks
Incubation period: 1-2 weeks
Diagnosis: Clinical ( Primary multiplication in tonsils ) , no symptoms

32
 ( inapparent abortive) , invasion of blood stream & nervous tissue (
non - paralytic, aseptic meningitis ) , destruction of anterior horn
cell ( flaccid paralysis ) and laboratory diagnosis made by
serology& viral isolation form throat swab , stool , CSF.
Prevention: Active immunization ( Sabin’s trivalent oral polio vaccine).

Dengue( Break-bone) fever

Infection agents: Dengue virus type 1-4 ; RNA virus , Elvelope(+)
Tissue tropism: Endothelial lining of small blood vessels
Source-Reservoir: man , mosquito
Mode of transmission : Vector borne , bite of infected female Aedes aegypti
Incubation period: 1-3 weeks
Diagnosis: Clinical (Dengue fever ; saddle back type , severe pain in back,
joints, muscle, eyeball ) Hess test positive.
Dengue haemorrhagic fever- Fever with Coffee ground Vomittus, rash and petechiae on 3 rd 4th
day, malena, fever subsides rapidly after 2-7 days.
Dengue shock syndrome ; shock , DIC
laboratory diagnosis - made by serology, PCV,
Prevention : Anti- mosquito measures , personal protection , health education

Rabies
Infectious agents: Rabies virus; RNA virus, bullet shape. Envelope(+), contains
protein spike.
Tissue tropism: Sub-maxillary salivary glands, central nervous system , pancreas ,
kidney, heart , retina, cornea
Reserviors: All warm-blooded animals
Mode of transmission : By bite of rabid animal , inhalation ( droppings of vampire bat ),by
direct contact of infected saliva through pre-existing scratches or
skin abrasion , corneal transplant
Incubation period : Depend on age , genetic background , immune status , viral strain ,
amount of inoculum, severity of lacerations , and the distance the
virus has to travel from site of entry to the CNS
Diagnosis: Clinical (a short prodromal phase; non-specific symptoms, sore

33
 throat, photophobia stc., an acute neurologic phase; nervousness,
sympathetic overactivity; lacrimation, pupil dilatation, excessive
salivation, perspiration, hydrophobia , convulsive seizures, coma,
death) and laboratory diagnosis made by finding of Negri bodies in
the brain or spinal cord.
prevention: Pre-exposure & post-exposure propylaxis with Anti-rabies vaccine
& Rabies immune globulin ( HRIG), anti-rabies serum.
Treatment: No successful treatment for clinical rabies.

Parasitology

It is the study of protozoa and helminthes and diseases caused by them.

Protozoa: A single cell like unit which is morphologically and functionally complete 3
organs of locomotion present; pseudopodia, flagella, cilia.
An active trophozoite --> inactive cyst (Encystment)
Reproduction; asexual, sexual
Helminths: Multicellular; cestodes, trematodes, nematodes
Common Protozoa of medical importance
1. Entamoeba histolytica Amoebiasis
2. Trichomonas vaginalis Trichomoniasis (vaginitis in female , urethritis in male)
3. Giardia intestinalis Giardiasis (diarrhoea , stearrhoea, acute enterocolitis)
4. Plasmodium species Malaria
5. Toxoplama gondii Toxoplasmosis

Amoebiasis
Infectious agent: A protozoan parasite; Entamoeba histolytica, exists in 2 forms: the hardy ,
infective quadrinucleated cyst and the more fragile, potentially pathogenic
trophozoite.
Reservoir: Humans, chronic patients or asymptomatic cyst passer

34
Mode of transmission:By ingestion of faecally contaminated food or water containing amoebic
cysts, which are relatively chlorine resistant. It may occur sexually
by
oral-anal contact.
Incubation peroid: 4 -5 days
Diagnosis: Clinical and bacteriological confirmation. Most infections are
asymptomatic. Intestinal disease varies from acute dysentery with fever, chills and bloody or
mucoid diarrhoea (amoebic dysentery- Anchovy sauce Pus) to mild abdominal discomfort with
alternating constipation & diarrhoea containing blood and mucus. Amoebic colitis may mimic
inflammatory bowel disease. Amoebic granuloma is sometimes mistaken for carcinoma .
Extra - intestinaloamoebiasis occurs as acute amoebic hepatitis, abscesses in liver, lung , brain
and ulceration of the skin .
Prevention: Health education & personal hygiene .

Malaria

Human malaria parasites Diseases

Plasmodium falciparum Malignant tertian malaria , pernicious malaria , falciparum malaria
Plasmodium vivax Benign tertian malaria , vivax malaria
Plasmodium malariae Quartan malaria , malariae malaria
Plasmodium ovale Ovale tertian malaria
Life cycle
2 hosts: Definitive host; Female anopheline mosquito ( sexual reproduction)
Intermediate host ; Man ( asexual reproduction )
Life cycle in man ( Schizogony)
Infective from to man ; Sporozoite
Pre- erythrocytic schizogony ( in Liver):Trophozoite, immature schizont , mature schizont
--> merozoite
Erythrocytic schizogony (in RBC): Young , old trophozoite --> immmature , mature schizont
-> merozoite
Repeated cycles , one cycle last 48 hrs
Exo-erythocytic schizogony: Absent in p-falcipaiun , present in p-vivax ,after one cycle of pre-
erythrocytic schyzogony --> some merozoite invade liver cell again ->RBC --> relapse
Gametogony : After certain period , some merozoites --> RBC --> male + female gametocytes

35
 Lifecycle of malaria parasite

Life cycle in mosquito (Sporogony )

Infective from to mosquito : Male & Female mature gametocytes
Fertilization -->sporozoites
Clinical features : Febrile paroxysm(completion of erythrocytic schizogony--> RBC rupture
-->release of merozoites , haemozoin pigments , malarial toxin ),
Splenomegaly ( macrophages --> phagocytosis ) ,
Anaemia
Pernicrious malaria :A series of phenomenon occurs during the course of an infection of p-
falciparum which , if not effectively treated , treatens the life of the patients within 1-3
days .
1. Cerebral malaria : hyperpyrexia , confusion , coma

36
2. Algid manaria : cold & clammy extremities with collapse
(a) Gastric type : Vomiting
(b) Choleric type: Diarrhea
(c) Dysenteric type:Blood in faces
3. septicaemic malaria : DIC, shock

Laboratory Diagnosis
Specimen : Peripheral blood
Time of specimen collection :P-falcipaiun: admission ,Fever with chills and rigor, a few hours
after the febrile paroxysm
p-vivax: any time
Microscopic examination : Thick film for screening . Thin film for species identification

Toxoplasma & Toxoplasmosis

Infectious agent : Toxoplasma gondii:Trophozoite and cyst forms
Life cycle : Definitive host : Cat , intermediate host : mammals , birds , man
Infective form : Tissue & faecal cyst , trophozoites
Mode of transmission:Ingestion , inhalation (trophozoite in sputum), inoculation through skin
Clinical features : Mild lymphatic form , acute fulminating disseminated infection , chronic
toxoplasmosis. Congenital : Abortion , still –birth, Intracerebral calcification , choroidoretinitis ,
hydrocephaly , microcephaly, convulsion.
laboratory diagnosis : Lymph-node biopsy , microscopic exam -spleen, bone marrow , CSF
,Serology
Prevention & control :Health eduction especially to pregnant woman

Trichomonas & trichomoniasis

Infectious agent : Trichomonas vaginalis :Genital flagellate , trophozoite only
Infective form: Trophozoite
Mode of transmission: Sexual contact
Clinical features : Vaginitis , urethritis ; frothy yellow discharge , pruritus , irritation , pain
Laboraatory diagnosis: Female --> frsh vaginal discharge , urine

37
 Male --> urethral discharge , prostatic massage , semen
Prevention & control :Same as STDs

Giardia & Giardiasis

Infectious agent : Giardia intestinalis ( G-lamblia);Intestinal flagellate; trophozoite & cyst
forms
Infective form: Mature quadrinucleated cyst
Mode of transmission: Ingestion
Clinical features: Asymptomatic , diarrhea, steatorrhoea(watery ,semisolid , greasy,
bulkyfoul smelling), vitamin deficiency especially vitamin A, acute enterocolitis
Laboratory diagnosis: Microscopic examination of stool or duodenal aspirate -->cyst/
trophozoite
Prevention & control: Personal hygiene & health education

Helminths
Difference between Cestodes & Nematodes

Cestodes Nematodes
Shape Tape like , segmented Elongated, cylindrical, unsegmented
Sexes Not separate Separate
Heat Suckers + ,hooks often+ No suckers , no hooks

38
Principal features of (a) nematodes (b)cestodes (c) tematodes

39
 w
Common Helminthic infection s:Cestodes & Intestinal nematodes

Transmission Infective form Clinical condirions

Intestianal Nematodes
Ascaris lumbricoides Ingestion Embryonated egg Larva:pneumonia alergy
Inhalation Adultworm:Spoliative,toxic,
mechanical ectopic ascariasis
Trichuris trichiura same same Diarrhea, prolapse rectum in
children
Strongyloides stercoralis Penetration, Filariform larva Larva:rash,pruritus,pneuminia
Autoinfection Adult:diarrhea,hyperparasitism
Hookworms same same Larva:dermatitis,bronchopneu
-monia
Adult: Anaemia,malabsorption
abdominal pain,mental
&physi -cal retardation
Enterobius vermicularis Ingestion, Egg containing Pruritus ani,GI disturbance,ps
inhalation Tadpole larva -ychologicalproblem,migrating
Autoinfection female--> GUT
Retroinfection Salpingitis,urethritis,nocturmal
enuresis etc.

Cestodes
Taenia solium Ingestion-pork Cysticercus GI symptoms, cerebralcysticce
cellulosae -rcosis--> epilepsy, SOL sympt
Taenia saginata Ingestion-beef cysticercus vibis -oms retinal detachment GI
symptoms
Hymenolepis nana Hand-->mouth embryonated egg
(Haxacanth embryo -Enteritis

40
 Ascaris lambricoides Eggs

Taenia Solium and Taenia Saginata

Key to the diagnosis of intestinal nematodes

Stool RE: Eggs in stool --> Bile stained (Ascaris numbricoides,Trichuris trichiura)
--> Colourless (Hookworms, Enterobius vermicularis )
Eggs on perineal skin -->enterobius vermiculris
Larvae in stool --> strongyloides stercoralis

41
Pervention & control

1. Proper disposal of excreta

2. Treatment of parasitized individual
3. Proper cooking of food and drinking of boiled water
4. Personal hygiene & health education

Tissue nematodes
Wuchereria Bancrofti & Filariasis
Infectious agent: Wuchereria bancrofti
Infective form: Third stage larva
Life cycle: Definitive host: man, Intermediate host: Mosquito (Culex pipiens
fatigans)
Mode of transmission: Inoculative method by the bite of mosquito
Clinical featres:
Classical filariasis (due to developing worms & adult); allergic manifestation ,
lymphangiovarix, lymphorrhea, chylorrhagia, elephantiasis, secondary bacterial infection

42
Occult filariasis (due to microfilaria): allergic manifestaion (eosinophilic granuloma )
Laboratory diagnosis : Detection of mocrofilaria in peritheral blood ( specimen take
between 10 Pm to 2 am ) , Chylous urine , exudates of lymph varix & hydrocele fluid, detection
of adult worms in lymph node biopsy , calcified worm by X-ray, Serology .
Prevention & control :Anti-mosquito measure , personal protection

Common Trematode infection

Species Habitat Clinical manifestion

Schistosoma haematobium Blood Haematuria,Ca bladder

Schistoma mansoni Blood Dysentery
Schistosoma japonicum Blood Dysentery, Ca liver

Faciola Hebatic Liver Biliary colic

Paragonimus westermani Lunch Haemoptysis

Skin and wound infections

Bacteria Fungi Viruses

Skin
Pyoderma Streptococcus pyogenes
Bullous Staphylococcus aureus
Folliculitis Staph . / Pseudomonas Candida albicans
Acne Propionibacterium
Furuncles Staphylococcus aureus
Carbuncles Staphylococcus aureus
Erysipelas Streptococcus pyogenes
Cellulitis Streptococcus pyogenes
Syaphylococcus aureus
Haemophilus influenzar
Intertrigo Staphylococcus aureus Candida albicans
Enterobacteriaceae
Chronic Treponema pallidum Herpes virus
Haemophilus ducreyi

43
 Norcardia
Mycobacterium ulcerum
Mycobacyerium marinum
Wounds
Surgical (Cleam) Staphylococcusa aureus
Streptococcus pyogenes
Entetrobacteriaceae
Surgial (dirty) Staphylococcus aureus
Eentreobacteriaceae
Bacteroides
Traumatic Clostridium
Pseudomonas
Post-partum endometritis Clostridium
Bacteroides
Streptococcus pyogenes
Umbilical sepsis Staphylococcus aureus
Clostridium tertani
Burns Pseudomnas
Staphylococcus aureus Candida albicans
Enterobacteriaceae
Animal bites Pasteurella

Diagnosis
Specimen collection: Needle aspiration of pus, wound swap collected in sterile tightly
closed container . Anaerobic infection should be suspected when foul smelling discharge with
gas and necrotic tissue are present especially infections after bowel surgery , pulmonary
aspiration , abortion or animal bite . In that case , suitable transport media is needed .

44
 Eye , ear & sinus Infection

Major infectious causes of eye disease

Site Disease Bacteria Viruses Fungi Parasites

Eyelid Blepharits Staph.aureus

Lacrimal sac Dacryocystitis Staph. aureus

Congunctivititis Strep. pneumoniae

Conjunctiva Keratitis Strep. pneumoniae Adeno Aspergilus Acantha

Haemophilus Herpes -moeba
Cornea Keratoconjunctivitis Strep. pyogenes Measles
Both Staph . aureus Varilella zoster
Chlamydia
Neisseria
pseudomonas Candida

Aqueous or Enophthalmitis Staph. aureus Aspergillus

Vitreous humor Gram negative orgs

Uveal tract Uveitis

iris,ciliary body Iridocyclitis T.pallidul Herpes
Varicella zoster
Choroid+(retina) Choroidoretinitis Myco.tuberculosis Cytomegalo HistoplasmaToxoplas
Herpes Coccidoides -ma
Candida Toxocara
-canis
Soft tissue Periorbital cellulitis Staph. aureus
Haemophilus
Strep. Pyogenes
Common causes of ear infections
Otitis externa : Pseudomonas aeruginosa , proteus , escherichia coli, staphylococcus
aureus, Aspergillus

45
Acute otitis media: Sterptococcus pneumoniae , Haemophinus influenzae , staphylococcus
aureus pseudomonas aeruginosa , group B sterptococci
Chronic otitis media; Mixed flora

Common causes of sinus infection:

Acute sinusitis: Sterptococcus pneumoniae , Haemophinus influenzae (comon ),
Staphylococcus aureus, sterptococcus pyogenes
Chronic sinusitis: Same as for acute ; also gram negative enteric bacteria , mixed aerobic &
anaerobic bacteria , mucor in immunocompronised patient

Dental & Periodontl infections

Dental caries : Is the single greatest cause of tooth loss in the child and young adult . The
newly erupted tooth is most susceptible to the carious process .
The factors involved are
1. a susceptible host or tooth
2. The proper microflora ( plaque bacteria ) on the tooth ( streptococcus , anaerobic vibrio,
spirochetes , gram negative anaerobes ) and
3. a substrate from which the plaque bacteria can produce the organic acids that result in
tooth mineralization

Gingivitis : Inflammation spread to the marginal gingival. Acute necrotizing uncerative

gingivitis : Rapid ulceration of the tinter dental area of gingiva ,
painful & associated with poor oral hygiene and stress
Periodontitis : Inflammation around the necks of the teeth with progressive loss of teeth suport

Infectious of the respiratory tract

Upper respiratory infections & their causal organisms

Disease viruses Bacteria Fungi

Rhinitis Rhino Rare Rare
Adeno

46
 Corona
Parainfluenza
Influenz;
Respiratory syncytial
Coxsackie A

Pharyngitis /Tonsillitis Adeno Streptococcus pyogenes

Parainfluenza Corynebacterium diphtheriae
Influenza Neisseria gonrrhoeae
Rhino
Coxsackie A or B
Herpes simplex
Epstein Barr

Stomatitis Herpes simplex Spirochetes Candida

species
Coxsackie A Oral anaerobes
Peritonsillar/ None Streptococcus pyogenes
Retropharyngeal abcess Oral anaerobes
Staphylococcus aureus(area)
Haemophilus(usually in infant)

Middle respiratory tract infection & their causal organisms

Diseases Viruses Bacteria

Epiglottitis Rare Haemophilus influenzae
Streptococcus pyogenes
Streptococcus pneumoniae
Corynebacterium diphtheriae
Neisseria meningiditis

47
Laryngitis Parainfluenza Rare
Influenza
Adeno
Layngotracheitis/ Same as laryngitis Haemophilus influenzae
Layngotracheobronchitis Staphylococcus aureus
Bronchitis Parainfluenza Bordetella pertussis
Influenza Haemophilus influenzae
Repiratory syncytial Mycoplasma pneumoniae
Adeno Chlamydia pnemoniae
Measles
Lower respiratory tract infections & their causal organisms

Diseases Viruses Bacteria Fungi other

Acute pneumonia Influenza Streptoccus pneumoniae Candida albicans Mycplasma
Parainfluenza Staphylococcus aureus Aspergillus
Chlamydia Adeno Haemophilus influenzae Pneumocystis
carinii
Resp. syncytial Pseudomonas aeruginosa
Enterobactericeae
Mixed anaerobes
(Aspiration)
Chronic pneumoniaRare Myco.tuberculosis Coccidoides Paragonimus
Other Mycobacteria Cryptococcus
Nacardoa Histoplasma

Lung abscess None Mixed anaerobes Aspergillus sp; Entamoeba

histolytica
Actinomicetes
Nocardia
Staphylococcus aureus
Pseudomonas aeruginosa
Enterobactericeae
Empyema None Mixed anaerobes Rare

48
 Staphylococcus
Streptococcus pneumoniae
Pseudomonas aeruginosa
Enterobactericeae
Clinical features: Fever, sore throat , and cough with or without sputum, weight loss

Diagnosis:
1. Specimens: Throat swab for URTI ; it is best to take before treatment, before gurgle
or lozenges if possible. A good light is required to illuminate the throat. A clean wooden tongue
depressor or the handle of a clean spoon is used to press down the tongue. The throad swab is
then quickly placed in the throat and rubbed gently , but firmly over the tonsils, the posterior
pharyngeal
wall and particulary on any areas of purulent exudates. Swab must not contaminate with saliva.
Sputam for LRTI ; it is best collected in the morning soon after the patients wakes and
before any mouth wash and asked to cough deeply to produce sputum not saliva. Take care to
prevent the spread of infection while collecting sputum and collect in wide mouth screw capped
container . Label and send to the laboratory as soon as possible with the request form.

2. Direct microscopic examination , culture & Sensitivity testing , serology

Infection of the central nervous system

Types of infection
Meningitis: Infection of the meninges
Encephalitis: Direct invasion of the brain tissue
Brain abscess: Localized collection of pus in brain substance

Causal Agents
Bacterial
. Escherechia coli , Group B beta-haemolysing streptpococci ,Listeria monocytogenes,
Stretococcus pneumoniae, Haemophilus influenzae (Type b), Neisseria meningitides, Myco
bacterium tuberculosis , Treponema pallidum , Leptospira interrogans,
Staphylococci.

49
Vial
. Herpes simplex virus, Varicella zoster virus, Cytomegalovirus, Poliovirus, Measles
virus, Rabies virus

Fungal
. Cryptococcus neoformans, Candida albicans
Protozoal
. Entamoeha histolytica, Toxoplasma gondii

Mode of spread
. Haematogenous e.g., Neisseria meningitides
. Direct invasion via nerves e.g., Herpes simplex virus, Rabies virus
. Direct spread from a local focus of infection e.g., mastoiditis, otitis media, sinusitis

Clinical features: Headache, fever, vomiting, photophobia, neck stiffness, decreased level of
consciousness

Laboratory Diagnosis
Specimens- cerebrospinal fluid (CSF) 5-10 ml by lumbar puncture collected under aseptic
condition in 3 sterile screw-capped bottles with rubber liner (2 for Microbiology lab, 1 for
Pathology lab).Send as soon as possible. If delay, put in incubator at 37C.
Blood , Pus from abscess
Direct microscopic examination
Culture & Sensitivity
Infection of the gastrointestinal tract

Normal flora -Lactobacilli, Escherechia coli , Klebsiella, Proteus, Clostridium

Common GI infection: Food-borne infection
1. Bacterial food poisoning
a. Infection type; Salmonella food poisoning

50
 b. Toxin type -Staphylococcus aureus (dairy product, meat, salads, custard),
Bacillus cereus (reheated fried rice), Clostridium perfringens (under-cooked meat)
Clostridium botulinum (canned food, honey, smoked fish), Vibrio
parahaemolyticus (sea food)
2. Gastroenteritis: A syndrome characterized by vomiting and diarrhoea
3. Diarrhoea: Frequent loose or watrery stools & often vomiting & fever.
a. Bacteria- E. coli (ETEC, EPEC, EHEC, EIEC), Yersinia enterocolitica, Campylo
bacter
b. Virus -Roat virus, Adeno virus.
c. Fungi -Candida albican
d. Protozoa -Giardia lamblia, Cryptosporidium
e. Helminth -Round worns, Tape worms
4. Dysentery: E.coli (ETEC,EPEC,EHEC,EIEC), Yersinia enterocolitica ,
Campylobacter - abdominal pain & tenemus.
a. Bacillary dysentery- Shigella species, Escherechia coli 015:h7
b. Amoebic dysentery- Entamoeba histolytica
c. Ciliate dysentary- Balantidium coli.
d. Algid type Pernicious malaria- Plasmodium falciparum
From a practical clinical stand point , diarrheal illnesses can be divided into six clinical
presentation:
1. Simple diarrhea, managed by oral rehydration with solutions water, glucose &
electrolytes, with its specific etiology not important in management.
2. Bloody diarrhea (dysentery)
3. Persistent diarrhea that last at least 2 weeks
4. Severe purging as seen in ( cholera ).
5. Minimal diarrhea, associated with vomiting , typical of some (viral GE;) & toxin type of
food poisoning
6. Hemorrhagic colitis, with watery diarrhea containing gross blood but with no fever or
fecal leukocytes .

Food - borne disease are recognized by the occurrence of illness within a usually short, but
variable period of time (from a few hours to a few weeks) after consumption , among
individuals who have consumed foods in common. Prevention and control is regardless of the
specific cause& based on the same principle .

51
”Ten golden rules for safe food preparation
(WHO)”
(1) Choose foods processed for safety .
(2) Cook food thoroughly .
(3) Eat cooked foods immediately .
(4) Store cooked foods carefully .
(5) Reheat cooked foods thoroughly .
(6) Avoid contact between raw food and cooked food .
(7) Wash hands repeatedly .
(8) Keep all kitchen surfaces meticulously clean .
(9) Protect food from insects , rodents and other animals.
(10) Use safe water .

Diagnosis : Culture & sensitivity

Specimen: Stool, rectal swab, vomitus , food
Collection :In a sterile container with a tight , leak proof lid that must be sent as soon as
possible not longer than two hrs after collection . If any delay , put the specimen into the
suitable transport medium

Infection of the cardiovascular system

Infective endocarditis: Infection of the endocardium of the heart usually including valves
Bacteraemia: Transient presence of bacteria in the blood strean .
Septicaemia : Presence of actively multiplying bacteria and their toxins in the blood stream with
signs and symptons of shock .
Causal organisms of infective endocarditis :
Streptococcus viridans , Streptococcus faecalis , Staphylococcus epidermidis ,
Escherichia coli, Coxiella burletti, Candida albicans.

52
Pathogenesis: Valve damage ( e.g. , rheumatic fever , congenital anomalies ) or prosthetic valve
deposition of fibrin to which organism attach during transient bacteraemia ( e.g. , tooth
extraction).
Clinical features: Fever,night sweats,malaise,anaemia,anorexia
Causal organisms of septicaemia:
Staphylococcus aureus , Streptoccoccus pneumoniae , Neisseria gonorrhoeae,
Neisseria meningitidis , Salmonella typhi , Proteus species, pseudomonas aeruginosa,
Bacteroides spp.
Clinical features: Signs of shock ( hypotension, tachycardia, cold & clammy extremi
ties, disseminated intravascular coagulopathy in gram
negative
septicaemia)
Diagnosis: Blood culture & sensitivity . Prior to taking blood sample , skin
must be disinfected with solution I ( soap & water ), III(water iodine solution ) and II
( methylated spirit ). 5ml of blood then taken out with sterile disposable needle and inoculated
into blood culture bottle Label and send to laboratory promptly . Do not refrigerated for
2hrs.

Urinary tract infection

Infection of urinary tract: Urethra , Bladder , Ureter , Kidney
Causal organisms: Escherichia coil , proteus , Pseudomonas , Klebsiella , Staphylococcus
epidermitis, Staphylococcus aureus, Stapylococcus saprophyticus, Streptococcus faecalis,
Mycobacterium tuberculosis , candida albicans.
Predispofing factors
. Female > male
. Diabetes
. Pregnancy
. Tumors
. Benign prostatic hypertrophy

53
 . Stone
. Catheterization , instrumentation e.g. , cystoscopy
Clinical features: Dysuria , fever with chills & rigor , urgency , frequency , pain in supra
pubic region
Mode of transmission: Endogenous: ascending from perianal region , from blood steram
Exogenous: Catheter, cystoscope
Diagnosis :
Specimen: Early morning first voided , mid stream urine sample with clean catch
method ( male --> clean the glans penis , female --> clean the labia & seprate the labia )
must be collected into sterile wide mouth screw capped container . If delay in examination ,
keep at 4 C.
Macroscope exam: Color , turbidity , haematuria
Microscope exam : Unstained wet cover slip preparation (pus+bacteria + --> UTI RBC + -->
infection , stone , tumor , injury, blood disorder e.g. , ITP , viper
bite )
Prevention : Catheterization must be done only if necessary under strict aseptic precau
tion. Close drainage system preferable . Treat underlying cause .

Sexually transmitted diseases

Causal organisms Disease
Treponema pallidum Syphilis (Chancre )
Haemophilus ducreyi Chancroid
Chlamydia trachomatis LI - L 3 Lymphogranuloma venereum
Neisseria gonorrhoeae Gonorrhoeae
Chlamydia trachomatis D - K Non - gonococal urethritis
Ureaplasma urealyticum Non - gonococal urethritis
Candida albicans Candida vaginitis
Trichomonas vaginalis Trichomonas vaginalis
Entamoeba histolytica Amoebic vaginitis
Herpes simplex virus Genital herpes

54
Human papilloma virus Condylomata accuminata
Hepatitis B virus Viral hepatitis B
Human immuno deficiency virus Acquired immunodeficiency syndrome
Clinical features
1. genital ulcer e.g., chancre , chancroid , genital warts
2. discharge e.g., gonorrhoea , NGU (Non Gonococcal Urethritis)
3. others e.g., hepatitis , AIDS , cancer
Complications: Infertility ( gonorrhoea , NGU) , Abortion , still - brith
(Syphilis) , congenital infections by vertical transmission
(Syphilis , HIV ,HBV) Maligancy (HIV , HBV )
Diagnosis
Specimen: Discharge , exudates from ulcer , blood
Collected on a swab or inoculation wire loop
Vaginal discharge --> posterior fornix , cervical discharge -->
endocervix
Transport media needed for fastidious organism
1. Direct microscopic examination
2. Culture & sensitivity
3. Immunodiagnosis

Prevention & control :

1. Avoid multiple sex ,
2. Use mechanical prophylaxis ( condon ) ,
3. Early detection of patient & treatment

Bio - weapons

55
 Biological weapons are unique in their ability to inflict large number of casualties over a
wide area with animal logistics requirements and by means which can be virtually
untraceable .The ease and low cost to produce the agent , the difficulty and detecting its present
and protection (and treating its intented vicitms , and the potential to selectively target humans ,
animals , or plants conspire to make defense against this class of weapon particularly difficult .
Intrinsic features of biological agent which influence their potential for use as weapons include
pathogenicity ( infectivity & transmissibility ) , incubation period stability .
Biological agents
. Bacteria
. viruses
. Rickettsiae
. Chlamydia
. Fungi
. Toxins
Method of dissemination
. Aerosol: respiratory exposore , alimentary exposure , dermal exposure
. Contaminaton of food & water
. Others : through live arthropod vectors , through person to person spread
Defense
General: sanitation
Detection :attack indicators, diagnostic sampling
. Environmental sampling
. Specimen collection
. Specimen labeling
. Specimen handling & shipments
. Countermeasure
. Protective equipment : individual , collective
. Immunprophylaxis & chemoprophylaxis
. Management
. Decontamination of exposed personnel : primary , secondary
. Treatment : general supportive, barrier nursing , antibotic, antiviral , anti
toxin therapy
. Protection of health care personnel
. Handling of contaminated remains

56
 Microbiology of water
Drinking water supplies liable to contamination with sewage or other excreted matter
may cause outbreaks of intestinal of intestinal infection of pathorgentic organism e.g . , S. typhi
is the most direct prove of dangerous contamination but these parthogens , when present, are
scanty , and makes the test impracticable for ordinary purposes . Therefore , faecal pollutions are
tested for the presence of commensal intestinal bacteria, e.g . coliform bacilli, Escherichia coli,
Streptococcus faecalis or Clostridium perfringens.
Chorinated water supply : If the test reveals the presence of coliform bacili in 100 ml water
sample water treatment should be considered insufficient.
Non - chlorinated piped supplies: the presence if coliform count is between 10-25 ml of
water,and Escherichia coli is present in minimal numbers.
Water - borne Infections & causal organisms
1. Cholera Vibrio cholerae
2. Escherichia coli gastroenteritis EPEC, ETEC, EIEC
3. Enteric fever Salmonella typhi , paratyphi A, B,C
4. Bacillary dysentery Shigella species
5. Poliomyelitis Polioviruses types 1,2 and 3.
6. Viral hepatitis A&B Hepatitis A&B viruses
7. Amoebiasis Entamoeba histolytica
8. Giardiasis Giardia lamblia
9. Ascariasis Ascaris lumbricoides
10. Trichuriasis Trichuris trichiura
11. Hymenolepiasis nana Hymenolepis nana

MYCOLOGY

57
 * Eucaryotic organisms
* Microscopic ( mushrooms) or microscopic ( yeast, mycelia)
* Few cause human disease

Fungal Infections & their causal organisms

Superficial Malassesia furfur
Cutaneous Candida sp , Dermatophytes
Systemic Histoplasma capsulatum
Opportunistic Candida sp, cryptococcus sp , aspergillus sp

Laboratory diagnosis
Specimen: Superficial (skin scraping , hair including follicles , nail clipping , materia unter
nailbed ). Vaginal discharge , throat swap , tissue biopsy
Serum for serology , antigen detection
Direct microscopy : KOH mount , Gram stam
Culture
Serology

Malassesia furfur :
A part of normal flora , thick walked budding cells , curve hyphae +
Causes ptyriasis versicolor ; a superficial scaly skin infection with depigmentation

Dermatophytes : a group of related filamentous fungi

1. Epidermophyton Infects skin ( tinea corporis ) , nails tinea anguiun) , groin
(tinea cruris ) , feet (tinea pedis )
2. Microscoprum Infects hair , skin
3. Trichophyton Infects skin , hair , nail
Reservior: Man , animals , soil
Mode of transmission : Direct & indirect contact

Candida albicans : Commensal of mouth , gastrointestinal tract

58
Sources : endogenous
Clinical conditions:
1. Superfical : common , thrush , vaginal , skin , nail candidiasis
2. Invasive ( opportunistic) : Abscess in various organs , GIT , lungs , UTI
Predisposing factors : Diabetes, prolonged use of antibiotics , steroid theraby ,
immuncompromised state ; cancer , AIDS , radio theraty , prosthetic material (IV catheter ,
peritoneal dialysis cannula )
Prevention & control : avoid interfering with the normal balance of microbial flora &
normal host defense
Cryptococcus neoformans: Inhalation of soil contaminated with bird droppings
Clinical conditions
1. Primary infection --> lungs , usually symptomatic
2. Fungaemia in AIDS --> lungs (acute pneumonia ) meninges ( menigitis )
Aspergillus : A number of species
Mode of transmission: Inhalation of spores
Clinical conditions: Common in immunocompromised state
1. Diffuse lung infection / aspergilloma
2. Allergic alveolitis ( fever , cough , bronchospasm )
3. Chronic ear infection
4. Can disseminate into liver , kidneys , brian
5. Ca liver (aflatoxin )
Histoplasma capsulatum: dimorphic fungus
Mode of transmission: Inhalation of spores ( in caves with bat droppings )
Clinical conditions :
1. A self - limiting pulmonary infection
2. Chronic pulmonary disease with cavitations ( like TB) in patients with underlying
lung disease
3. Disseminated histoblasmosis ( liver , bone , brain , skin ) in
immunocompromised patients

MEDICAL ENTOMONOGY

59
 The study of insects of medical importance
Medical importance mosquitoes
1. Pests of man : Discomfort , sleep disturdancs
2. Local lesion :Erythema , swelling , itchiness , secondary infection
3. Vectors or diseases
(a) Malaria ( anophelas )
(b) Dengue hemorrhagic fever ( aedes )
(c) Filariasis ( culex )
(d) Japanese B Encephalitis ( culex )
Control measures
1. Elimination or reduction of breeding ground
* Drainge , dumping , intermittend , irrigation , canalization
* Removal of vegetation from surfaces of streama & ponds
* Growing of big trees
2. Destruction of lavae
* Oiling , larvicides , breeding of larvicidal fishes
3. Destuction of adult mosquitoes
* Insecticide ( contact & stomach poison ) , residual spraying
Medical importance of house files
1. Intestinal & genitourinary myiasis
2. Mechanical vector of diseases
(a) Enteric fever
(b) Dysentery
(c) Cholera
(d) Bacterial food poisoning
(e) Viral hepatitis A,E
(f) Congunctivitis
(g) Trachoma
Control measures
1. Elimination or reduction of breeding places
* Sanitary disposal of human feces
* Proper disposal of animal manure
2. Destruction of maggods ( larvae ) : By sodium arsenite
3. Destruction of adult flies : By trops , insecticides
Orthers
1. Rat flea: Biological vecter of bubonic plague
2. Louse : Pediculosid , conjunctivitis , as vector of certain bacterial disease
3. Pubic louse: Local itchiness , spread by sexual contact
4. Bed bug : Local itchiness , asthma , sleep disturbances. May act as
mechanical vector : hepatitis , leprosy

60
5. Ticks : As vector of certain bacterial & viral diseases
6. Mite : As vector of scrub typhus

MICROBIOLOGY

61
S.NO CONTENTS Page No

I GENERAL MICROBIOLOGY 1
II INFECTION
- DEFINATION 2
- SIX LINKS OF INFECTION
III STERILIZATION & DISINFECTION
(1) PHYSICAL METHODS
(2) CHEMICAL METHODS
IV IMMUNE RESPONSES 6
- FUNCTIONS OF THE IMMUNE SYSTEM
- ANTIGEN
- ANTIBODY / IMMUNOGLOBULIN
- DIFFERENT TYPES OF DEFENSE MECHANISM+IMMUNITY
- HYPERSENSITIVITY
V BACTERIA 16
- ANATOMY
- PHYSIOLOGY
- SYSTEMATIC CLASSIFICATIONS
- COMMON BACTERIAL INFECTIONS
VI VIRUSES 26
- VIRUSES IN GENERAL CLASSIFECATION
- VIRAL HEPATITIS
- ACQUIRED IMMUNO DEFECIENCY SYNDROME
- MYXOVIRA INFECTIONS
VII PARASITOLOGY 34
- COMMON PROTOZA OF MEDICAL IMPORTANCE
- AMOEBIASIS
- MALARIA
- HELMINTHICS

62
 - SKIN & WOUND INFECTIONS 43
- EYE , EAR & SINUS INFECTIONS 45
- DENTAL & PERIODONTAL INFECTIONS 46
- INFECTIONS OF THE RESPIRATORY TRACT 46
- INFECTIONS OF THE CENTRAL NERLOUS SYSTIM 49
- INFECTIONS OF THE GASTRO INTESTINAL TRACT 50
- INFECTIONS OF THE CARDIOVASCULAR SYSTEM 52
- URINARY TRACT INFECTIONS 53
- SEXUALLY TRANSMITTED INFECTIONS 54

VIII GENERAL
- BIO-WEAPONS 56
- MICROBIOLOGY OF WATER 57
- MYCOLOGY 58
- MEDICAL ENTOMOLOGY 60

63