Microbiology notes for competitive examinations

virus1Dr. Sabitha Vijayan BHMS, MD

  1. The first person to observe bacteria – Anton von leuwen hock
  2. The earliest discovery of pathogenic micro organism was probably made by – Augustino Bassi
  3. The development of bacteriology as a scientific discipline date from Louis Pasteur
  4. The kingdom Protista has been divided into two groups – prokaryotes and Eukaryotes
  5. Bacteria and blue green algae are Prokaryotes while fungi, algae, slime moulds and protozoa are Eukaryotes.
  6. The types of staining that may be toxic and that which kills bacteria is called supravital staining.
  7. Bacteria have an affinity to basic dyes due to acidic nature of protoplasm.
  8. Acid fast staining discovered by Ehrlich and modified by Zeil and Neelssen.

According to shape bacteria are classified into

  • 1. Cocci –  spherical shaped bacteria
  • 2. Bacilli –  rod shaped cells
  • 3. Vibrio –  comma shaped cells
  • 4. Spirilla- rigid spiral forms
  • 5. Spirochetes- flexuous spiral forms
  • 6. Actinimycetes –  branching filamentous form.
  • 7. Mycoplasma – lacks cell wall. Hence do not possess stable morphology.

Cultural media may be a complex medic if ingredients are added for special purpose of growth.


  •  Refers to resistance exhibited by host towards injury caused by microorganisms and their products.
  • Innate immunity is inborn.
  • Acquired immunity may passive and active immunity.
  • Active immunity developed by an individual due to antigenic stimulus . once developed it is long lasting.
  • In PASSIVE immunity no antigenic stimulus; preformed ontibodies are administered.
  • An antigen has been defined as any substance when introduced parenterally into the body stimulates the production of antibodies. The smallest unit of antigenicity is called an epitope
  • Antibodies are immunoglobulins 
  • IgG :- this is major serum immunoglobulin. Its level is raised in chronic malaria, kala azar, or myeloma. IgG is only maternal immunoglobulin that is normally transported across the placenta and provides natural passive immunity in newborn.
  • IgA:-it is the second most abundant class of immunoglobulin seen in body fluids such as colostrums, saliva and tears. 
  • IgM:- is called ‘millionaire” molecule. It is not transported across the placenta hence presence of IgM in the foetus or newborn indicates diagnosis of congenital infection such as syphilis, rubella, HIV and toxoplasmosis.
  • IgM antibodies are short lived, hence their presence in serum indicates recent infection. 
  • IgE:- greatly elevated in atopic (Type I allergy) conditions such as asthma, hay fever, eczema, and also in children having high load of intestinal parasites. 
  • In general
  •             IgM – protects body fluids
  •             IgA – protects body surfaces
  •             IgM – protects blood stream
  •             IgE –  mediates reagenic hypersensitivity
  • Bence jones proteins are abnormal light chain immunoglobulins seen in multiple myeloma.
  • Coomb’s test – antiglobulin test- dirct commb’s test is positive in haemolytic disease of newborn due to Rh incompatibility
  • Idirect commb’s test is positive in Brucellosis 
  • Wasserman reaction (Serodiagnosis of syphilis) is a complement fixation test
  • The term hypersensitivity means injurious consequence in sensitized host following contact with specific antigens. Mainly classified into
  • Immediate – B-cell or antibody mediated and Delayed – t cell mediated 
Immediate hypersensitivity Delayed hypersensitivity
1. Appears rapidly and recedes rapidly2. Induced by antigens or happens by any route3. Circulating antibodies are present and responsible for reaction4. So antibody mediated reaction 1. Appears slowly and lasts longer2. Induced by infection, ingestion of antigen or happen intradermally3. Antibodies absent4. Cell mediated reaction
  1. In anaphylactoid reactions there is no immunological basis.
  2. Shwartzan reaction is not an immune reaction but reaction resembles immune inflammation.
  3. Auto immunity is a condition in which structural or functional damage is produced by action of immunologically competent cells or antibodies against normal components of body.
  4. Rose water test is used for the detection of rheumatic fever.


  • Gram positive
  • Occurs in ‘grape like clusters’
  • Enzyme coagulase present

Common culture media is nutrient ogar and organization shows ‘oil –paint’ appearance in medica. Main exotoxins of S.aureus are cytolytic toxin, enterotoxin and exfoliative toxins. Entero toxin causes staphylococcal food poisoning (milk and milk products are responsible for common food items)

Exfoliative toxins causes TSS (toxic shock syndrome)

And SSSS  – Staphylococcal scalded skin syndrome- seen in infants – Ritter’s disease


  1. Localized skin lesions including furuncles, styes, boils, abscesses, carbuncles, impetigo.
  2. Sepsis in burns and wounds
  3. Acute osteomyelitis
  4. Tonsillitis, pharyngitis, pneumonia, especially bronchopneumonia secondary to some respiratory infections
  5. Breast abscess in lactating mothers
  6. Tropical myositis- in young adults of tropics multiple abscess in voluntary muscles.
  7. In staphylococcal food poisoning diarrhea and vomiting starts with in 6 hours of taking contaminated food
  8. Exfoliative diseases such as impetigo, pemphigus neonatorum, Ritter’s disease, toxic epidermal necrolysis.
  9. Non pathogenetic staphylococci- staphylococcus epidermitidis


  • Gram positive
  • It causes SPREADING PYOGENIC INFECTIONS  and non suppurative lesions sucj as rheumatic fever and glomerulonephritis
  • 3 types
  • Alpha haemolytic s.cocci
  • Beta haemolytic s.cocci
  • Gamma haemolytic s.cocci (non haemolytic)
  • Streptococci form several exotoins and ensumes. The two haemolysins are haemolysin ‘O’ and ‘S’.
  • Streptolysin ‘O’ is oxygen labile. Streptolysin regularly appear in sera following streptococcal infection –  ASO tite
  • Strepto lysine S is not antigenic
  • Erythrogenic toxin is also called Dick , scarlatinal or pyrogenic toxin.

DICK TEST:- this test is used to identify children susceptible to scarlet fever (scarlet fever is a type of acute pharyngitis with extensive rash caused by str.pyogens

SCHULRZ CHARTON reaction:- blanching of rash on localinfection convalescent serum. This is used as a diagnostic test in scarlet fever.

The enzyme sternodornase present in the str.cocci helps to liquefy pus and hence responsible for serous character of pus.


  • Respiratory infection including sore throat, tonsillitis, pharyngitis
  • Extension of infection from  throat to surrounding tissues causes ASOM, mastoiditis , quinsy, Ludwig’s angina, suppurative adenitis
  • Skin and subcutaneous infection –  Variety of suppurative infection including infection of wounds or burns.
  • 2 typical streptococcus infections are Erysipelas and impetigo (impetigo are vesicular pin head like infection with exfoliation.)
  • Streptococcal subcutaneous infection range from cellulites to necrotizing fascitis.
  • Genital infection including puerperial sepsis and abscess in internal organs such as brain, kidneys etc.
  • Non suppurative leisions such as rheumatic fever and acute glomerualonephritis.
  • In rheumatic fever, a connective tissue degeneration of heart valve and inflammatory myocardial leisions causes Aschoff nodules
  • Str. Viridans normally residing in mouth and upper respiratory tract


  • It is gram positive
  • Single most prevalent bacterial genera in pneumonia, otitis media, acute sinusitis, meningitis, and other infectious processes
  • Cultural characters :- on blood agar draughtsman or carom coin appearance. It exhibits capsule swelling reaction called quelling reaction.
  • The toxins are oxygen labile haemolysin and a leucosidin


  • Lobar pneumonia
  • Bronchopneumonia following viral infections
  • Acute exacerbation of chronic bronchitis (haemophilus influenza also causes this)
  • Empyema, pericarditis, ASOM, otitis media, sinusitis, conjunctivitis, suppurative arthritis


  • Gram negative cocci
  • N.meningitidis
  • Causes meningococcal meningitis or cerebrospinal fever
  • Oval or spherical in shape
  • Grows only on enriched media such as blood agar, chocolate agar
  • Modified  Thayer-Martin media is a useful selective media 


  • Cerebrospinal meningitis
  • Meningococcal septicemia
  • In meningococcal septicemia there occurs adrenal haemorrhage and shock. This is Water house – Frederickson syndrome

N. gonorrhoea

            Causes veneral disease gonorrhoea. Here also Thayer – Martin media is used.


            Gonorrhoea is acquired by sexual contact. c/c urethritis lead to stricture formation. The may spread to periurethral tissue causing abscess and multiple discharging sinuses. (Water can perineum)

  • In women causes Bartholinitis and salpingitis
  • Proctitis, conjunctivitis, arthritis, ulcerative endocarditis and meningitis
  • Non veneral infection is gonococcal ophthalmia in newborn


Causative organisms are

  1. Chlamydia trachomatis
  2. Ureaplasma urealyticum
  3. Mycoplasma hominis 


  • Gram positive
  • Non acid fast, non motile rods
  • C.diphtheria :- syn. (Loffler’s bacillus)
  • Having Chinese letter of cuneiform arrangement
  • Usual media –  Loeffler’s serum slope and tellurate blood agar

3 types –

  • Gravis – most fatal infections
  • Intermediate
  • Mitis

Universally used strain is Park william’s strain


Site of infection

  1. Faucial
  2. Laryngeal
  3. Nasal
  4. Otitic
  5. Conjunctival
  6. Genital
  7. Cutaneous
  • Faucial diphtheria is the commonest type. Classified into malignant or hyper toxic diphtheria in which there is sever toxaemia with marked adenitis – bull neck. Death occurs due to circulatory failure.
  • Septic- which leads to ulceration, cellulitis, gangrene
  • Haemorrhagic – characterized by bleeding from edge of membranes
  • Common complication – asphyxia, acute circulatory failure, post diphtheritic paralysis
  • SHICK TEST- susceptibility test for diphtheria


  • Rod shaped bacteria
  • 2 types
  • Aerobic bacilli and anaerobic bacillus
  • Gram positive

B.anthracis :- first pathogenic bacteria observed under microscope and it is the first bacillus to be isolated in pure culture and first bacterium used for preparation of attenuated vaccine.

M-Fayden’s reaction:- used for presumptive diagnosis of anthrax in animals

Culture media:- on agar media frosted glass appearance with locks of matted hair called medusa head appearance, on gelatin slab having ‘inverted fir tree’ appearance when grown on solid media ‘ strings of pearl reaction’.

ANTRAX is a zoonosis

3 types

1. Cutaneous 2. Pulmonary 3. Intestinal

  • All types leads to fatal septicemia.
  • Cutaneous anthrax
  • Follows infection through skin. Leisions are called ‘malignant pustule’ or black eschar
  • Disease is common in dock workers carrying loads of hides and skins on bare back. Hence called hide porter’s disease.


Wool sorter’s disease due to inhalation of dust from infected wool. There is haemorrhagic pneumonia. Haemorrhagic meningitis is a complication.

Intestinal anthrax is rare. Occurs mainly in primitive communities which uses undercooked meat.

Lab diagnosis is by immunofluoroscence

Bacillus cereus – causes food borne disease characterized by diarrhea and abdominal pain associated with consumption of cooked rice, usually fried rice from Chinese restaurant.

Gram positive

  • Anaerobic sphere forming bacilli
  • Genus responsible for  3 major diseases : 1.     Gas gangrene. 2. Food poisoning 3. Tetanus
  • Spores may be central or equatorial.  Eg. Cl. Bifermingens
  • Oval or terminal   Tennis racket  eg. Cl. Tertian
  • Spherical and terminal – drum stick appearance eg. Cl. Tetani

Useful media :   Robertson’s cooked meat broth

cl. perfingens –  Gas gangrene (malignant oedema)

  • Wound contamination
  • Septic abortion
  •  Anaerobic myositis
  • Food poisoning and
  • Necrotizing enteritis

In litmus reaction fermentation of lactose causes stormy fermentation

cl. perfingens show ‘Nagler reaction’ due to specific lecithinase effect

Food poisoning starts between 8-24 hours – self limiting illness

cl.noviji (cl.oedematiens)

Also causes gangrene characterized by high mortality and large amount of oedema fluid with little or no observable gas.

Clostridium tetani

  1. Drumstick appearance
  2. Media: robertson’s cooked meat broth
  3. 2 toxins: tetanolysin which is haemolysin and tetanospasmin which is a powerful  neurotoxin
  4. Tetanus toxins block synaptic inhibitors in spinal cord. While  strychnine acts post synaptically.
  5. Abolition of spinal inhibition causes uncontrolled spread of impulses initiated any where in CNS. This results in muscle rigidity and spasm.
  6. Sometimes tetanus may be due to local suppuration called otogenic tetanus.

Clostridium botulinum
Causes food poisoning – exotoxin is responsible for pathogenicity. It acts by blocking acetylcholine at synapse and neuromuscular junction. Hence onset marked by diplopia, dysphagia and dysarthria

Botulinum – 3 type

  1. Food borne botulism
  2. Wound botulism
  3. Infantile botulism

Food borne botulism– 12- 36 hours after ingestion

  •  Vomiting, thirst, constipation, ocular paresis, difficulty in swallowing, speaking, breathing, coma or delirium
  • Death is due to respiratory failure.
  • Wound botulism – Rare. Symptoms similar to food borne botulism except GIT symptoms
  • Infant botulism –  Infants less than 6 months are affected. Manifestations are constipation, poor feeding, lethargy, weakness, pooled oral secretion, weak or altered cry, loss of head control.


Enterobacteria – proteus

Mc conkeney’s medium

E coli- pathogenesis

  • Neonatal meningitis
  • Septicemia

Clinical features:

  1. UTI
  2. Pylonephritis and hypertension in pregnant women
  3. For diagnosis –  Mid stream urinalysis
  4. Diarrhea – traveller’s diarrhea
  5. Enterohaemorrhagic colitis – frank dysentery
  6. Pyogenic infection and septicemia

KLEBSIELLA (fried –landler’s bacillus)

            -Pneumonia, UTI, septicemia and rarely diarrhea 


            Shigella causes bbacillary dysentery

            Short incubation period – 1-7 days; usually 48 hours

  • Enterobacteria  – Salmonella
  • Salmonella typhi:- causes typhoid fever.
  • Enteric fever :- typhoid and paratyphoid fever- salmonella paratyphi A,B,C
  • Widal reacton
  • Leucopenia
  • Diazo test of urine

Slamonella gastroenteritis

Poultry, meat, milk, cream and eggs

Short incubation period – less than 24 hours


  • Gram negative; comma shaped
  • Described by Koch as ‘fish in stream’ vibrio colonies are identified by ‘string test’
  • Biochemical reaction- cholera rod reaction
  • In cholera – watery diarrhea, vomiting with hypovolumic shock and death in less than 2 hours
  • Stool has fishy odour and it is described as ‘rice watery’ stool.


  1. Bacillus pyocyanius
  2. Gram negative
  3. Pyocyanis forms blue pus ; self limiting illness –  shanghai fever
  5. Yersinia safety pin appearance
  6. On nutrient agar –  stalactile growth
  7. Yersinia causes plague
  8.  Pandemic plague causes black death due to extensice cutaneous haemorrhage and gangrene.
  9. 3 forms :     Bubonic, pneumonic and septicemic
  10. Vector is rat flea – xenophilla cheopis


  • Gram negative bacillus
  • Cultural media is blood agar and shows Satelletism in media


  • Meningitis
  • Otitis media
  • Pneumonia
  • Arthritis
  • Endocarditis, pericarditis
  • Bronchitis

Haemophilus ducreyi

Cause chancroid or soft sore. Veneral disease. Bacilli are arranged in groups called school of fish or rail road track appearance

BORDETELLA PERTUSIS ( bordet- gengou glycerine –potatoe blood agar

‘Bisected pearls’ or mercury drops’ with ‘aluminium paint’ appearance

Pathogenesis: Pertusis  or whooping cough.


Acute brucellosis ; undulant fever

                        Malta fever

                        Relapsing fever

Caused by B. melitensis – Brucellosis is primarily a disease of reticuloendothelial system

Lab investigation:- castinada method of blood culture.


  • Gram positive
  • Acid fast bacillus
  • In children it causes primary complex.
  • Ghon’s focus :- subpleural focus of tuberculous pneumonia in lung parenchyma
  • Adult type TB is due to reactivation of primary infection.
  • In mantoux test 0.1 ml. purified protein derivative is injected intracutaneously on flexor aspect of forearm. Site is examined after 48-72 hours
  • If induration of diameter 10mm or more – positive mantoux test
  • If induration is 5 mm. or less than 5mm. – negative
  • If induration is between 6-9 mm it is doubtful case. 

Caused by gram positive mycobacterium leprae. Organism is arranged in parallel rows are having ‘cigar bundle’ appearance. Masses of bacilli are called globi. The globi appear in virchow’s lepra cell or foamy cell.

Leprosy is a chronic granulomatous disease.

4 types

  1. Lepromatous
  2.  Tuberuloid
  3. Dimorphous
  4. Indeterminate
  • Lepromatous variety is most infectious type. Lepromin test is negative in lepromatous leprosy due to deficient cell mediated immunity.
  • In Tuberculoid leprosy patient is having high resistance. Good prognosis. Lepromin test is positive. Few skin lesions but neurological symptoms are more and deformity occurs early.
  • The term borderline or dimorphous refers to lesions possessing characteristic of both tuberculoid and lepromatous type.
  • The indeterminate type is early unstable tissue response to the microorganism. Lesions undergo spontaneous healing.
  • Classification according to Reiding & jopteng scale of classification
  • Lepromin test is described by metsuda
  • Biphasic events
  • First phase –  early reaction –  Fernandes reaction. Ie. Erythema and induration developing in 24-48 hours.
  • Late phase –  Mitsuda reaction –  starting 1 or 2 weeks later. It consists of indurated skin nodule which may ulcerate.
  • Lepromin test is positive in Tuberculoid leprosy
  • Lepromin test is negative in lepromatous leprosy
  • Lepromin test is variable in dimorphous and indeterminate varieties


  1.  Treponema pallidum causing syphilis
  2.  Treponema pertenue  causes yaws
  3.  Treponema carateum  causes pinta
  • Staining reaction is silver impregnation method
  • Syphilis is a veneral disease
  • Primary lesion is chancre
  • Lymph nodes are characteristically rubbery in consistency
  • Secondary syphilis starts after 2-6 weeks, characterized by roseolar skin rashes
  • After secondary syphilis there is a stage of latent syphilis. During this period diagnosis is possible by serological test. There occurs cardiovascular lesions including aneurysm.
  • Tertiary syphilis – delayed hypersensitivity reaction mainly tabes dorsalis and general paralysis of insane.

Serological test for diagnosing syphilis

  • A.    Reagin test
  • B.    Kahn test (floaculation test)
  • C.    VDRL test (veneral disease research laboratory test)
  • D.    Rapid plasma regain test is the first modified VDRL

First reagen test is Wasserman reaction


Causes relapsing fever

2 types

  • Louse borne relapsing fever
  •  Tick borne relapsing fever
  • Louse borne relapsing fever is caused by Borellia recurrentis
  • Borellia vincenti causes ulcerative gingivostomatitis or oropharyngitis called – vincent’s angina or cancre oris
  • Borellia burgdorferi causes lyme disease
  • Rat bite fever caused by spirillum minus or streptobacillus moniliformis


  1. Leptospira icterohaemorrhagica causes Weil’s disease which causes hepatorenal damage.
  2. Antibodies appear in serum towards the end of first week of disease and increase till 4th week. Caonicola fever is caused by leptospira canicola.


  •  Smallest free living microorganism. Organism in colony have ‘fried egg’ appearance.
  • Mycoplasma causes pneumonia and genital infection especially of children and adolescents.


  • Gram positive. Between bacteria and fungi
  • It causes ‘lumpy jaw’ in cattle.

Actinomycosis is a chrnic granulomatous infection characterized by development of indurated swelling mainly in connective tissue with suppuration and discharge of sulphur granules. Actinomycosis in human being is an endogenous infection. Actinomycetes Israeli is the causative organism.

3 forms

1. Cervico fascial

2. Thoracic

3. Abdominal

Pelvic actinomycosis is associated with the use of IUCD (intra uterine contraceptive device)

Actinomycetes mycetoma( Madura mycosis)
It is a localized chronic granulomatous involvement of subcuteneous and deeper tissue affecting foot and less commonly hands and presenting as a tumour with multiple discharging sinuses.

Helicobacter pylori associated with antral gastritis and peptic ulcer disease.

Legionella pneumonia is caused by Legionella pneumophilia. Human infection is typically caused by inhalation of aerosols produced by airconditioners and shower heads.


Gram negative organism

Weil – Felix raction used for diagnosis of rickettsial infection.

Scrub typhus –   Rickettsiae tsu tsu gambusti

Epidemic typhus

            Rickettsiae prowazekii (vector is louse or pediculus humanis)

  • Recrudescent typhus is activated latent infection called Brill- Zeinsser disease
  • Rocky mountain spotted fever  – Rickettsia rickettsi
  • Endemic typhus is caused by rickettsiae typhi  ( r. mooseri)
  • Transmitted by xenopsyla cheopis or rat flea
  • Trench fever  is caused by Rickettsiae Quintana
  • Transmitted by body louse
  • Q fever is caused by coxellia burnetti


  • Main pathogenitic varieties are
  • Chlamydiae psittaci
  • hlamydiae pneumoniae

Trachomatis causes

  1. Trachoma which is a chronic keratoconjunctivitis  (lab diagnosis by Hp bodies)
  2. Inclusion benorrhoea (neonatal form of inclusion conjunctivitis)
  3. Pool conjunctivitis
  4. Lymphogranuloma venerum

Chlamydia psittaci
Causes psittacosis – consumption of infected poultry products leads to this disease

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