Microbiology

Marathon

Dr. Priyanka Sachdev

 Overview

• General Microbiology

• Immunology

• Bacteriology

• Virology

• Parasitology

• Mycology
Overview

• General Microbiology

• Immunology

• Bacteriology

• Virology

• Parasitology

• Mycology
 Study of Bacteria

Unstained (Wet) Preparations Stained Preparations

Lack of
contrast

Motility
Morphology
Common Staining Techniques

1. Simple stains

2. Negative staining

3. Impregnation methods

4. Differential stains
1. Simple stains

• Same colour to all the bacteria

• Eg. Methylene blue or Basic fuchsin

 2. Negative staining
• Background is stained, while the structure to be demonstrated is not
stained

• Eg. Indian ink and Nigrosin dyes

Spirochetes Capsulated bacteria

3. Impregnation methods
• Bacterial cells and structures that are too thin to be seen under the light
microscope
• So they are thickened by impregnation of silver on surface
• e.g. bacterial flagella and spirochaetes

Impregnation
Simple Negetive Impregnation
Differential
 4. Differential stains

• Different colours to different bacteria

1. Gram stain

2. Acid-fast stain

3. Albert stain
 Gram Positive Gram Negative

Transparent

1. Primary Stain (Violet)

2. Mordant (Iodine)

PG 3. Decoloriser (Alcohol/ PG
Acetone)

4. Secondary stain (Red)

GP GN
Acid fast organisms Non acid fast organisms

1. Transparent

1. Primary Stain (red)

2. Mordant (Heat)

Mycolic Mycolic
3. Decolouriser (20% H2SO4) acid -
acid +

4. Secondary Stain (Blue)

 AFO
Non AFO
 Gram Stain Acid Fast Stain
Gentian violet (primary stain) Carbol fuschin (primary stain)

Iodine (Mordant) Heat (Mordant)

Acetone or ethanol (decoloriser) 20% sulphuric acid (Decoloriser)

Carbol fuchsin (Counterstaining) Methylene blue (Counterstain)

Retain Take colour Retain fuschin Take methylene blue

primary stain of counterstain (Red color) (blue colour)
(violet) (red)
Acid fast Non Acid fast
Gram Positive Gram Negative organisms organisms
 Gram Positive Gram Negative

Coccus (sphere) Bacillus (rod)

 Gram Gram Gram Gram
Positive Cocci Negative Cocci Positive Bacilli Negative Bacilli
(GPC) (GNC) (GPB) (GNB)
• Staphylococcus • Neisseria • Actinomyces • Enterobacteriacease
• Streptococcus • Moraxella • Bacillus • Vibrio
• Clostridium • Pseudomonas
• Diptheria • Burkholderia
• Listeria • Haemophilus
Miscella neous • Mycobacteria • Brucella
• Bordetella
• Spirochetes
• Legionella
• Rickettsiae
• Helicobacter
• Chlamydiae • Campylobacter
• Mycoplasma
AFO Non AFO
Acid - Fast Organism
Modification in percentage of sulfuric acid:

• 5% H2SO4 → Mycobacterium leprae

• 0.5 – 1% H2S04 → Nocardia

• 0.25-0.5% H2S04 → Oocysts of cryptospora, isospora, cyclospora and

bacterial spores.

• M. leprae is less acid fast than M. tuberculosis.

Acid - Fast Organism
 4. Differential stains

• Different colours to different bacteria

1. Gram stain

2. Acid-fast stain

3. Albert stain
 Alberts Stain

• Differentiates bacteria having metachromatic granules from other

bacteria that do not have them.

MSC Garden in Agra

 Mycobacterium
 Spirillum volutants
 Corynebacterium diphtheiiae
 Gardernella vaginalis
 Aglobacterium tumefaciens
 Gram Stain

Gram Positive Gram Negative

Acid fast stain
Violet Red
Ziehl-Neelsen stain

Acid fast organisms Non Acid fast organisms

Red Blue
Albert stain

Albert Positive Albert Negative

Green bacteria with Transparent bacteria with

blue granules no granules
Simple Negetive Impregnation
Differential
Bipolar Staining (Safetypin Appearance)
• Accumulation of dye at poles of cells
Capsulated Bacteria
Yes Very Killer Bacterias Have Preety Nice Capsule

Yersinia
V. parahemolyticus
Kleibsella
Bordetella
Polysaccharide
Bacillus anthrax  Polypeptide (glutamate)
H. influenza
Pneumococcus
N. meningococci
CI. perfringes and butyricum
Flagella

• Thread like structures composed of a protein (flagellin)

• Organ of locomotion
• Confer motility to the bacteria
Flagella types

Polar Peritrichous

Monotrichous

Lophotrichous

Amphitrichous
Motile with polar flagella:
Motile with peritrichous flagella:
Very Polar Solution HCL
Cute Baby SLEP

 Vibrio  Clostridia all except cl.perfringens

 Pseudomonas  Bacillus except b.antrax
 Spirochetes  Salmonella except salmonella gallenarum – pullorum
 H.pylori  Listeria monocytogen
 Campylobacter  E.Coli
 Legionella  Proteus
Types of Motility
 Darting - V. cholera, Campylobactor

 Tumbling - Listeria at 25°C

 Cork screw - T. pallidum

 Swarming - P. mirabilis, P. vulgaris, CI. tetani, Bacillus cereus

 Darting Tumbling

Cork screw Swarming

Spore Producing Bacteria

BSC Chemistry
Bulging Non Bulging
Central
 B. anthrax and subtilis
 Sporosarcina Subterminal
 Clostridia
 Coxiella Bumetti Terminal
Sterilisation  An article is made free of all microorganisms either in
the vegetative or spore form
• Complete absence of microorganism

Disinfection  Destruction of all pathogens or organisms capable of

producing infections but not necessarily spores
• All organisms may not be killed but the number is reduced to a level
that is no longer harmful to health

• Unlike sterilization, disinfection is not sporicidal (does not kill spores)

 Heat
Dry heat Moist heat
Red heat
Flaming
Incineration
Hot air oven

Below 100°C At 100°C Above 100°C

Pasteurisation Boiling Autoclave
Inspissation Tyndallisation
Vaccine bath Steam sterliser
LTSF
Hot Air Oven

• Electrically heated  hot air is created

• 160°C for two hours (holding time)

Uses 
1. Glasswares like glass syringes, petridishes, flasks, pipettes and
test tubes.

2. Chemicals  oily fluids such as liquid paraffin, fats, grease, dusting

powder
 Sterilisation control

1. Biological control  Spores of “Bacillus subtilis subsp. Niger”

2. Chemical indicator Browne’s tubes No. 3 containing red solution

is inserted in each load and a color change from red to green is
observed, which indicates proper sterilization
 Heat
Dry heat Moist heat
Red heat
Flaming
Incineration
Hot air oven

Below 100°C At 100°C Above 100°C

Pasteurisation Boiling Autoclave
Inspissation Tyndallisation
Vaccine bath Steam sterliser
LTSF
Autoclave

Sterilization by steam under pressure (modified Pressure cooker)

• Temperature — 121 °C
• Chamber pressure — 15 lb per square inch
• Holding time —15 minutes

Uses 

1. Culture media

2. Rubber material

3. Aprons , gowns, dressing, gloves etc.

4. Surgical instruments except sharps

Sterilisation control

1. Biological control  Spores of Bacillus stearothermophilus

2. Chemical indicators  Browne’s tube contains red solution

which turns green, when exposed to temperature of 121°C for 15
minutes in autoclave
 Hot air oven Autoclave
Principle

Temp.

Time

Pressure

Uses

Contol
 Overview

• General Microbiology

• Immunology

• Bacteriology

• Virology

• Parasitology

• Mycology
Definition

• Resistance offered by host against micro-organisms or foreign

substances.
 Immunity

Cell mediated Humoral

Types of Antigen

Complete Ag → can induce Ab formation as well as can react with Ab

Incomplete Ag/ Haptans→ NOT induce Ab formation but can react with
Ab
• Molecular weight < 100 KD

• Not immunogenic but they became immunogenic when linked to

large carrier proteins (protein in nature)
 +

Hapten Carrier
Complete Antigen
Epitope and Paratope
Superantigen
• Potent activators of T-lymphocytes without relation to their epitope
specificity.

• Activate T cells directly without being processed by antigen

presenting cells (APCs).

• Receptor for superantigens  Variable β region of T cell receptor (vβ

of TCR)
Bacterial superantigen
• Staphylococcal toxin  Toxic shock syndrome toxin-1(TSST-1); Exfoliative toxin; Enterotoxins
• Streptococcal toxin  Streptococcal pyrogenic exotoxin (SPE)-A and C
• Mycoplasma arthritidis mitogen-I
• Yersinia enterocolitica
• Yersinia pseudotuberculosis

Viral superantigen
• Epstein-Barr virus associated superantigen
• Cytomegalovirus associated superantigen
• Rabies nucleocapsid
• HIV encoded superantigen (nef- negative regulatory factor)
Fungal superantigen
• Malassezia furfur
Antibody

GAMDE

• IgG
• IgA
• IgM
• IgD
• IgE
Fab
Variable
Amino

Fc
Constant
Carboxy
Valency of antibody

Serum  2
2
2 2

Secretions  4 Theoritically  10
Practically  5
 IgA

Serum IgA Secretory IgA

 Monomer  Dimer
 Pound in serum  Two monomer units
arc joined together
by a glycopeptide
J chain
 IgM

Theoretical valency Effective valency

10 5
Immunoglobulin class H. Chain L. Chain

IgG γ (gamma) K/λ

IgA α (alpha) K/λ

IgM μ (mu) K/λ

IgD δ (delta) K/ λ

IgE ε (epsilon) K/ λ
Property IgG IgA IgM IgD IgE

Heavy chain Gamma Alpha Mu Delta Epsilon

Light Chain K or L K or L K or L K or L K or L

Molecular weight 150,000 160,000 900,000 180,000 190,000

Sedimentation coefficient(S) 7 7 19 7 8

Serum concentration (mg/ml) 12 2 1.2 0.03 0.00004

Half life 23 days 6-8 days 5 days 3 days 2-3 days

Placental transport + - - - -

Present in milk + + - - -

Heat stability (56oC) + + + + -

Property IgG IgA IgM IgD IgE

Heavy chain

Light Chain

Molecular weight

Sedimentation coefficient(S)

Serum concentration (mg/ml)

Half life

Placental transport

Present in milk

Heat stability (56oC)

Hypersensitivity Reactions

• Hypersensitivity is defined as an exaggerated state of normal

immune response which results in adverse effects on the body.
Type I: Examples
All Allergies
+
PCTS (proximal convulated tubules)

P - PK rxn
C - Casoni test
T - Theoblad smith phenomena
S - Schultz Dale phenomenon
Type II: Examples

My Myasthenia gravis
Blood Blood transfusion reactions
Group Goodpasture syndrome and Graves' disease
Is Insulin resistant diabetes, ITP
R Rheumatic fever
H Hyperacute graft rejection
Positive Pemphigus vulgaris
Type III: Examples

S Serum sickness, Schick test and SLE

H Henoch-Schonlein Purpura

A Arthus reaction

R Reactive arthritis, Raji assay

P Polyarteritis nodosa (PAN) and Post Streptococcal

glomerulonephritis (PSGN)
Type IV: Examples

John gave TU LIP and Pop Corn to Hashi

John mote reaction

Tuberculin reaction

LePromin reaction

Pernicious anaemia

Contact dermatitis

Hashimoto thyroiditis
 Transplant Immunology

Transplantation  transfer of a
graft or transplant (cells, tissues,
or organs) from one site to
another.

• Individual from whom the

transplant is taken  Donor

• Individual to whom it is
transplanted  Recipient
Autograft (autogenic graft): Graft from self

Isograft (syngraft): Graft from genetically identical person.Eg.

monozygotic twins

Allograft (homograft or allogenic graft): Graft from genetically unrelated

member of same species

Xenograft (heterograft): Graft from different species

Overview

• General Microbiology

• Immunology

• Bacteriology

• Virology

• Parasitology

• Mycology
 Gram Gram Gram Gram
Positive Cocci Negative Cocci Positive Bacilli Negative Bacilli
(GPC) (GNC) (GPB) (GNB)
• Staphylococcus • Neisseria • Actinomyces • Enterobacteriacease
• Streptococcus • Moraxella • Bacillus • Vibrio
• Clostridium • Pseudomonas
• Diptheria • Burkholderia
• Listeria • Haemophilus
Miscella neous • Mycobacteria • Brucella
• Bordetella
• Spirochetes
• Legionella
• Rickettsiae
• Helicobacter
• Chlamydiae • Campylobacter
• Mycoplasma
 Bacterias Selective media
Bacillus cereus MYPA medium
Bordetella Bordet Gengou medium
Brucella Serum dextrose agar, Trypticase soy agar,
Potato infusion agar, Castaneda method

Campylobacter jejuni Campy BAP, Skirrow's or Butler's media

H. Pylori Skirrow's media
Chlamydia HeLa cells
Clostridia (anaerobes) Robertson's cooked meat broth
Corynebacterium diphtheriae Tellurite blood agar, Tinsdale media
Leptospira Semisynthetic media such as EMJH, Stuart's, Korthoff s
media

Listeria Mueller-Hinton agar

Legionella, Nocardia BCYE medium
Neisseria Thayer-Martin medium
gonorrhoeae

Pseudomonas NYC medium

Shigella Deoxycholate Citrate agar (DCA)
Spirochaetes Smith Noguchi's medium
Staphylococcus Ludlum's, polymixin, salt, mannitol
Pasturella/Yersinia Ghee broth
Vibrio TCBS
Salmonella Wilson-Blair
E coli 0157, H-7 Sorbitol, Mac Conkey media
Mycobacterium TB LJ media
Proteus CNA agar media
 Gram Gram Gram Gram
Positive Cocci Negative Cocci Positive Bacilli Negative Bacilli
(GPC) (GNC) (GPB) (GNB)
• Staphylococcus • Neisseria • Actinomyces • Enterobacteriacease
• Streptococcus • Moraxella • Bacillus • Vibrio
• Clostridium • Pseudomonas
• Diptheria • Burkholderia
• Listeria • Haemophilus
Miscella neous • Mycobacteria • Brucella
• Bordetella
• Spirochetes
• Legionella
• Rickettsiae
• Helicobacter
• Chlamydiae • Campylobacter
• Mycoplasma
Staphylococcus Streptococcus
Staphylococcus Streptococcus
Gram positive Cocci

• Staphylococcus
• Streptococcus
 Gram Gram Gram Gram
Positive Cocci Negative Cocci Positive Bacilli Negative Bacilli
(GPC) (GNC) (GPB) (GNB)
• Staphylococcus • Neisseria • Actinomyces • Enterobacteriacease
• Streptococcus • Moraxella • Bacillus • Vibrio
• Clostridium • Pseudomonas
• Diptheria • Burkholderia
• Listeria • Haemophilus
Miscella neous • Mycobacteria • Brucella
• Bordetella
• Spirochetes
• Legionella
• Rickettsiae
• Helicobacter
• Chlamydiae • Campylobacter
• Mycoplasma
Staphylococcus
Staphylococcus
Intrinsic pathway Extrinsic pathway

Injury to Tissue factor

blood vessels
VII
XII Xlla
VIIa
XI XIa

IX IXa
VIII
Ca²⁺
X Xa
Va
Prothrombin Thrombin
Ca²⁺
(II)
Fibrinogen Fibrin
Cross-
(I) linking

Blood clot
 Catalase test
Staphylococcus Coagulase test

Negative

Positive

Sen. S. epidermis
Streptococcus Novobiocin
CONS
S. Aureus Rest S. Saprophy
Staphylococcus
 Gram positive cocci
Catalase test

(+ve) (-ve)
Staphylococci Streptococci

Coagulase Test

(+ve)
(-ve)
S. Aureus Coagulase negative Staphylococci

Novobiocin susceptible

(+ve) (-ve)
S. S. saprophyticus
Epidermidis
1. GPC 

2. GPC, Catalase negative 

3. GPC, Catalase positive 

4. GPC, Catalase positive, Coagulase positive 

5. GPC, Catalase positive, Coagulase Negetive 

6. GPC, Catalase positive, Coagulase Negetive,Novobioci succeptibility 

7. GPC, Catalase positive, Coagulase Negetive,Novobioci Resistant 

S. Aureus
 Toxins

Cytolytic T. Enterotoxins TSTT-1 Epidermolytic T

α
A-E, G-I TSS SSSS
β cold
hot 8 types ,vagus
γ pheno.
δ Super Ag
Panton-Valentine [P-V] leukocidin
Pathogenesis

1. Cutaneous I. (Cytolytic T. )

2. Food poisoining (Enterotoxins)

3. TSS (TSTT-1 )

4. SSSS (Epidermolytic T)
Cutaneous Infections
Food poisoning
• 2-6 hours

• Meat and fish, or milk and

milk products

• Site of action: The toxin stimulates

the vagus nerve and vomiting
center of the brain.
Toxic shock syndrome (TSS)
• Multisystem disease

• Young women

• Most cases occur in menstruating

women who use tampons

• Characterised by high fever,

hypotension, vomiting, diarrhoea and
scarlatiniform rash
Staphylococcal scalded skin syndrome’
(SSSS)
• Exfoliative skin diseases.

• 0uter layer of epidermis

gets separated from the
underlying tissues.

Nikolsy sign
 CONS
Staphylococcus epidermidis  novobiocin sensitive
• Most common cause of prosthetic valve endocarditis (early onset,
upto 12 months).

Staphylococcus Saprophyticus  novobiocin resistant

• Common cause of UTI in sexually active young women
 Gram Gram Gram Gram
Positive Cocci Negative Cocci Positive Bacilli Negative Bacilli
(GPC) (GNC) (GPB) (GNB)
• Staphylococcus • Neisseria • Actinomyces • Enterobacteriacease
• Streptococcus • Moraxella • Bacillus • Vibrio
• Clostridium • Pseudomonas
• Diptheria • Burkholderia
• Listeria • Haemophilus
Miscella neous • Mycobacteria • Brucella
• Bordetella
• Spirochetes
• Legionella
• Rickettsiae
• Helicobacter
• Chlamydiae • Campylobacter
• Mycoplasma
 Streptococci

Hemolysi
s

Alpha Gamma
Bet
Str. Pneumoniae Enterococci
a
Str. viridans
C carbohydrate antigen
20  Lancefield group  (A to H and
K to V)
Group A -Streptococcus LC
pyogenes

M protein
>100  Griffith types  (1,2,3, etc.) GM
Alpha Beta Gamma
 Hemolysis

Alpha (a) Beta (b) Gamma (g)

Greenish discolouration with Colourless zone of complete No hemolysis
Partial hemolysis around the hemolysis
Colonies Enterococci (grp D)
Str. pyogenes (grp A)
Str. Pneumoniae Str. agalactiae (grp B)
Str. viridans
 Hemolysis

Alpha (a) Beta (b) Gamma (g)

Greenish discolouration with Colourless zone of complete No hemolysis
Partial hemolysis around the hemolysis
Colonies Enterococci (grp D)
Str. pyogenes (grp A)
Str. Pneumoniae Str. agalactiae (grp B)
Str. viridans
Str. Pneumoniae

Diplococcus pneumoniae 
• Flame-shaped or lanceolate appearance
• capsule encloses each pair.
Blood Agar
• After incubation for 18 hours  Alpha hemolysis

• On further incubation  Draughtsman or carrom coin

appearance / central umbonation

Carron Coin
appearance/
Draughtsman
appearance
 Bile Solubility Optochin Sensitivity Inulin Fermentation
(Autolytic amidase)

BOI
 Hemolysis

Alpha (a) Beta (b) Gamma (g)

Greenish discolouration with Colourless zone of complete No hemolysis
Partial hemolysis around the hemolysis
Colonies Enterococci (grp D)
Str. pyogenes (grp A)
Str. Pneumoniae Str. agalactiae (grp B)
Str. viridans
Str. Viridans

BOI  Negetive

1. Dental caries

2. Subacute endocarditis
 Hemolysis

Alpha (a) Beta (b) Gamma (g)

Greenish discolouration with Colourless zone of complete No hemolysis
Partial hemolysis around the hemolysis
Colonies Enterococci (grp D)
Str. pyogenes (grp A)
Str. Pneumoniae Str. agalactiae (grp B)
Str. viridans
Str. pyogenes (grp A)

PYR +ive

Bacitracin sensitive (unlike other

streptococcus)
 Pathogenesis

Suppurative Nonsuppurative

Respiratory Infections Rheumatic

fever Skin Infections
PSGN
i. “Strep throat” – Pharyngitis with streptococcus
pyogenes

Petechiae Pus deposits

 Impetigo Erysipelas

Honey
Comb Peau d’ orange
 Hemolysis

Alpha (a) Beta (b) Gamma (g)

Greenish discolouration with Colourless zone of complete No hemolysis
Partial hemolysis around the hemolysis
Colonies Enterococci (grp D)
Str. pyogenes (grp A)
Str. Pneumoniae Str. agalactiae (grp B)
Str. viridans
Str. agalactiae (grp B)

Single most common cause of neonatal sepsis and meningitis

Hippurate hydrolysis test CAMP

Test
 Hemolysis

Alpha (a) Beta (b) Gamma (g)

Greenish discolouration with Colourless zone of complete No hemolysis
Partial hemolysis around the hemolysis
Colonies Enterococci (grp D)
Str. pyogenes (grp A)
Str. Pneumoniae Str. agalactiae (grp B)
Str. viridans
Enterococci (grp D)

Bile esculin hydrolysis test

Hospital acquired infections

 Gram positive cocci

Catalase

Positive Negative

Staphylococci Strptococci

Coagulase Hemolysis

Positive Negative Alpha Beta Gamma

6.5% NaCl
Staph. Aureus • Bile • Bacitracin • CAMP Test
Novobiocin
soluble sensitive 40% bile
• Hippurate Hydrolysis
• Optochin
pH 9.6
• Inulin fer
Sen Resist
Bile esculin hyd.
Pneumococci S.Pyogenes S. agalactiae
S. Epidermidis S. Saprophyticus Enterococcal Group D
 Staphylococcus

Catalase

Positive Negative

Staphylococci Strptococci

Coagulase Hemolysis

Positive Negative Alpha Beta Gamma

6.5% NaCl
Staph. Aureus • Bile • Bacitracin • CAMP Test
Novobiocin
soluble sensitive 40% bile
• Hippurate Hydrolysis
• Optochin
pH 9.6
• Inulin fer
Sen Resist
Bile esculin hyd.
Pneumococci S.Pyogenes S. agalactiae
S. Epidermidis S. Saprophyticus Enterococcal Group D
 Streptoccocus

Catalase

Positive Negative

Staphylococci Strptococci

Coagulase Hemolysis

Positive Negative Alpha Beta Gamma

6.5% NaCl
Staph. Aureus • Bile • Bacitracin • CAMP Test
Novobiocin
soluble sensitive 40% bile
• Hippurate Hydrolysis
• Optochin
pH 9.6
• Inulin fer
Sen Resist
Bile esculin hyd.
Pneumococci S.Pyogenes S. agalactiae
S. Epidermidis S. Saprophyticus Enterococcal Group D
 Gram positive cocci

Catalase

Positive Negative

Staphylococci Strptococci

Coagulase Hemolysis

Positive Negative Alpha Beta Gamma

6.5% NaCl
Staph. Aureus • Bile • Bacitraci • CAMP Test
Novobiocin
soluble n • Hippurate 40% bile
• Optochin sensitive Hydrolysis pH 9.6
• Inulin fer
Sen Resist
Bile esculin hyd.
Pneumococ S.Pyogene S.
S. Epidermidis S. Saprophyticusci s agalactiae Enterococcal Group D
 Gram Gram Gram Gram
Positive Cocci Negative Cocci Positive Bacilli Negative Bacilli
(GPC) (GNC) (GPB) (GNB)
• Staphylococcus • Neisseria • Actinomyces • Enterobacteriacease
• Streptococcus • Moraxella • Bacillus • Vibrio
• Clostridium • Pseudomonas
• Diptheria • Burkholderia
• Listeria • Haemophilus
Miscella neous • Mycobacteria • Brucella
• Bordetella
• Spirochetes
• Legionella
• Rickettsiae
• Helicobacter
• Chlamydiae • Campylobacter
• Mycoplasma
N. Meningitidis N. Gonorrhoeae

Diplococci Diplococci

Half moon shaped Kidney | bean shaped

One capsule around each pair → 12 No capsule

types
N. meningitidis N. gonorrhoeae
Capsulated Non capsulated

Lens-shaped/half moon-shaped Kidney-shaped (diplococci with

(diplococci with adjacent sides flattened) adjacent sides concave)

Catalase and Oxidase Positive Catalase and Oxidase Positive

Ferments glucose and maltose Ferments only glucose

Virulance factor - Capsule Virulance factor - Pilli

Habitat—nasopharynx Habitat—genital tract (urethra,

cervix), rarely pharynx
 Pathogenesis of N. Meningitidis
Pyogenic meningitis: Young children (3–5
years of age).

Rashes: A non blanching rash (petechial or

purpuric)

Septicemia

Waterhouse-Friderichsen syndrome: severe

form of fulminant meningococcemia,
characterized by large purpuric rashes
(purpura fulminans), shock, DIC, bilateral
adrenal hemorrhage and multi-organ failure.
Pathogenesis of N. Gonorrhoeae
Gonorrhoea

In men: acute urethritis, prostate, seminal vesicles

and epididymis, abscesses and multiple discharging
sinuses (‘watercan perineum’)

In women: Cervicitis , Acute salpingitis, PID, Peritoneal

spread may produce a perihepatic inflammation (Fitz–
Hugh–Curtis syndrome)

In Prepubertal girls : Vulvovaginitis

In Infants (infected birth canal of mother during

vaginal delivery): Ophthalmic neonatorum
N. meningitidis N. gonorrhoeae
 Gram Gram Gram Gram
Positive Cocci Negative Cocci Positive Bacilli Negative Bacilli
(GPC) (GNC) (GPB) (GNB)
• Staphylococcus • Neisseria • Actinomyces • Enterobacteriacease
• Streptococcus • Moraxella • Bacillus • Vibrio
• Clostridium • Legionella
• Diptheria • Helicobacter
• Listeria • Campylobacter
Miscella neous • Mycobacteria • Pseudomonas
• • Burkholderia
Spirochetes
• Haemophilus
• Rickettsiae
• Brucella
• Chlamydiae
• Bordetella
• Mycoplasma
 Species Disease Vector Rash Weil Felix
R. prowazeki Epidemic Typhus Louse Except OX 19 ++++
palm,sole

R. typhi Endemic Typhus Flea Trunk OX 19 ++++

extremities
R. rickettsii Rocky mountain Tick Palm and OX 19 ++, OX
spotted fever (RMS) sole 2++

R.Conori Indian tick typhus Tick Maculopapul

(ITT) ar OX 19 ++, OX
146
2++

R.akari Rickettsial Pox Mite Vesicular/ All negative

 Overview

• General Microbiology

• Immunology

• Bacteriology

• Virology

• Parasitology

• Mycology
DNA viruses → 6 families →HHAPPPy

Hepadnaviridae : Hepatitis-B virus

Herpesviridae : HSV-1, HSV-2, varicella-zoster, EBV,

CMV, HTLV-1, RK-virus

Adenoviride : Adenovirus

Poxviridae : Variola, vaccinia, cowpox, monkeypox,

tanapox, molluscurr contagiosum

Parvoviridae : Parvovirus B19

Papovaviridae : Papilloma virus, Polymavirus

RNA viruses 15 families ABC2D F2OR3 TP2H
DNA viruses RNA viruses

HHAPPP A B C2 D F2 O R3 T P2H

ss ds
ss ds
Remember
• All DNA viruses have ds DNA, except Parvovirus which has ss DNA

• All RNA viruses have ss RNA, except reoviridae which has ds RNA.
 DNA viruses RNA viruses

HHAPPP A B C2 D F2 O R 3 T P 2

Smalles Largest Smalles Largest

t t
 DNA viruses RNA viruses

HHAPPP A B C2 D F2 O R3 T P2H

Smallest Largest Smallest Largest

 REMEMBER

• Smallest virus  Parovovirus

• Largest virus  Poxvirus

• Smallest DNA virus  Parovovirus

• Largest DNA virus  Poxvirus

• Smallest RNA virus  Picornavirus

• Largest RNA virus  Paramyxovirus
DNA viruses RNA viruses

HHAPPP A B C2 D F 2 O R 3 T P2

Envelope Nacke Envelope Nacke

d d d d
DNA viruses RNA viruses

HHAPPP A B C2 D F 2 O R 3 T P2

Envelope Nacke Envelope Nacke

d d d d
 Viruses

DNA Viruses RNA Viruses

Enveloped Non-Enveloped Enveloped Non-Enveloped

• Hepadnaviridae • Parvoviridae • Togaviridae • Picoronaviridae
(HBV) • Adenoviridae • Flaviviridae • Calciviridae
• Herpesviridae • Papovaviridae • Coronaviridae • Reoviridae
• Poxviridae • Filoviridae
PAP • Paramyxoviridae PCR
• Orthomyxoviridae
• Bunyaviridae
• Arenaviridae
• Retroviridae
• Rhabdovirus
• Deltavirus
 DNA viruses RNA viruses

HHAPPP A B C2 D F2 O R3 T P2H

Segmented Segmented
 Segmented nucleic acid
BORA

Bunyaviridae: 3 segments

Orthomyxoviridae (influenza): 8
segments

Reoviridae : 10-12 segments

Arenaviridae: 2 segments
Symmetry
• 3 types of symmetry 
 DNA viruses RNA viruses

HHAPPP A B C2 D F2 O R3 T P2H

Helical IH Helical IH
Complex Complex
 Viruses

DNA Viruses RNA Viruses

Enveloped Non-Enveloped Enveloped Non-Enveloped

• Hepadnaviridae • Parvoviridae • Togaviridae • Picoronaviridae
(HBV) • Adenoviridae • Flaviviridae • Calciviridae
• Herpesviridae • Papovaviridae • Coronaviridae • Reoviridae
• Poxviridae • Filoviridae
PAP • Paramyxoviridae PCR
• Orthomyxoviridae
• Bunyaviridae
• Arenaviridae
• Retroviridae
• Rhabdovirus
• Deltavirus
 RNA viruses
DNA viruses
A B C2 D F 2 O R3 T
HHAPPP
P2H
ss ds ss ds

Smallest Largest Smallest Larges

Enveloped Enveloped
Nacked Nacked
Segmented Segmented

Helical IH Helical IH
Replication of Viruses

1. Adsorption

2. Penetration

3. Uncoating

4. Biosynthesis

5. Maturation and

6. Release
Inclusion bodies:

• Structures with distinct size, shape,

location and staining properties that
can be demonstrated in virus
infected cells under the light
microscope.

• Represent sites of viral

multiplication in a bacterium or
a eukaryotic cell
Types

1. Intracytoplasmic inclusion bodies

2. Intranuclear inclusion bodies

3. Intranuclear and intracytoplasmic inclusion bodies

Host cell Host cell Host cell

Intracytoplasmic Intranuclear Intracytoplasmic and Intranuclear

Intracytoplasmic inclusion bodies

1. Rabies virus (Negri bodies)

2. Vaccinia (Guarnieri bodies)

3. Variola (Paschen bodies)

4. Fowlpox (Bollinger bodies)

5. Molluscum contagiosum (Henderson-

Patterson bodies)
Intranuclear inclusion bodies
Cowdry type A (Granular) 

• Herpes simplex virus (Lipschutz bodies)

• Varicella zoster virus

• Yellow fever (Torres bodies)

Cowdry type B (circumscribed) 

• Polio virus

• Adenovirus
Intranuclear and intracytoplasmic inclusion
bodies:

• Measles virus (Warthin–Finkeldey bodies)

• Cytomegalovirus (Owl's eye appearance)

 Inclusion bodies

Intracytoplasmic Intranuclear Intranuclear and

intracytoplasmic
 Viruses

DNA Viruses RNA Viruses

Enveloped Non-Enveloped Enveloped Non-Enveloped

• Hepadnaviridae • Parvoviridae • Togaviridae • Picoronaviridae
(HBV) • Adenoviridae • Flaviviridae • Calciviridae
• Herpesviridae • Papovaviridae • Coronaviridae • Reoviridae
• Poxviridae PAP • Filoviridae PCR
• Paramyxoviridae
• Orthomyxoviridae
• Bunyaviridae
• Arenaviridae
• Retroviridae
Small pox
 Small pox rash Chicken pox rash

Centrifugal distribution Centripetal distribution

Non-pleomorphic Pleomorphic rash

Deep seated & Multilocular Superficial & Unilocular

No inflammation around vesicles Inflammation around vesicles present

Affects extensor surfaces, spares axilla Affects flexor surfaces, involves axilla

Affects palms and soles Spares palms and soles

Slow evolution Rapid evolution

Scabs form after 10-14 days Scabs form after 4-7 days
Pox- Variola Herpes - Varicela zoster

Centrifugal Centripetal

Spares axilla Spares palms and soles

 Non-pleomorphic Pleomorphic

Deep & Multilocular Superficial & Unilocular

No inflammation
Inflammation seen
 Molluscum Contagiosum

Non cultivable  It does not grow in Egg,

tissue culture or animals

Molluscum Contagiosum disease 

• Umblicated nodule  It presents with

pink or pearly white nodule with central
umblication
 Viruses

DNA Viruses RNA Viruses

Enveloped Non-Enveloped Enveloped Non-Enveloped

• Hepadnaviridae • Parvoviridae • Togaviridae • Picoronaviridae
(HBV) • Adenoviridae • Flaviviridae • Calciviridae
• Herpesviridae • Papovaviridae • Coronaviridae • Reoviridae
• Poxviridae PAP • Filoviridae PCR
• Paramyxoviridae
• Orthomyxoviridae
• Bunyaviridae
• Arenaviridae
• Retroviridae
Diseases

1. Fetus  Severe anemia ( transient aplastic crises),

PRCA, Congestive heart failure , Hydrops fetalis

2. Children  Fifth disease, erythema infectiosum,

slapped cheek fever

3. Adults  Rash and arthralgias (MC wrist )

 Viruses

DNA Viruses RNA Viruses

Enveloped Non-Enveloped Enveloped Non-Enveloped

• Hepadnaviridae • Parvoviridae • Togaviridae • Picoronaviridae
(HBV) • Adenoviridae • Flaviviridae • Calciviridae
• Herpesviridae • Papovaviridae • Coronaviridae • Reoviridae
• Poxviridae PAP • Filoviridae PCR
• Paramyxoviridae
• Orthomyxoviridae
• Bunyaviridae
• Arenaviridae
• Retroviridae
Retroviridae (HIV)

Envelope: Present  Lipoprotein

• Lipid part: host cell membrane

derived

• Protein part: 2 components:

a) GP 120  projected as
knob like spikes on the
surface
b) GP 41  anchoring
transmembrane
pedicles.
Receptor Attachment
Main receptor Entry
• Binding of gp120 to the
CD4 receptor

Co-receptor  Fusion

Binding of gp 41 to 
 CXCR4  on T
lymphocytes
 CCR5  on macrophage
•
Overview

• General Microbiology

• Immunology

• Bacteriology

• Virology

• Parasitology

• Mycology
Parasite
Parasites are organisms that obtain food & shelter by living on or
within another organism (host) and harm host
 Parasites

Based on cellularity

Unicellular
Multicellular

Protozoa Metazoa / Helminths

 Parasites

Based on cellularity

Unicellular
Multicellular

Protozoa Metazoa / Helminths

 Protista

Protozoa

Sarcomastigophora Apicomplexa Ciliophora Microspora

Amoeba Flagellates sporozoans Cilliates Microsporidia

 Amoeba

Pathogenic Nonpathogenic Free living

Entamoeba histolytica Entamoeba coli Naegleria fowleri

Entamoeba gingivalis Acanthamoeba
Entamoeba dispar Balamuthia M.
Entamoeba hartmanni
Endolimax nana
Iodamoeba buetschlii
 Flagellates

Intestinal Genital
Haemoflagellates

Giardia lamblia Trichomonas

Leishmania

T. brucei

T. cruzi
 Sporozoans

Plasmodium
Babesia
Toxoplasma gondii
Sarcocystis
Isospora belli
Cyclospora cayetanensis
Cryptosporidium parvum
 Cilliates

Balantidium coli  largest protozoa

Microspora

Microsporidia
 Parasites

Based on cellularity

Unicellular
Multicellular

Protozoa Metazoa / Helminths

 Metazoa / Helminths

Platyhelminthes Nemathelmithes

Cestode Trematode Nematode

Tapeworms Flukes Round worms
Cestodes Trematodes Nematodes
 Cestode
(Tapeworms)

Intestinal Tissue
Taenia saginata Echinococcus granulosus
Taenia solium
Hymenolepsis nana
Diphyllobothrium latum
 Trematoda
(Flukes)

Intestinal Blood Tissue

Fasciolopsis buski species Hepatic flukes
Schistosoma • Fasciola hepatica
•Clonorchis sinensis
Hematobiu
•Opisthorchis
m
Mansoni Lung flukes
japonicum • Paragonimus
westermani
 Class : Nematoda
(Roundworms)

Intestinal Tissue
Large intestine • Trichinella spiralis
• Trichura trichisis • Dracunculus medinensis
• Enterobius vermicularis • Filarial Nematodes
Small intestine  Wuchereria bancrofti
• Ascaris lumbricoides  Brugia malayi
• Necator americanus  Loa loa
• Ancylotoma duodenale  Onchocerca volvulus
• Strongyloides stereorails  Mansonella
 Parasites
Protozoa Metazoa
Amoeba Flagellates Sporozoans
Nematodes
E. histolytica IntestinalG. lamblia Plasmodium
Intestinal Genital T. vaginalis Babesia Intestinal Tissue
Hepatic Hemo Leishmania Toxoplasma
N. fowleri Viceral Spora A. D.
Acanthamoeb Cutaneous Isospora lumbricoides medinensis
a N. americanus T. spiralis
Balmuthia Mucocutaneous Cyclospora A. duodenale Filarial
S. stercoralis - W.
- T. brucei Cryptospora
Trematodes E. bancrofti
- T. cruzi vermicularis - B. malayi
Cestodes
T. trichuris - Loa loa
- O. volvulus
Intestinal Tissue Intestinal Blood Tissue-
T. solium E. Mansonella
F. buski Schistosoma F. hepatica
T. saginata granulosus Hematobium C. sinensis
H. Nana Mansoni Opistorchis
D.latum japonicum P. westermani
 Eggs in parasitology

Bile stained Saturated solution of Nacl

 Cestode
(Tapeworms)

Intestinal Tissue
Taenia saginata Echinococcus granulosus
Taenia solium
Hymenolepsis nana
Diphyllobothrium latum
• All cestodes eggs  Egg shell and three pair of hooklets except D.
latum eggs
• D. latum eggs  Operculated

Operculum Three pairs of hooklets

Embryophore

Embryo
Knob

Egg of D. latum Egg of other cestodes

 Trematoda
(Flukes)

Intestinal Blood Tissue

Fasciolopsis buski species Hepatic flukes
Schistosoma • Fasciola hepatica
•Clonorchis sinensis
Hematobiu
•Opisthorchis
m
Mansoni Lung flukes
japonicum • Paragonimus
westermani
S. Haematobium S. Mansoni S. japonicum
Eggs of all the trematodes (Except
schistosomes)  Operculated
 Class : Nematoda
(Roundworms)

Intestinal Tissue
Large intestine • Trichinella spiralis
• Trichura trichisis • Dracunculus medinensis
• Enterobius vermicularis • Filarial Nematodes
Small intestine  Wuchereria bancrofti
• Ascaris lumbricoides  Brugia malayi
• Necator americanus  Loa loa
• Ancylotoma duodenale  Onchocerca volvulus
• Strongyloides stereorails  Mansonella
Ascaris lumbricoides
 Ancylostoma and Necator

Contains a segmented ovum with four

blastomeres.
Strongyloides stereorails

• Ovi-viviparous  As soon as the eggs are laid,

the rhabditiform (first stage) larvae start
hatching  eggs are not detected in the faeces

• Rhabditiform larvae come out of the mucous

membrane
Enterobius vermicularis
Planoconvex

Tadpole-like larva.
 Trichura trichisis

• Barrel shaped with a projecting mucous plug at each pole.

• Plugs are colourless.

NON BILE STINED EGGS

N  Necator Americanus

E  Enterobius Vermicularis

H  H. Nana

A  Ancylostoma Douodenale
Filarial Parasites
Seven species

1. Wuchereria bancrofti
2. Brugia malayi
3. Loa loa
4. Onchocerca volvulus
5. Mansonella ozzardi
6. M. perstans
7. M. streptocerca
Overview

• General Microbiology

• Immunology

• Bacteriology

• Virology

• Parasitology

• Mycology
 Classification based on pathogenesis

Superficial Subcutaneous Systemic Opportunistic Mycotoxicoses

mycoses mycoses mycoses mycoses

• • Aspergillus
• Dermatophytosis Histoplasmosis
• • Claviceps
• Tinea versicolor Blastomycosis
• Coccidiodomycosis Purpurea
• Tinea nigra
• Piedra • Paracoccidioidomycosis
• Candidiasis
• Cryptococcosis
• Mycetoma • Zygomycosis
• Sporotrichosis • Aspergillosis
• Chromoblastomycosis • Penicilliosis
• Rhinosporidiosis • Pneumocystis
 Classification based on pathogenesis

Superficial Subcutaneous Systemic Opportunistic Mycotoxicoses

mycoses mycoses mycoses mycoses

• • Aspergillus
• Dermatophytosis Histoplasmosis
• • Claviceps
• Tinea versicolor Blastomycosis
• Coccidiodomycosis Purpurea
• Tinea nigra
• Piedra • Paracoccidioidomycosis
• Candidiasis
• Cryptococcosis
• Mycetoma • Zygomycosis
• Sporotrichosis • Aspergillosis
• Chromoblastomycosis • Penicilliosis
• Rhinosporidiosis • Pneumocystis
 Tinea versicolor Tinea nigra Piedra
Dermatophytosis

Introduction

Causative agent

Pathogenesis

Clinical features

Lab diagnosis

Treatment
Tinea Versicolor / Pityriasis versicolor
1. Flat-round scaly patches of hypo to
hyperpigmentation of skin
• Non-inflammatory
• Non-pruritic
• Areas involved  rich in sebaceous
glands (neck, chest, or upper arms)

2. Seborrheic dermatitis: erythematous

pruriticscaly lesions called dandruff in adults
and cradle cap in babies.
Laboratory Diagnosis
1. Direct microscopy

2. Culture

3. Wood’s lamp examination

1. Direct microscopy:
Mixture of budding yeasts and short septate hyphae are seen 
spaghetti and meatballs appearance
2. Culture:
SDA with olive oil overlay is the ideal media for culture
(Malassezia furfur lipophilic)  Typical ‘fried egg’ colonies
appear after incubating for 5–7 days at 32–35°C
3. Wood’s lamp examination: scaly lesions show golden yellow
fluorescence.
Tinea nigra
• Painless, black, non-scaly patches

• Agent  Hortaea werneckii ( black-colored yeast like fungus)

• Site: Palms and sole

Piedra

• Irregular nodules in hair shaft

• Black piedra - Piedraia hortae
• White piedra - Trichosporon beigelii
 Tinea versicolor Tinea nigra Piedra
Dermatophytosis

Introduction

Causative agent Malassezia furfur Hortaea werneckii Piedraia hortae

Clinical features

Lab diagnosis

Treatment
Dermatophytoses

• Also called as Tinea or Ringworm

• Infection of skin, hair and nail (keratinized structures)

Genera Site of infection

Trichophyton Skin, Hair, Nail
Microsporum Skin , Hair
Epidermophyton Skin , Nail
Dermatophyt Macroconidia Microconidia
es

Trichophyton Pencil shaped Abundant

Microsporum Spindle shaped Absent

Epidermophyton Club shaped Absent

 Tinea versicolor Tinea nigra Piedra
Dermatophytosis

Introduction

Causative agent Malassezia furfur Hortaea werneckii Piedraia hortae

Clinical features
Lab diagnosis
Treatment
 Classification based on pathogenesis

Superficial Subcutaneous Systemic Opportunistic Mycotoxicoses

mycoses mycoses mycoses mycoses

• • Aspergillus
• Dermatophytosis Histoplasmosis
• • Claviceps
• Tinea versicolor Blastomycosis
• Coccidiodomycosis Purpurea
• Tinea nigra
• Piedra • Paracoccidioidomycosis
• Candidiasis
• Cryptococcosis
• Mycetoma • Zygomycosis
• Sporotrichosis • Aspergillosis
• Chromoblastomycosis • Penicilliosis
• Rhinosporidiosis • Pneumocystis
 Mycetoma Chromoblastomycosis Rhinosporidiosis Sporotrichosis

Introduction

Causative agent

Pathogenesis

Clinical features

Lab diagnosis

Treatment
 Classification based on pathogenesis

Superficial Subcutaneous Systemic Opportunistic Mycotoxicoses

mycoses mycoses mycoses mycoses

• • Aspergillus
• Dermatophytosis Histoplasmosis
• • Claviceps
• Tinea versicolor Blastomycosis
• Coccidiodomycosis Purpurea
• Tinea nigra
• Piedra • Paracoccidioidomycosis
• Candidiasis
• Cryptococcosis
• Mycetoma • Zygomycosis
• Sporotrichosis • Aspergillosis
• Chromoblastomycosis • Penicilliosis
• Rhinosporidiosis • Pneumocystis
 Histoplasmosis Blastomycosis Coccidioidomycosis
Paracoccidioidomycosis

Introduction

Causative agent

Pathogenesis

Clinical features

Lab diagnosis

Treatment
 Classification based on pathogenesis

Superficial Subcutaneous Systemic Opportunistic Mycotoxicoses

mycoses mycoses mycoses mycoses

• • Aspergillus
• Dermatophytosis Histoplasmosis
• • Claviceps
• Tinea versicolor Blastomycosis
• Coccidiodomycosis Purpurea
• Tinea nigra
• Piedra • Paracoccidioidomycosis
• Candidiasis
• Cryptococcosis
• Mycetoma • Zygomycosis
• Sporotrichosis • Aspergillosis
• Chromoblastomycosis • Penicilliosis
• Rhinosporidiosis • Pneumocystis
 Candidiasis
Most common fungal infection in humans  both in HIV and
non-HIV infected people

Candida  pseudohyphae

Species :
• Candida albicans  most common
• C. Tropicalis
• C. Glabrata
• C. Krusei
• C. Parapsilosis
• C. Dubliniensis
• C. viswanathii
Germ tube test Dalmau plate culture: CHROM agar
cornmeal agar
Cryptococcosis

Cryptococcus

• Negetive stain  India ink

 Compare
Zygomycosis Aspergillus
(Rhizopus, Mucor) (A.fumigatus,A.flavus,A.niger)

• Broad hyaline hyphae • Narrow hyaline hyphae

• Wide angle branching • Acute angle branching

• Aseptate • Septate
Penicilliosis

LPCB mount 
• Brush border appearance  conidiophore and its branches give rise
to elongated metulae, from which flask-shaped phialides originate
which bear chain of conidia.
Pneumocystis

• Cysts resemble black colored

crushed ping-pong balls, against
the green background
 Candidiasis Cryptococcosis Zygomycosis Aspergillosis Penicilliosis Pneumocystis

Introduction

Causative agent

Pathogenesis

Clinical features

Lab diagnosis

Treatment
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