π¦ Complete Microbiology
NEET PG Master Guide β All Topics
SECTION 1: BACTERIOLOGY BASICS
Gram Staining β The First Step
| Gram Positive (purple) | Gram Negative (pink/red) |
|---|
| Thick peptidoglycan wall | Thin peptidoglycan + outer membrane (LPS) |
| No outer membrane | Outer membrane present |
| Teichoic acids present | No teichoic acids |
| Retain crystal violet | Decolourised β take safranin |
Gram stain steps: Crystal violet β Gram's iodine (mordant) β Acetone/alcohol (decolouriser) β Safranin (counterstain)
Cell Wall Structures
Peptidoglycan (Murein):
- NAM (N-acetylmuramic acid) + NAG (N-acetylglucosamine) linked by Ξ²-1,4 bonds
- Cross-linked by peptide bridges
- Target of: Penicillin (inhibits transpeptidase/PBP), Vancomycin (binds D-Ala-D-Ala)
- Lysozyme cleaves Ξ²-1,4 bond between NAM and NAG
Teichoic acids (Gram +ve only):
- Lipoteichoic acid (LTA) - anchored to membrane
- Wall teichoic acid - anchored to peptidoglycan
- Important virulence factors, activate complement
LPS (Gram -ve only):
- Lipid A (toxic) + Core + O-antigen
- Endotoxin activity via TLR4/MD-2/CD14
Special Staining Techniques
| Stain | Organisms |
|---|
| Ziehl-Neelsen (ZN) | Mycobacterium (acid-fast due to mycolic acid) |
| Modified ZN (weak acid) | Nocardia (weakly acid-fast), Cryptosporidium, Cyclospora, Isospora |
| Albert's stain | C. diphtheriae (metachromatic granules - blue-black) |
| India ink / Nigrosin | Cryptococcus neoformans (capsule - halo effect) |
| Dark-field microscopy | Treponema pallidum, Leptospira (too thin for Gram) |
| Silver stain (Warthin-Starry) | T. pallidum, H. pylori, Legionella |
| PAS (Periodic Acid-Schiff) | Tropheryma whipplei (Whipple's disease), fungi |
| Giemsa | Malaria, Leishmania, Rickettsia, Chlamydia (intracellular) |
| Lactophenol cotton blue | Fungi |
| Gomori methenamine silver (GMS) | Pneumocystis jirovecii, fungi |
| Mucicarmine | Cryptococcus capsule |
Culture Media
| Medium | Organisms | Purpose |
|---|
| Blood agar | Most organisms | General purpose, shows haemolysis |
| Chocolate agar | Neisseria, H. influenzae | Heat-lysed RBCs release factor V (NAD) + X (haemin) |
| MacConkey agar | Gram-negative enteric bacteria | Lactose fermenters = pink (E. coli); non-fermenters = colourless |
| TCBS (Thiosulphate Citrate Bile Sucrose) | Vibrio cholerae (yellow) | Selective |
| CLED agar | Urinary pathogens | Non-swarming |
| LΓΆwenstein-Jensen (LJ) | Mycobacterium tuberculosis | Growth in 4-8 weeks |
| Middlebrook 7H10/7H11 | Mycobacteria | Faster growth |
| BACTEC | M. tuberculosis | Radiometric/fluorescent, fastest (1-2 weeks) |
| Bordet-Gengou | B. pertussis (dewdrop colonies) | Selective |
| Tellurite/Hoyle's medium | C. diphtheriae (black colonies) | Selective |
| BCYE (Buffered Charcoal Yeast Extract) | Legionella pneumophila | Needs L-cysteine + iron |
| Sabouraud Dextrose Agar (SDA) | Fungi | Acidic pH, antifungal antibiotics added |
| Fletcher's/Ellinghausen's | Leptospira | Semi-solid |
| Thayer-Martin | Neisseria gonorrhoeae | Vancomycin + colistin + nystatin |
| XLD / DCA | Salmonella, Shigella | Selective/differential |
Bacterial Growth & Kinetics
Growth curve phases:
- Lag phase - adaptation, no division
- Log (exponential) phase - rapid doubling, most sensitive to antibiotics
- Stationary phase - growth = death, nutrients depleted
- Decline/Death phase - cells die
Spore formation: Only in Bacillus (aerobic) and Clostridium (anaerobic)
- Most heat-resistant biological structure
- Autoclave (121Β°C, 15 psi, 15 min) required for sterilisation
SECTION 2: GRAM-POSITIVE COCCI
Staphylococcus
Coagulase test - differentiates S. aureus (positive) from others (negative)
Staphylococcus aureus
- Coagulase positive (slide + tube)
- Beta-haemolytic on blood agar
- Golden yellow colonies (carotenoid pigment)
- Catalase positive
- Protein A - binds Fc region of IgG β evades opsonisation
- MRSA - mecA gene β altered PBP2a (low affinity for beta-lactams)
Diseases:
- Skin: Folliculitis, furuncle, carbuncle, impetigo, cellulitis
- SSSS (Scalded Skin Syndrome) - exfoliative toxin, desmoglein-1
- Food poisoning (1-6 hrs, preformed toxin, vomiting dominant)
- TSS (TSST-1, superantigen)
- Pneumonia (post-influenza), bacteraemia, endocarditis
- Osteomyelitis (most common cause in all ages)
Lab ID: Catalase +, coagulase +, beta-haemolysis, golden colonies, Mannitol fermentation (MSA), PVL for CA-MRSA
Coagulase-Negative Staphylococci (CoNS)
| Species | Disease | Key Feature |
|---|
| S. epidermidis | Prosthetic valve endocarditis, catheter infections | Biofilm former, novobiocin sensitive |
| S. saprophyticus | UTI in young sexually active women | Novobiocin resistant |
| S. haemolyticus | Endocarditis | - |
Streptococcus
Classification:
- By haemolysis: Alpha (partial, green), Beta (complete, clear), Gamma (none)
- By Lancefield grouping: A, B, C, D, F, G (based on cell wall carbohydrate)
S. pyogenes (Group A Streptococcus)
- Beta-haemolytic, Lancefield A
- Bacitracin sensitive (A disc)
- M protein - major virulence factor, antiphagocytic, basis of serotyping
Diseases:
- Pharyngitis, tonsillitis
- Impetigo (school sores)
- Scarlet fever (SPE erythrogenic toxin, phage-encoded)
- Necrotising fasciitis
- Streptococcal TSS (SPE superantigen)
- Post-streptococcal: Rheumatic fever, Post-streptococcal GN (PSGN)
PSGN: Nephritogenic strains (M types 12, 49) β subepithelial "humps" on EM β β complement (C3) β haematuria, hypertension, oedema. ASO titre elevated.
Rheumatic fever - Jones Criteria (major):
- Carditis, Polyarthritis (migratory), Sydenham's chorea, Erythema marginatum, Subcutaneous nodules
- CATCHES = Carditis, Arthritis, Chorea, Erythema marginatum, Subcutaneous nodules
S. agalactiae (Group B Streptococcus)
- Beta-haemolytic, Lancefield B
- CAMP test positive (arrowhead haemolysis with S. aureus beta-lysin)
- Hippurate hydrolysis positive
- Normal vaginal flora in 20-30% women
Diseases:
- Neonatal meningitis + sepsis (most common cause)
- Neonatal pneumonia
- UTI in pregnant women
- Diabetic foot infections
Prevention: GBS screening at 35-37 weeks gestation; intrapartum IV penicillin if positive
S. pneumoniae
- Alpha-haemolytic (green on blood agar)
- Lancet-shaped diplococci
- Bile solubility test positive (autolysis in bile/deoxycholate)
- Optochin sensitive
- Inulin fermentation positive
- Quellung reaction (capsular swelling) - for serotyping
Virulence factors:
- Capsule - most important (prevents phagocytosis)
- IgA protease, pneumolysin, surface proteins
Diseases:
- Lobar pneumonia (most common cause in adults)
- Meningitis (most common in adults + elderly)
- Otitis media (most common in children)
- Sinusitis
- Most common cause of CAP at all ages
Viridans Streptococci
- Alpha-haemolytic (partially), bile insoluble, optochin resistant
- Normal oral flora
- Most common cause of Subacute Bacterial Endocarditis (SBE) - S. sanguis, S. mutans, S. mitis
- S. bovis (now S. gallolyticus) - associated with colorectal carcinoma (always colonoscopy!)
- S. mutans - dental caries
Enterococcus (Group D)
- Alpha or gamma haemolytic
- Grows in 6.5% NaCl and bile esculin positive
- Intrinsically resistant to many antibiotics
- VRE (Vancomycin-Resistant Enterococcus) - major hospital pathogen
- Diseases: UTI, endocarditis, biliary infections
SECTION 3: GRAM-POSITIVE BACILLI
Bacillus species (Aerobic, Spore-forming)
Bacillus anthracis
- Bamboo-cane appearance (jointed rods)
- Non-motile (unlike other Bacillus)
- Non-haemolytic on blood agar
- Capsule made of poly-D-glutamic acid (not polysaccharide)
- Medusa head / Frosted glass colonies
- String of pearls test (penicillin inhibition forms spheroplasts)
- Toxins: PA + EF (oedema toxin), PA + LF (lethal toxin)
Forms of anthrax:
- Cutaneous (most common, 95%) - malignant pustule β black eschar
- Inhalational (Woolsorter's disease) - widened mediastinum on CXR
- GI anthrax - from ingestion of spores
Bacillus cereus
- Food poisoning - 2 types:
- Emetic type (1-5 hrs, vomiting) - rice dishes (cereulide toxin, heat stable)
- Diarrhoeal type (8-16 hrs, diarrhoea) - meat/vegetables (enterotoxin, heat labile)
Clostridium species (Anaerobic, Spore-forming)
| Species | Spore position | Disease |
|---|
| C. tetani | Terminal (drumstick) | Tetanus |
| C. botulinum | Subterminal/oval | Botulism |
| C. perfringens | Subterminal/oval | Gas gangrene, food poisoning |
| C. difficile | Subterminal | Pseudomembranous colitis |
C. tetani
- Terminal spore (drumstick/tennis racket appearance)
- Tetanospasmin (plasmid) β retrograde to spinal cord β blocks GABA/glycine β spastic paralysis
- Tetanolysin - haemolysin
- Generalised tetanus: trismus β risus sardonicus β opisthotonus
- Neonatal tetanus - umbilical stump infection, poor immunisation of mother
C. botulinum
- Subterminal spore
- Most potent biological toxin (LD50 ~1 ng/kg)
- Blocks ACh at NMJ β flaccid descending paralysis
- Infant botulism - most common form in USA; honey β spores germinate in gut
- Home-canned food - classic adult botulism (type A, B, E)
C. perfringens
- Stormy fermentation in litmus milk (rapid gas production)
- Nagler reaction positive (lecithinase activity on egg-yolk agar)
- Double zone of haemolysis on blood agar
- Alpha toxin (lecithinase) - most important
- Type A: gas gangrene, food poisoning
- Type C: Necrotising enteritis (Pig-bel disease, Papua New Guinea)
C. difficile
- Yellow, horse-manure smell colonies on CCFA medium
- Toxin A (enterotoxin) + Toxin B (cytotoxin)
- Glucosylates Rho GTPases β cytoskeletal disruption
- Pseudomembrane on colonoscopy (yellow plaques)
- Associated with clindamycin, fluoroquinolones, broad-spectrum antibiotics
- Diagnosis: Stool PCR (most sensitive), EIA for toxins
- Treatment: Oral vancomycin or fidaxomicin (first line), bezlotoxumab (prevents recurrence)
Corynebacterium diphtheriae
- Club-shaped (Chinese letter arrangement)
- Albert's stain - metachromatic (volutin) granules at poles
- Tellurite medium - black/grey colonies (reduces tellurite)
- Elek's test - immunodiffusion to detect toxin production
- Toxin only produced in lysogenic strains (infected by Ξ²-corynephage)
- Toxin: ADP-ribosylates EF-2 β blocks protein synthesis β myocarditis, neuropathy
Clinical: Bull-neck, pseudomembrane (bleeds on removal), Schick test
Listeria monocytogenes
- Small Gram-positive rod
- Tumbling motility at room temperature (22Β°C), non-motile at 37Β°C
- Cold enrichment - grows at 4Β°C (refrigerator temperature)
- Actin rocket motility inside host cells
- Umbrella-shaped motility in semi-solid agar
Diseases:
- Neonatal meningitis + sepsis (along with GBS)
- Meningitis in elderly + immunocompromised
- Granulomatosis infantiseptica (disseminated in neonates)
- Food-borne (soft cheeses, deli meats, raw vegetables)
- Treatment: Ampicillin + Gentamicin (NOT cephalosporins - intrinsically resistant)
SECTION 4: GRAM-NEGATIVE COCCI
Neisseria
N. meningitidis
- Diplococci (kidney-shaped pairs), intracellular in CSF
- Requires chocolate agar or blood agar with COβ
- Polysaccharide capsule - key virulence factor (13 serogroups: A, B, C, W, Y most important)
- Ferments glucose + maltose (distinguishes from N. gonorrhoeae)
- IgA protease
Diseases:
- Meningitis (most common bacterial meningitis in meningitis belt Africa)
- Meningococcaemia with Waterhouse-Friderichsen syndrome (bilateral adrenal haemorrhage, purpuric rash, DIC)
- Petechiae/purpura is the hallmark
- Terminal complement deficiency (C5-C9) β recurrent Neisseria infections
Treatment: Penicillin G (IV), ceftriaxone
Prophylaxis for contacts: Rifampicin or Ciprofloxacin or Ceftriaxone (single dose)
N. gonorrhoeae
- No polysaccharide capsule
- Ferments glucose only (not maltose)
- Thayer-Martin medium (chocolate agar + antibiotics)
- Pili - type IV, antigenic variation (pilE gene)
- Protein II (Opa proteins) - mediate attachment to epithelial cells
- IgA protease - cleaves secretory IgA
- Beta-lactamase (plasmid) - penicillin resistance
Diseases:
- Urethritis, cervicitis
- PID, salpingitis (Fitz-Hugh-Curtis syndrome - perihepatitis)
- Ophthalmia neonatorum (treated with erythromycin eye ointment)
- Disseminated gonococcal infection (DGI): septic arthritis, skin lesions, tenosynovitis
- Treatment: Ceftriaxone IM (DOC now due to widespread resistance)
SECTION 5: GRAM-NEGATIVE BACILLI
Enterobacteriaceae (Lactose fermenters vs Non-fermenters)
MacConkey agar:
- Pink colonies (lactose fermenters): E. coli, Klebsiella, Enterobacter, Citrobacter
- Colourless (non-fermenters): Salmonella, Shigella, Proteus
Escherichia coli
Normal colonic flora but pathogenic strains:
| Strain | Toxin/Mechanism | Disease |
|---|
| ETEC | LT (βcAMP) + ST (βcGMP) | Traveller's diarrhoea, infant diarrhoea |
| EPEC | A/E lesion (attaching-effacing), no toxin | Infant diarrhoea (developing countries) |
| EHEC (STEC) | Shiga-like toxin (verotoxin), O157:H7 | Bloody diarrhoea β HUS |
| EIEC | Intracellular invasion (like Shigella) | Dysentery (bloody diarrhoea, fever) |
| EAEC | Aggregative adherence, ST-like | Persistent diarrhoea in children |
| DAEC | Diffuse adherence | UTI, mild diarrhoea |
Other E. coli diseases:
- UTI (most common cause) - fimbriae, P pili (uropathogenic)
- Neonatal meningitis (K1 capsular antigen)
- Neonatal meningitis: E. coli K1 + GBS = top 2 causes
Klebsiella
- Large mucoid colonies, thick capsule (mucoviscosity)
- Currant jelly sputum (haemorrhagic, mucoid)
- FriedlΓ€nder's pneumonia - upper lobe, alcohol/diabetes
- UTI (hospital-acquired, catheter)
- K. granulomatis (formerly Calymmatobacterium) β Granuloma inguinale (Donovanosis)
- Donovan bodies in macrophages
Salmonella
Salmonella typhi (Typhoid fever)
Pathogenesis:
- Ingested β invades Peyer's patches (ileum) β M cells β macrophages β blood
- Bacteraemia β seeded to liver, spleen, bone marrow, Peyer's patches
Clinical (weeks):
- Week 1: Fever, step-ladder pattern, headache, relative bradycardia
- Week 2: Rose spots (anterior chest), splenomegaly, hepatomegaly
- Week 3: Complications - intestinal haemorrhage/perforation, myocarditis
- Week 4: Resolution
Lab:
- Week 1: Blood culture (most sensitive early)
- Week 2-3: Stool + urine culture
- Widal test: O agglutinins (active disease), H agglutinins (past infection/vaccination)
- Significant: O titre β₯1:160; H titre β₯1:320
Treatment: Azithromycin (first line outpatient), Ceftriaxone (severe), Ciprofloxacin (if sensitive)
Carrier state: Bile β faecal carrier (chronic carriage in gallbladder)
Non-typhoidal Salmonella
- Food poisoning (poultry, eggs)
- Gastroenteritis (self-limiting, 2-3 days)
- Bacteraemia in sickle cell disease (Salmonella osteomyelitis)
Shigella
4 species by decreasing severity:
- S. dysenteriae (most severe, Shiga toxin, HUS) > S. flexneri > S. boydii > S. sonnei (mildest, most common in developed world)
Pathogenesis:
- Very small inoculum (10-100 organisms)
- Invades colonic mucosa β intracellular spread via actin rockets
- Causes dysentery (bloody diarrhoea + mucus + pus)
Lab: Non-lactose fermenter, non-motile, non-gas producing, HβS negative
Treatment: Azithromycin / Ciprofloxacin (antibiotics always indicated - reduces duration)
Vibrio
Vibrio cholerae
- Comma-shaped, oxidase positive
- TCBS agar - yellow colonies (sucrose fermenter)
- Serotype O1 (classic + El Tor biotypes) and O139 cause epidemics
- Darting motility (shooting star appearance)
- Dark-field microscopy - characteristic motility
- Toxin: Cholera toxin (CT) - phage-encoded (CTXΟ), βcAMP
- Rice-water diarrhoea, severe dehydration, "washerwoman's hands"
- Treatment: Oral rehydration salts (primary); Doxycycline (antibiotic shortens duration)
V. parahaemolyticus
- Seafood consumption (raw shellfish, crabs)
- Watery or bloody diarrhoea
- Blue-green colonies on TCBS (non-sucrose fermenter)
V. vulnificus
- Most virulent Vibrio
- Necrotising soft tissue infections in coastal areas
- Liver disease patients β fatal septicaemia from raw oysters
Campylobacter
Campylobacter jejuni
- Most common bacterial cause of food-borne diarrhoea globally
- S-shaped / gull-wing-shaped rods
- Microaerophilic (5% Oβ)
- 42Β°C optimal growth temperature (selective advantage)
- Darting motility (corkscrew)
- Campy-BAP medium (blood agar + antibiotics, 42Β°C)
Diseases:
- Bloody diarrhoea (invasive)
- Post-infectious complications:
- Guillain-BarrΓ© syndrome (GBS) - molecular mimicry, ganglioside antibodies
- Reactive arthritis
- C. jejuni serotype O:19 most associated with GBS
Treatment: Azithromycin or Erythromycin
Helicobacter pylori
- Spiral-shaped, microaerophilic
- Urease positive (most important virulence factor - produces ammonia, neutralises acid)
- CLO test (Campylobacter-like organism test) - biopsy urease test
Virulence factors:
- Urease, flagella, adhesins
- CagA (cytotoxin-associated gene A) - associated with gastric cancer + peptic ulcer
- VacA (vacuolating cytotoxin) - mucosal damage
Diseases:
- Peptic ulcer disease (duodenal 95%, gastric 70%)
- Chronic gastritis (type B antral gastritis)
- Gastric adenocarcinoma (IARC Group 1 carcinogen)
- MALT lymphoma (eradication alone can cure early MALT lymphoma)
Diagnosis:
- Urea breath test (UBT) - best non-invasive test, best for test of cure
- Stool antigen test (non-invasive)
- Serology (IgG ELISA) - cannot distinguish active vs past
- Endoscopic biopsy: CLO test + histology + culture (most specific)
Treatment (Triple therapy):
- PPI + Clarithromycin + Amoxicillin (or Metronidazole) for 14 days
Pseudomonas aeruginosa
- Oxidase positive, non-fermenter
- Blue-green pigment (pyocyanin) + fluorescent pigment (pyoverdin)
- Grape-like/fruity odour (2-aminoacetophenone)
- Grows at 42Β°C (selective advantage)
- Mucoid strains in cystic fibrosis (alginate capsule)
Virulence: Exotoxin A (blocks EF-2), Exoenzyme S, alkaline protease, phospholipase C, pyocyanin (damages cilia, generates free radicals)
Diseases:
- Nosocomial pneumonia (ventilator-associated)
- Burn wound infections
- Malignant otitis externa (diabetics, elderly)
- Cystic fibrosis lung infections
- Hot tub folliculitis
- UTI (catheterised patients)
- Ecthyma gangrenosum (black necrotic skin lesion in immunocompromised)
Treatment: Piperacillin-tazobactam, Carbapenems, Aminoglycosides, Ciprofloxacin (anti-pseudomonal)
Haemophilus influenzae
- Small pleomorphic Gram-negative coccobacillus
- Requires Factor X (haemin) + Factor V (NAD) for growth
- Chocolate agar (blood heated to 80Β°C releases X and V factors)
- Satellitism around Staph aureus colonies on blood agar
- Type b capsule (polyribose ribitol phosphate) - most virulent, vaccine-preventable
Diseases:
- Meningitis (before Hib vaccine - most common in children)
- Epiglottitis (type b) - "thumb sign" on lateral neck X-ray
- Pneumonia (non-typeable strains, adults with COPD)
- Otitis media, sinusitis
- Conjunctivitis (non-typeable)
Treatment: Ceftriaxone (meningitis), Amoxicillin-clavulanate (URTI)
Bordetella pertussis
- Small Gram-negative coccobacillus
- Bordet-Gengou medium (potato blood glycerol agar) - mercury drop colonies
- Filamentous haemagglutinin (FHA) - major adhesin
- Pertussis toxin (PT), tracheal cytotoxin, adenylate cyclase toxin
Clinical stages (whooping cough):
- Catarrhal phase (1-2 weeks) - most infectious, mild cold symptoms
- Paroxysmal phase (2-6 weeks) - paroxysmal cough + inspiratory whoop + post-tussive vomiting
- Convalescent phase (weeks-months) - gradual recovery
Lab: Lymphocytosis (absolute), PT causes lymphocytes to stay in blood
Treatment: Azithromycin (drug of choice), Erythromycin
Prevention: DTaP (children), Tdap (adults, especially pregnant women)
Legionella pneumophila
- BCYE agar (L-cysteine + iron required)
- Cannot be seen on Gram stain easily (takes up safranin poorly)
- Dieterle silver stain used for tissue
- Intracellular pathogen (multiplies in macrophages + protozoa)
- Source: Air conditioning cooling towers, water heaters, hospital water
Clinical (Legionnaires' disease):
- Severe pneumonia (especially in middle-aged men, smokers, immunocompromised)
- Relative bradycardia, hyponatraemia, elevated LFTs, diarrhoea, confusion
- "Pontiac fever" = mild flu-like illness (same organism, no pneumonia)
Diagnosis:
- Urinary antigen test (most rapid, detects serogroup 1)
- Culture on BCYE (gold standard, slow)
- DFA (direct fluorescent antibody)
Treatment: Azithromycin or Fluoroquinolones (macrolides or quinolones, NOT beta-lactams)
Brucella
- Obligate intracellular (facultative)
- Gram-negative coccobacillus
- Zoonosis - from cattle (B. abortus), goat/sheep (B. melitensis - most virulent), pigs (B. suis), dogs (B. canis)
- Transmission: unpasteurised milk/cheese, contact with infected animals
Clinical: Undulant fever (fever spikes every 2-3 days), hepatosplenomegaly, lymphadenopathy, arthritis, orchitis
Lab: Blood culture (prolonged incubation 4-6 weeks), serology (Wright's agglutination test)
Treatment: Doxycycline + Rifampicin (6 weeks) or Doxycycline + Streptomycin
Yersinia
Yersinia pestis (Plague)
- Gram-negative coccobacillus, bipolar staining (safety-pin appearance) with Wayson's stain
- Reservoir: Rodents; Vector: Rat flea (Xenopsylla cheopis)
- Forms: Bubonic (most common, bubo = inguinal lymph node), Pneumonic (most dangerous, droplet spread), Septicaemic
Y. enterocolitica
- Cold-enrichment, grows at 4Β°C
- Mimics acute appendicitis (mesenteric lymphadenitis)
- Bloody diarrhoea, fever
Francisella tularensis (Tularaemia)
- Most infectious bacterium (10 organisms cause disease)
- Gram-negative coccobacillus
- Reservoir: Rabbits, rodents; Vector: Ticks, deer flies
- Transmission: tick bite, handling infected animals, inhalation
- Requires cysteine for growth
- Forms: Ulceroglandular (most common), Pneumonic, Oculoglandular, Typhoidal
SECTION 6: ANAEROBIC BACTERIA
Bacteroides fragilis
- Most common anaerobe in human colon
- Polysaccharide capsule (only anaerobe with a capsule)
- Metronidazole - drug of choice
- Important in intra-abdominal infections, peritonitis
Fusobacterium
- Long pointed rods
- Associated with Lemierre's syndrome (septic thrombophlebitis of internal jugular vein after pharyngitis)
- Also in periodontal disease (along with Treponema - ANUG)
SECTION 7: SPIROCHETES
Treponema pallidum (Syphilis)
- Cannot be cultured on artificial media
- Too thin for Gram stain
- Dark-field microscopy (corkscrew motility)
- Silver stain (Warthin-Starry, Levaditi) for tissue sections
Stages of syphilis:
| Stage | Features | Serology |
|---|
| Primary | Painless chancre (indurated, clean base), inguinal lymphadenopathy | VDRL may be negative early |
| Secondary | Maculopapular rash (palms + soles), condylomata lata, mucosal patches, alopecia, fever | VDRL strongly positive |
| Latent | Asymptomatic (early <1yr, late >1yr) | Positive |
| Tertiary | Gummas, CV syphilis (aortic regurgitation, aortic aneurysm), neurosyphilis | VDRL may be negative |
Serological tests:
- Non-treponemal (screening): VDRL, RPR - become negative after treatment (used for monitoring)
- Treponemal (confirmatory): TPHA, FTA-ABS, TPPA - remain positive lifelong
- Biological false positives (VDRL): SLE, antiphospholipid syndrome, malaria, pregnancy, TB, infectious mononucleosis
Neurosyphilis: CSF-VDRL (specific but insensitive), treat with IV penicillin G
Congenital syphilis:
- Hutchinson's teeth, interstitial keratitis, sensorineural deafness (Hutchinson's triad)
- Saddle nose, sabre tibia, Clutton's joints
Treatment: Benzathine penicillin G (primary, secondary, early latent)
Leptospira (Leptospirosis)
- Hooked ends (question mark appearance)
- Fletcher's medium (semi-solid)
- Dark-field microscopy
Transmission: Contact with urine of infected rodents/animals (Weil's disease from rats)
Weil's disease (severe leptospirosis): Jaundice + renal failure + haemorrhage
Treatment: Penicillin G (severe), Doxycycline (mild/prophylaxis)
Borrelia
Borrelia burgdorferi (Lyme disease)
- Vector: Ixodes tick (deer tick)
- Giemsa stain, Barbour-Stoenner-Kelly (BSK) medium
Stages:
- Stage 1: Erythema migrans (bulls-eye rash) at tick bite site
- Stage 2: Dissemination - Bell's palsy, meningitis, carditis (heart block)
- Stage 3: Arthritis (large joints, esp. knee), chronic neurological (Lyme encephalopathy)
Treatment: Doxycycline (stages 1-2), Ceftriaxone (stage 3/neurological)
Borrelia recurrentis (Relapsing fever)
- Vector: Body louse (epidemic relapsing fever)
- Giemsa stain during febrile episodes
- Antigenic variation of OspC protein β relapsing fever
SECTION 8: INTRACELLULAR BACTERIA
Rickettsia
Obligate intracellular, Gram-negative
Arthropod vectors (tick, mite, louse, flea)
Giemsa stain, Weil-Felix reaction (agglutination with Proteus strains)
| Disease | Organism | Vector | Weil-Felix |
|---|
| Rocky Mountain Spotted Fever | R. rickettsii | Tick | OX-2, OX-19 |
| Epidemic typhus | R. prowazekii | Body louse | OX-19 |
| Endemic (murine) typhus | R. typhi | Rat flea | OX-19 |
| Scrub typhus | Orientia tsutsugamushi | Trombiculid mite | OX-K |
| Q fever | Coxiella burnetii | Inhalation (no vector) | Negative |
Key features:
- Scrub typhus - eschar at bite site, characteristic; Indian Ocean islands, Asia
- Q fever - atypical pneumonia + hepatitis + no rash + no vector; phase I/II antigen; Weil-Felix negative
- Epidemic typhus - louse-borne, war/crowded conditions, Brill-Zinsser disease (recrudescence)
- RMSF - petechial rash starts on wrists and ankles β spreads centrally
Treatment: All rickettsial diseases β Doxycycline (drug of choice)
Chlamydia
Obligate intracellular, Gram-negative (no peptidoglycan in cell wall)
Two forms:
- Elementary body (EB) - infectious, metabolically inert, extracellular
- Reticulate body (RB) - replicating, intracellular, metabolically active
Staining: Giemsa (mauve intracytoplasmic inclusions)
Chlamydia trachomatis (serovars)
| Serovars | Disease |
|---|
| A, B, Ba, C | Trachoma (leading cause of infectious blindness) |
| D-K | Urethritis, cervicitis, PID, epididymitis, neonatal conjunctivitis, neonatal pneumonia |
| L1, L2, L3 | Lymphogranuloma venereum (LGV) |
Trachoma: Follicular conjunctivitis β pannus formation β scarring β entropion β blindness
LGV: Painless genital ulcer β inguinal lymphadenopathy (buboes, "groove sign")
C. pneumoniae (TWAR strain)
- Atypical pneumonia (mild, walking pneumonia)
- Associated with atherosclerosis
C. psittaci
- Psittacosis/Ornithosis - from birds (parrots, pigeons)
- Atypical pneumonia + systemic features
Treatment: Doxycycline or Azithromycin (all Chlamydia)
- Trachoma: Azithromycin single dose (SAFE strategy)
Mycoplasma
No cell wall β not seen on Gram stain, resistant to penicillin/beta-lactams
Mycoplasma pneumoniae
- Cold agglutinins (IgM against I antigen on RBCs) - positive in ~50%
- Causes autoimmune haemolytic anaemia
- Atypical pneumonia ("walking pneumonia")
- Eaton agent - grows on Eaton's medium (SP4 medium)
- Fried-egg colonies on Eaton's medium
Clinical: Gradual onset fever, dry cough, bilateral patchy infiltrates
Complications: Stevens-Johnson syndrome, encephalitis, haemolytic anaemia, erythema multiforme
Treatment: Azithromycin or Doxycycline (NOT penicillin)
Mycoplasma genitalium
- NGU (non-gonococcal urethritis)
- Emerging resistance to azithromycin; moxifloxacin used
Ureaplasma urealyticum
- NGU, splits urea
- Associated with premature delivery
SECTION 9: MYCOBACTERIUM
Mycobacterium tuberculosis
Cell wall: Rich in mycolic acid (wax D) β acid-fast (retain carbol fuchsin after acid-alcohol decolourisation)
Growth characteristics:
- Strict aerobe
- Slow growth (generation time 16-20 hrs)
- LJ medium (eggs + glycerol + malachite green) - 4-8 weeks
- Buff, rough, dry, crumbly colonies
Virulence factors:
- Cord factor (Trehalose 6,6'-dimycolate) - inhibits PMN migration, toxic to mitochondria, causes serpentine cord growth
- Wax D (mycolic acid) - acid-fastness, adjuvant property
- Sulfatides - inhibit phagolysosome fusion
- Lipoarabinomannan (LAM) - scavenges free radicals, inhibits T cell activation
Pathogenesis:
- Droplet nuclei (<5 ΞΌm) β alveoli β ingested by macrophages (but resists killing)
- Primary complex (Ghon focus = parenchymal lesion + hilar lymph node = Ranke complex)
- Hypersensitivity (Type IV, delayed, Th1-mediated) = tuberculin sensitivity
- Caseation necrosis, granuloma (epithelioid cells, Langhan's giant cells)
Diagnosis:
- Sputum AFB smear (ZN stain, most rapid, but needs 5,000-10,000 bacilli/mL)
- Culture on LJ medium (gold standard, but slow)
- BACTEC/MGIT (liquid culture, fastest - 1-3 weeks)
- Xpert MTB/RIF (PCR-based, detects TB + rifampicin resistance simultaneously, 2 hours) - WHO recommended first test
- Tuberculin skin test (Mantoux) - inject 5TU PPD intradermally, read at 48-72 hrs
- β₯5 mm: HIV, recent contact, fibrotic lesion on CXR
- β₯10 mm: High-risk groups (healthcare workers, immigrants, homeless)
- β₯15 mm: No risk factors
Tuberculin false positives: BCG vaccination, NTM (non-tuberculous mycobacteria)
Tuberculin false negatives: Immunocompromised (HIV, malnutrition, old age), miliary TB, sarcoidosis
Treatment (DOTS):
- Intensive phase (2 months): HRZE (Isoniazid + Rifampicin + Pyrazinamide + Ethambutol)
- Continuation phase (4 months): HR (Isoniazid + Rifampicin)
Drug adverse effects:
| Drug | Adverse Effects |
|---|
| Isoniazid (H) | Peripheral neuropathy (B6), hepatitis, drug lupus, seizures |
| Rifampicin (R) | Orange secretions, hepatitis, flu syndrome, enzyme inducer |
| Pyrazinamide (Z) | Hyperuricaemia, hepatotoxicity |
| Ethambutol (E) | Optic neuritis (retrobulbar, colour blindness), avoid in children |
| Streptomycin (S) | Ototoxicity (vestibular > cochlear), nephrotoxicity |
Mycobacterium leprae (Leprosy)
- Cannot be cultured on artificial media (like T. pallidum)
- Grown in armadillo footpads (in vivo)
- Acid-fast (ZN stain, also Wade-Fite stain)
- Fite-Faraco stain used in tissue sections
Ridley-Jopling classification:
| Type | Immunity | Bacilli | Lepromin test | Features |
|---|
| Tuberculoid (TT) | High (Th1) | Few (paucibacillary) | Positive | 1-2 anaesthetic, hypopigmented lesions; thick nerves |
| Borderline tuberculoid (BT) | β | Few | + | - |
| Mid-borderline (BB) | Intermediate | Intermediate | Β± | Unstable |
| Borderline lepromatous (BL) | β | Many | - | - |
| Lepromatous (LL) | Low (Th2) | Many (multibacillary) | Negative | Diffuse infiltration, leonine facies, madarosis, nerve damage bilateral |
Lepromin test (Mitsuda test):
- Tests cell-mediated immunity, not diagnosis
- Positive = TT (good prognosis), Negative = LL (poor prognosis)
Complications:
- Type 1 reaction (reversal reaction) - upgrading or downgrading, treat with prednisolone
- Type 2 reaction (ENL - Erythema Nodosum Leprosum) - immune complex, treat with thalidomide/prednisolone
Treatment (WHO regimen):
- Paucibacillary (PB): Rifampicin (monthly supervised) + Dapsone (daily) Γ 6 months
- Multibacillary (MB): Rifampicin + Clofazimine (monthly supervised) + Dapsone + Clofazimine (daily) Γ 12 months
Non-Tuberculous Mycobacteria (NTM)
| Organism | Disease |
|---|
| M. avium-intracellulare (MAC) | Disseminated infection in AIDS (CD4 <50) |
| M. kansasii | Pulmonary TB-like disease |
| M. marinum | Swimming pool granuloma, fish tank granuloma |
| M. ulcerans | Buruli ulcer (painless ulcers) |
| M. fortuitum, M. chelonae, M. abscessus | Rapidly growing, post-injection abscesses, LASIK keratitis |
| M. scrofulaceum | Cervical lymphadenitis in children |
SECTION 10: VIROLOGY
DNA Viruses (mnemonic: HHAPPPY)
Herpesvirus, Hepadnavirus, Adenovirus, Papillomavirus, Poxvirus, Parvovirus, Yest (fungus, not virus!)
Herpes Viruses (HHV 1-8)
| Virus | Primary Disease | Latency Site | Reactivation |
|---|
| HSV-1 (HHV-1) | Oral herpes, gingivostomatitis | Trigeminal ganglion | Cold sores, herpes labialis |
| HSV-2 (HHV-2) | Genital herpes | Sacral ganglion | Genital recurrences |
| VZV (HHV-3) | Chickenpox | Dorsal root/cranial ganglia | Herpes zoster (shingles) |
| EBV (HHV-4) | Infectious mononucleosis, Burkitt's lymphoma | B lymphocytes | Lymphomas in immunocompromised |
| CMV (HHV-5) | Congenital CMV, mono-like illness | Monocytes/macrophages | Retinitis, pneumonitis, colitis in AIDS |
| HHV-6 | Roseola infantum (exanthem subitum) | T lymphocytes | Encephalitis in transplant |
| HHV-7 | Roseola, pityriasis rosea | T lymphocytes | - |
| HHV-8 (KSHV) | Kaposi's sarcoma | B lymphocytes | Kaposi's sarcoma in AIDS/transplant |
EBV (Infectious Mononucleosis):
- Fever + pharyngitis + lymphadenopathy + splenomegaly
- Monospot test (heterophile antibodies) - positive
- Atypical lymphocytes (Downey cells) on peripheral smear
- Ampicillin/amoxicillin β maculopapular rash in EBV (avoid!)
- Associated: Burkitt's lymphoma, Nasopharyngeal carcinoma, Post-transplant lymphoproliferative disorder, CNS lymphoma in AIDS
CMV:
- Most common congenital viral infection causing hearing loss
- Periventricular calcifications (congenital CMV) vs cortical calcifications (Toxoplasma)
- Owl-eye inclusions in infected cells
- CMV retinitis (AIDS, CD4 <50) - "pizza pie" or "ketchup & cheese" appearance
VZV:
- Chickenpox: Centripetal distribution, "dew drop on rose petal" vesicles, all stages simultaneously
- Herpes zoster: Dermatomal, painful, unilateral; Ramsay Hunt syndrome (VII nerve + ear)
- Tzanck smear - multinucleated giant cells (both HSV and VZV)
- Treatment: Aciclovir (all herpesviruses), Valaciclovir (higher bioavailability)
Hepatitis Viruses
| Virus | Type | Transmission | Chronicity | Key Feature |
|---|
| HAV | RNA (Picorna) | Faeco-oral | None | Self-limiting, no carrier |
| HBV | DNA (Hepadna) | Blood, sexual, vertical | 5-10% adults, 90% neonates | Dane particle, HBsAg, HBeAg, anti-HBc |
| HCV | RNA (Flavi) | Blood (IVDU, transfusion) | 70-80% | Most common cause of chronic liver disease in West |
| HDV | RNA (delta) | Blood, sexual | Only with HBV | Satellite virus, needs HBsAg |
| HEV | RNA (Hepevirus) | Faeco-oral | None | High mortality in pregnancy (20-25%) |
HBV markers:
| Marker | Meaning |
|---|
| HBsAg | Active infection (surface antigen) |
| Anti-HBs | Recovery/immunity (vaccination) |
| HBeAg | High infectivity, active replication |
| Anti-HBe | Low infectivity, seroconversion |
| Anti-HBc IgM | Acute HBV (also present in window period) |
| Anti-HBc IgG | Past infection or chronic |
| HBV DNA | Gold standard for viral replication |
Window period: HBsAg gone, Anti-HBs not yet appeared β only Anti-HBc IgM positive
Treatment HBV: Tenofovir or Entecavir (first line)
Treatment HCV: Direct-acting antivirals (DAAs) - Sofosbuvir + Ledipasvir or Sofosbuvir + Velpatasvir (~95% cure rate)
HIV
Classification: Lentivirus (Retrovirus family), RNA virus, reverse transcriptase
Receptor: CD4 + CCR5/CXCR4 (co-receptors)
- CCR5 - used by macrophage-tropic strains (M-tropic, R5 strains) - early infection
- CXCR4 - used by T-cell tropic strains (T-tropic, X4 strains) - late disease
- Delta 32 mutation in CCR5 β resistance to HIV (homozygous protective)
CD4 count and infections:
| CD4 count | Opportunistic infections |
|---|
| <500 | Candida, TB, HSV, HZV |
| <200 | PCP (P. jirovecii), Toxoplasma, Cryptosporidium, Microsporidium |
| <100 | Cryptococcus, Bartonella |
| <50 | CMV (retinitis), MAC (disseminated) |
Diagnosis:
- ELISA (4th generation - detects IgG + p24 antigen) - screening
- Western blot - confirmatory (bands at gp120, gp41, p24)
- HIV RNA PCR - viral load (monitors treatment), used in neonates (maternal antibodies confound serology for 18 months)
Treatment (ART): HAART - start in ALL patients regardless of CD4 count
- Standard first-line: 2 NRTIs + 1 INSTI (e.g., TDF + FTC + Dolutegravir)
Drug classes:
| Class | Examples | Key Side Effect |
|---|
| NRTIs | Zidovudine, Lamivudine, Tenofovir, Emtricitabine | Lactic acidosis, lipodystrophy; AZT β anaemia |
| NNRTIs | Efavirenz, Nevirapine | CNS effects (efavirenz), hepatotoxicity (nevirapine) |
| PIs | Lopinavir, Ritonavir, Atazanavir | Lipodystrophy, GI, jaundice (atazanavir) |
| INSTIs | Dolutegravir, Raltegravir | Well tolerated, weight gain |
| Fusion inhibitor | Enfuvirtide | SC injection, injection site reactions |
| CCR5 antagonist | Maraviroc | Only for R5 strains (tropism testing needed) |
Respiratory Viruses
| Virus | Disease | Key Facts |
|---|
| Influenza A, B | Flu, pneumonia | Haemagglutinin (HA) + Neuraminidase (NA) surface antigens |
| Respiratory Syncytial Virus (RSV) | Bronchiolitis (infants), pneumonia | Most common cause of bronchiolitis in infants <2 years |
| Parainfluenza | Croup (laryngotracheobronchitis), URI | Steeple sign on X-ray |
| Adenovirus | URI, pharyngoconjunctival fever, military recruits | DNA virus |
| Rhinovirus | Common cold | Picornavirus, most common cause |
| Coronavirus | SARS, MERS, COVID-19 | Spike protein, ACE2 receptor |
Influenza:
- Antigenic drift (minor changes in HA/NA, point mutations) β seasonal epidemics
- Antigenic shift (major reassortment of genome segments) β pandemics
- Reassortment between human + animal (avian/swine) strains
- Treatment: Oseltamivir (Tamiflu) - neuraminidase inhibitor, within 48 hours of symptoms
- Amantadine/Rimantadine (M2 inhibitors) - only influenza A, widespread resistance
Childhood Exanthems
| Disease | Virus | Rash | Other features |
|---|
| Measles | Paramyxovirus (Morbillivirus) | Maculopapular, centrifugal, appears 4th day of fever | Koplik spots (pathognomonic, before rash) |
| Rubella | Togavirus | Maculopapular, faceβtrunk, fine | Post-auricular lymphadenopathy, forchheimer spots, congenital rubella |
| Chickenpox | VZV | Vesicular, centripetal, all stages simultaneously | "Dew drop on rose petal" |
| Roseola infantum | HHV-6 | Rash after fever subsides | High fever β febrile seizures β rash |
| Erythema infectiosum | Parvovirus B19 | Slapped cheek β lacy rash | Aplastic crisis in sickle cell, hydrops fetalis |
| Hand-foot-mouth | Coxsackievirus A16 | Vesicles on hands, feet, mouth | Enterovirus |
Measles complications: Pneumonia, encephalitis, SSPE (Subacute sclerosing panencephalitis) - years later
Congenital rubella syndrome (CRS):
- Cataracts, patent ductus arteriosus (PDA), sensorineural deafness
- "Blueberry muffin" baby (dermal haematopoiesis)
- Prevention: MMR vaccine (live attenuated, avoid in pregnancy)
Enteroviruses (Picornaviridae)
- Poliovirus, Coxsackievirus, Echovirus, Enterovirus
- Faeco-oral transmission, replicate in intestine
- Poliovirus: Anterior horn cells β lower motor neurone lesion β flaccid paralysis
- OPV (oral, live attenuated) vs IPV (injectable, killed)
- Vaccine-associated paralytic poliomyelitis (VAPP) - rare, only with OPV
- Coxsackievirus A16 - Hand-foot-mouth disease, herpangina
- Coxsackievirus B - Myocarditis (most common cause of viral myocarditis), pleurodynia (Bornholm disease), neonatal sepsis
SECTION 11: MYCOLOGY (FUNGI)
Classification
Superficial: Malassezia furfur (tinea versicolor), Trichosporon (white piedra)
Cutaneous (Dermatophytes): Trichophyton, Microsporum, Epidermophyton β tinea (ringworm)
Subcutaneous: Sporothrix schenckii (sporotrichosis), Madurella (Madura foot)
Systemic: Histoplasma, Coccidioides, Blastomyces, Paracoccidioides
Opportunistic: Candida, Cryptococcus, Aspergillus, Mucor/Rhizopus, Pneumocystis
Key Fungi
Candida albicans
- Dimorphic - yeast at 37Β°C, hyphae/pseudohyphae in tissue
- Germ tube test (positive) - forms germ tubes in serum at 37Β°C
- Chlamydoconidia - on cornmeal agar
- Thrush (oral, oesophageal), vulvovaginitis, diaper rash, systemic candidiasis
- Risk factors: antibiotics, diabetes, immunosuppression, catheters
- Treatment: Fluconazole (superficial), Amphotericin B or Echinocandins (systemic)
Cryptococcus neoformans
- Encapsulated yeast, India ink - halo capsule
- Mucicarmine positive capsule (pink staining)
- Urease positive, phenol oxidase positive (melanin production)
- Source: Pigeon droppings (dried pigeon faeces)
- Meningitis in AIDS (CD4 <100) - "soap bubble" lesions in basal ganglia
- India ink - direct CSF exam
- Serum/CSF cryptococcal antigen (CrAg) - most sensitive
- Treatment: Amphotericin B + Flucytosine (induction) β Fluconazole (consolidation/maintenance)
Aspergillus fumigatus
- Septate hyphae with acute angle branching (45Β°)
- Conidiophore with vesicle and phialides (fruiting body)
- Source: Decaying vegetation, construction sites
- Diseases:
- Allergic bronchopulmonary aspergillosis (ABPA) - asthma/CF patients, IgEβ, central bronchiectasis
- Aspergilloma ("fungus ball") - in pre-existing cavity (old TB), aerial hyphae on CT
- Invasive aspergillosis - immunocompromised (neutropenic), "halo sign" on CT chest
- Treatment: Voriconazole (first line for invasive), Amphotericin B, Caspofungin
Mucor / Rhizopus (Zygomycetes/Mucormycosis)
- Non-septate (aseptate/pauci-septate) hyphae with right-angle (90Β°) branching
- Ribbon-like hyphae
- Risk factors: Diabetic ketoacidosis (DKA), iron overload, deferoxamine treatment, neutropenia
- Rhinocerebral mucormycosis (most common form) - black eschar on nasal turbinates, invades orbit
- Treatment: Amphotericin B (first line), surgical debridement
Pneumocystis jirovecii
- NOT a true fungus (originally thought to be a protozoan, reclassified)
- Cannot be cultured in standard media
- GMS (Gomori methenamine silver) stain - black cysts with "helmet" or "crushed ping-pong ball" appearance
- Causes PCP (Pneumocystis pneumonia) in AIDS (CD4 <200)
- CXR: bilateral interstitial infiltrates ("ground glass"), perihilar
- LDH elevated (marker of severity)
- Treatment: Co-trimoxazole (TMP-SMX) - first line, also prophylaxis when CD4 <200
- Alternatives: Pentamidine, Atovaquone, Primaquine + Clindamycin
Sporothrix schenckii
- Dimorphic - mould in environment, yeast in tissue
- Rose thorn injury (florists, gardeners)
- Lymphocutaneous sporotrichosis - nodules along lymphatics
- Treatment: Itraconazole (potassium iodide for cutaneous)
Histoplasma capsulatum
- Dimorphic - mould (25Β°C), yeast (37Β°C, intracellular in macrophages)
- Ohio-Mississippi River valley (bird + bat droppings)
- Resembles leishmaniasis on tissue (small intracellular yeasts)
- Treatment: Itraconazole (mild), Amphotericin B (severe)
Antifungal Drugs
| Drug | Mechanism | Spectrum | Key Side Effect |
|---|
| Amphotericin B | Binds ergosterol β pore formation | Broad (Candida, Aspergillus, Cryptococcus, Mucor) | Nephrotoxicity, hypokalaemia, infusion reactions |
| Azoles (Fluconazole, Itraconazole, Voriconazole) | Inhibit ergosterol synthesis (CYP51/14Ξ±-demethylase) | Varies by agent | Hepatotoxicity, drug interactions (CYP450) |
| Echinocandins (Caspofungin, Micafungin) | Inhibit Ξ²-glucan synthase β disrupts cell wall | Candida, Aspergillus (NOT Cryptococcus) | Minimal, well tolerated |
| Flucytosine (5-FC) | Converted to 5-FU β inhibits thymidylate synthase | Cryptococcus, Candida | Bone marrow suppression |
| Griseofulvin | Disrupts microtubules β inhibits mitosis | Dermatophytes only | Teratogenic, liver induction |
| Terbinafine | Inhibits squalene epoxidase | Dermatophytes | Hepatotoxicity |
SECTION 12: PARASITOLOGY
Malaria
Plasmodium species:
| Species | RBC affected | Fever cycle | Complications | Unique features |
|---|
| P. falciparum | All RBCs | Irregular/tertian (36-48 hr) | Cerebral malaria, ARDS, blackwater fever | Maurer's clefts, accolΓ© forms, multiple rings/RBC |
| P. vivax | Young (reticulocytes) | Benign tertian (48 hr) | Rupture spleen | SchΓΌffner's dots, hypnozoites (liver relapse) |
| P. ovale | Young | Benign tertian (48 hr) | Mild | SchΓΌffner's dots, oval RBCs, hypnozoites |
| P. malariae | Old RBCs | Quartan (72 hr) | Nephrotic syndrome (immune complex) | Band-form trophozoites |
| P. knowlesi | All | Quotidian (24 hr) | Severe | Zoonosis (macaques), SE Asia |
Diagnosis:
- Peripheral blood smear (thick = sensitivity, thin = species identification)
- RDT (Rapid Diagnostic Test) - HRP-2 antigen for P. falciparum
- PCR (most sensitive)
Treatment:
- Uncomplicated P. falciparum: Artemisinin-based Combination Therapy (ACT) - Artemether-lumefantrine
- Severe malaria: IV Artesunate (first line, replaced quinine)
- P. vivax/ovale (radical cure): Chloroquine + Primaquine (clears hypnozoites; check G6PD first!)
- Prophylaxis: Doxycycline, Mefloquine, Atovaquone-proguanil (Malarone)
Leishmania
| Species | Disease | Vector | Distribution |
|---|
| L. donovani | Visceral (Kala-azar) | Sandfly (Phlebotomus) | India, Africa |
| L. tropica, major | Cutaneous (Oriental sore) | Sandfly | Middle East, Asia |
| L. braziliensis | Mucocutaneous | Sandfly (Lutzomyia) | South America |
Kala-azar features: Fever, massive splenomegaly, hepatomegaly, weight loss, hyperpigmentation (kala-azar = black fever), pancytopenia, hypergammaglobulinaemia, post-kala-azar dermal leishmaniasis (PKDL)
Lab: Bone marrow/spleen aspirate - LD bodies (amastigotes in macrophages)
Treatment: Miltefosine (oral, first line in India), Liposomal Amphotericin B, Meglumine antimoniate
Trypanosomiasis
African (Sleeping sickness)
- T. brucei gambiense (West Africa, chronic) + T. brucei rhodesiense (East Africa, acute)
- Vector: Tsetse fly (Glossina)
- Chancre at bite β stage 1 (blood, lymph, winterbottom's sign = posterior cervical lymphadenopathy) β stage 2 (CNS)
- Treatment: Pentamidine/suramin (stage 1), Melarsoprol (stage 2)
American (Chagas disease)
- T. cruzi
- Vector: Triatomine bug (kissing bug/Reduviid bug), infects via faeces
- Chagoma, RomaΓ±a's sign (periorbital oedema)
- Chronic: Cardiomyopathy, megaoesophagus, megacolon
- Treatment: Benznidazole or Nifurtimox (acute phase)
Intestinal Parasites (Rapid Fire)
| Parasite | Disease | Key Features |
|---|
| Entamoeba histolytica | Amoebic dysentery, liver abscess | Flask-shaped ulcers, "anchovy sauce" pus, RBC in cysts, metronidazole treatment |
| Giardia lamblia | Giardiasis | Steatorrhoea, trophozoite = "falling leaf motility", cyst = 4 nuclei, duodenal aspirate |
| Cryptosporidium | Watery diarrhoea in AIDS | Oocysts on modified ZN, self-limiting in immunocompetent, nitazoxanide |
| Ascaris lumbricoides | Roundworm, LΓΆffler's syndrome | Largest intestinal nematode |
| Hookworm | Iron deficiency anaemia | Ancylostoma (buccal teeth), Necator (cutting plates) |
| Strongyloides | Diarrhoea, larva currens, hyperinfection in immunocompromised | Filariform larvae in stool, ivermectin treatment |
| Trichuris trichiura | Whipworm, rectal prolapse in children | Barrel-shaped eggs |
| Enterobius vermicularis | Pinworm, perianal pruritis | Scotch tape test, paddlewheel eggs |
| Taenia solium | Taeniasis + cysticercosis | Pork tapeworm, cysticercosis β neurocysticercosis |
| Taenia saginata | Taeniasis only | Beef tapeworm, no cysticercosis |
| Echinococcus | Hydatid cyst (liver, lung) | Dog tapeworm, Casoni test, "daughter cysts", Albendazole + PAIR procedure |
Tissue/Blood Parasites
| Parasite | Disease | Vector/Transmission | Key Diagnostic |
|---|
| Wuchereria bancrofti | Lymphatic filariasis, elephantiasis | Culex mosquito | Nocturnal periodicity, microfilariae in blood at night |
| Brugia malayi | Lymphatic filariasis | Mansonia mosquito | - |
| Loa loa | Loiasis, Calabar swellings | Chrysops (deer fly) | Microfilariae in blood daytime |
| Onchocerca volvulus | River blindness | Simulium (black fly) | Microfilariae in skin snips |
| Dracunculus medinensis | Guinea worm | Cyclops copepod | Worm emerges from skin; DEET + filtering water |
| Toxoplasma gondii | Toxoplasmosis | Cat faeces/raw meat | Congenital (periventricular calcifications), AIDS (ring-enhancing lesions) |
| Toxocara | Visceral larva migrans | Dog/cat faeces (eggs) | Eosinophilia, retinal granuloma |
SECTION 13: STERILISATION & DISINFECTION
Key Definitions
- Sterilisation: Destruction of ALL microorganisms including spores
- Disinfection: Destruction of most pathogens (not necessarily spores)
- Antiseptic: Used on living tissues
- Disinfectant: Used on inanimate objects
- Bactericidal: Kills bacteria
- Bacteriostatic: Inhibits growth
Methods
| Method | Temp/Details | Used For |
|---|
| Autoclaving | 121Β°C, 15 psi, 15 min | Gold standard sterilisation, kills spores |
| Hot air oven | 160Β°C Γ 1 hr or 180Β°C Γ 30 min | Glassware, oils, powders (NO steam) |
| Pasteurisation | 72Β°C Γ 15 sec (HTST) or 63Β°C Γ 30 min (Holder) | Milk, kills non-sporing pathogens |
| Tyndallisation | 100Β°C Γ 30 min on 3 consecutive days | Kills spores by repeated steaming |
| Incineration | Burning | Infected waste, carcasses |
| UV radiation | 260 nm | Air disinfection, laminar flow cabinets, creates thymine dimers in DNA |
| Gamma irradiation | 2.5 Mrad | Disposable syringes, sutures (cold sterilisation) |
| Ethylene oxide (EO) | 55Β°C, 4-8 hrs | Heat-sensitive equipment (endoscopes, catheters) |
| Glutaraldehyde (2%) | 4-10 hrs for sterilisation | High-level disinfection/sterilisation of endoscopes |
SECTION 14: IMMUNOLOGY (Micro-related)
Complement System
Classical pathway: Activated by antigen-antibody complex (IgG, IgM)
Lectin pathway: Activated by mannose-binding lectin (MBL)
Alternative pathway: Activated by bacterial surfaces, LPS (spontaneous)
All converge at C3 β C3 convertase β C5 convertase β MAC (Membrane Attack Complex) C5b-9
Functions:
- C3b - Opsonisation (most important)
- C3a, C5a - Anaphylatoxins (mast cell degranulation)
- C5a - Chemotaxis (PMN recruitment), most potent
- C5b-9 (MAC) - Lysis of Gram-negative bacteria
- C1q - clearance of immune complexes
Terminal complement deficiency (C5-C9): Recurrent Neisseria infections
Hypersensitivity (Gell & Coombs)
| Type | Mechanism | Mediators | Examples |
|---|
| Type I (Immediate) | IgE, mast cells, basophils | Histamine, leukotrienes | Anaphylaxis, asthma, urticaria, allergic rhinitis |
| Type II (Cytotoxic) | IgG/IgM + complement or ADCC | Complement, NK cells | Haemolytic anaemia, ITP, Goodpasture, ABO incompatibility |
| Type III (Immune complex) | IgG/IgM complexes + complement | C3a, C5a, neutrophils | SLE, PSGN, Arthus reaction, serum sickness |
| Type IV (Delayed/Cell-mediated) | T cells (CD4 Th1, CD8) | Lymphokines, macrophages | Tuberculin test, contact dermatitis, graft rejection, sarcoidosis |
Microbe-related hypersensitivity:
- PSGN β Type III (streptococcal antigen-antibody complexes)
- Tuberculin test β Type IV
- Rheumatic fever β Type II (molecular mimicry) + Type III
Immunoglobulins
| Ig | Key Features |
|---|
| IgG | Most abundant in serum, crosses placenta (only one), secondary response, 4 subclasses |
| IgM | Largest, first produced (primary response), best complement activator (classical), pentamer |
| IgA | Most abundant in secretions (secretory IgA = dimer + J chain + secretory component), protects mucosal surfaces |
| IgE | Lowest serum concentration, binds mast cells/basophils, type I hypersensitivity, anti-parasitic |
| IgD | B-cell surface receptor (with IgM), function largely unknown |
SECTION 15: HIGH-YIELD ONE-LINERS (NEET PG Favourite Facts)
Cannot be cultured:
- T. pallidum (dark-field microscopy)
- M. leprae (armadillo footpad)
- Rickettsia (cell culture only)
- Chlamydia (cell culture only)
- P. jirovecii (GMS stain)
Obligate intracellular:
- Viruses (all), Rickettsia, Chlamydia, Coxiella, Mycobacterium leprae (facultative), Leishmania, Toxoplasma, Plasmodium
Capsulated bacteria (SHiNE SKiS):
S. pneumoniae, H. influenzae, N. meningitidis, E. coli K1, Salmonella, Klebsiella, S. agalactiae
Oxidase positive: Neisseria, Pseudomonas, Vibrio, Campylobacter, Helicobacter, Brucella, Pasteurella
Oxidase negative: Enterobacteriaceae (E. coli, Salmonella, Shigella, Klebsiella)
Urease positive: H. pylori, Proteus, Klebsiella, Cryptococcus, Ureaplasma
Catalase positive: Staphylococcus, most Gram-negatives
Catalase negative: Streptococcus, Enterococcus (used to differentiate from Staph)
Coagulase positive: S. aureus only (among Staph)
CAMP test positive: S. agalactiae (Group B Strep)
Beta-haemolytic Streptococci: Group A (S. pyogenes), Group B (S. agalactiae), some Group C and G
Spore-forming bacteria: Bacillus (aerobic), Clostridium (anaerobic)
Zoonoses and their vectors:
| Disease | Organism | Animal/Vector |
|---|
| Plague | Y. pestis | Rat flea |
| Lyme disease | B. burgdorferi | Ixodes tick |
| RMSF | R. rickettsii | Dermacentor tick |
| Brucellosis | Brucella spp. | Cattle/goat/sheep |
| Q fever | Coxiella burnetii | Inhalation of animal aerosols |
| Leptospirosis | Leptospira | Rat urine |
| Anthrax | B. anthracis | Cattle/sheep spores |
| Tularaemia | F. tularensis | Rabbit/tick |
| Psittacosis | C. psittaci | Birds (parrots) |
| Hantavirus | Sin Nombre virus | Rodent aerosols |
Most common causes - quick reference:
- Most common bacterial meningitis (adults) β S. pneumoniae
- Most common bacterial meningitis (neonates) β GBS (S. agalactiae) + E. coli K1
- Most common meningitis (meningitis belt Africa) β N. meningitidis
- Most common UTI β E. coli
- Most common CAP β S. pneumoniae
- Most common food-borne diarrhoea (globally) β Campylobacter jejuni
- Most common nosocomial infection β UTI (CAUTI)
- Most common cause of osteomyelitis β S. aureus
- Most common organism in diabetic foot β S. aureus (polymicrobial in chronic)
- Most common cause of SBE β Viridans streptococci
- Most common cause of acute endocarditis β S. aureus
- Most common cause of prosthetic valve endocarditis (early, <60 days) β S. epidermidis
- Most common fungal infection in AIDS β Candida (oral thrush earliest)
- Most common cause of infectious blindness β Trachoma (C. trachomatis)
- Most common STI globally β HPV
- Most common STI in India β Trichomonas vaginalis
That covers all of Microbiology for NEET PG - bacteriology, virology, mycology, parasitology, immunology, and sterilisation. Want me to run a targeted quiz on any specific section to test your retention? π―