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Lab Diagnosis for 2nd Year MBBS Microbiology

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1. Giardiasis (Lab Diagnosis of Giardia duodenalis)

Specimens

• Stool (fresh or preserved — polyvinyl alcohol or sodium acetate-acetic acid formalin)
• Duodenal aspirate / string test (Enterotest) — less commonly used now
• Duodenal biopsy — for refractory/immunocompromised cases

A. Microscopy — Ova & Parasite (O&P) Examination

• Trophozoite: Pear-shaped (9–21 µm), 2 nuclei, 4 pairs of flagella, ventral concave sucking disc, falling-leaf motility
• Cyst: Oval (8–12 µm), 4 nuclei, retracted cytoplasm (giving a "halo"), axostyle, median bodies

⚠ Organisms are shed intermittently — examine 3 specimens collected on alternate days to improve sensitivity.

B. Antigen Detection (immunodiagnosis)

• DFA (Direct Fluorescent Antibody) — detects Giardia-specific antigens in stool; most sensitive antigen method
• EIA (Enzyme Immunoassay) — detects GSA 65 antigen; commercially available kits, higher sensitivity than routine O&P
• These are especially useful when O&P is negative but clinical suspicion remains high

C. Molecular Methods

• NAAT / PCR — highest sensitivity and specificity; can detect multiple parasites simultaneously (multiplex panels); increasingly used in clinical labs

D. Serology

• IgG ELISA — not routinely used for acute diagnosis; useful in epidemiological studies

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2. Bacterial Urinary Tract Infection (UTI)

Specimen Collection

• Midstream clean-catch urine (MSU) — method of choice; clean periurethral area before collection
• Catheter specimen — collected from catheter port (never from drainage bag) in catheterised patients
• Suprapubic aspiration — gold standard (avoids contamination); used in neonates or when MSU is unreliable

A. Urine Routine Examination (Urinalysis)

B. Urine Culture (Definitive Diagnosis)

• E. coli (most common — ~80% of community-acquired)
• Klebsiella pneumoniae, Proteus mirabilis, Enterobacter spp.
• Staphylococcus saprophyticus (young women, sexually active)
• Enterococcus spp., Pseudomonas aeruginosa (hospital-acquired)

C. Gram Stain of Urine

• Performed on uncentrifuged urine
• Helps guide initial empiric therapy (Gram-positive vs Gram-negative)

D. Antibiotic Sensitivity Testing (AST)

• Kirby-Bauer disc diffusion or MIC determination
• Essential in complicated UTI, recurrent cases, or after failed empiric therapy

E. Sterile Pyuria (important differential)

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3. Syphilis (Lab Diagnosis of Treponema pallidum infection)

Specimen

• Primary: Serous exudate from chancre (ulcer base/edge)
• Secondary: Skin lesion exudate, blood for serology
• CSF — for neurosyphilis
• Blood — for serology at all stages

A. Direct Detection of T. pallidum

1. Darkfield Microscopy ✦ (Most important in primary syphilis)

• Serous fluid from primary ulcer (chancre) or secondary lesions is examined under darkfield illumination
• T. pallidum appears as a tightly coiled corkscrew-shaped spirochete with characteristic rotatory and flexion motility
• To be seen readily, fluid must contain thousands of treponemes/mL; a negative result does not exclude syphilis
• Not used for oral/anal lesions (saprophytic spirochetes cause false positives)

2. Direct Fluorescent Antibody (DFA-TP)

• Uses fluorescein-labeled anti-T. pallidum antibodies
• More specific than darkfield; especially useful for oral lesions

3. PCR / NAAT

• Detects T. pallidum DNA; useful in neurosyphilis, congenital syphilis, extra-genital primary syphilis
• Increasing use in clinical settings

T. pallidum cannot be cultured on routine lab media; rabbit testicular inoculation is used only for experimental studies.

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B. Serological Tests (Main diagnostic tool for most stages)

I. Non-Treponemal Tests (NTTs) — Screening

• Become positive 1–4 weeks after chancre appears (early primary syphilis)
• Peak titre in secondary syphilis
• Used to monitor treatment response — titre falls with successful therapy and reverts to negative
• May revert to negative in late/tertiary syphilis
• False positives in: SLE, RA, antiphospholipid syndrome, pregnancy, viral hepatitis, infectious mononucleosis, malaria, leprosy, IV drug use (technical FP)
• Positive NTT must always be confirmed by a treponemal test

II. Treponemal Tests (TTs) — Confirmatory

• More specific than NTTs
• Remain positive for life (even after successful treatment) — cannot distinguish active from treated past infection
• FTA-ABS is highly sensitive for all stages including early primary
• Sensitivity of FTA-ABS: >95% in secondary and tertiary syphilis
• False positives (rare): Lyme disease, leptospirosis, other treponematoses (yaws, pinta)

C. Traditional vs. Reverse Algorithm

D. Stage-wise Serology Summary

E. CSF Examination (for Neurosyphilis)

• CSF-VDRL = standard (low sensitivity ~30–70%, but highly specific)
• CSF pleocytosis (lymphocytes), raised protein
• Positive CSF-TPHA/FTA-ABS supports diagnosis when VDRL negative

F. Congenital Syphilis

• Mother's and infant's titres compared — infant NTT titre ≥4-fold higher than mother's = suggestive
• IgM FTA-ABS-19S — detects infant's own antibodies (IgG crosses placenta; IgM does not) — sensitivity ~90%
• PCR on neonatal blood/CSF for definitive confirmation

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Quick Exam Summary Table

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14 Short Notes — 2nd Year MBBS Microbiology

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SN 1: Opportunistic Gastrointestinal Infections in HIV

Common Organisms & Features

Key Points for Cryptosporidiosis (Most Important)

• Specimen: Stool
• Diagnosis: Modified Ziehl-Neelsen (ZN) stain — oocysts stain pink-red on blue background; DFA, EIA, PCR
• Treatment: No effective Rx without immune reconstitution; nitazoxanide used; ART is cornerstone

Isosporiasis

• Modified ZN — large oocysts (25–30 µm) stain red-pink
• Treatment: Co-trimoxazole

CMV Colitis

• Endoscopic biopsy shows "owl-eye" intranuclear inclusions
• Treatment: Ganciclovir

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SN 2: Food Poisoning — Bacterial, Viral, Parasitic

A. Bacterial Food Poisoning

B. Viral Food Poisoning

C. Parasitic Food Poisoning

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SN 3: Hydatid Cyst

Aetiology

Life Cycle

• Definitive host: Dog (adult tapeworm in intestine)
• Intermediate host: Sheep, cattle, humans (accidental)
• Mode of transmission: Fecal-oral; humans ingest eggs from dog faeces → eggs hatch in duodenum → oncospheres penetrate intestinal wall → bloodstream → liver (most common), lungs, brain, bone

Structure of Hydatid Cyst (Diagram Below)

        ┌──────────────────────────────┐
        │  PERICYST (Host-derived)     │  ← Outermost fibrous layer (host reaction)
        │  ┌────────────────────────┐  │
        │  │  ECTOCYST / LAMINATED  │  │  ← Middle: thick, white, laminated, non-nucleated
        │  │       LAYER            │  │     (pathognomonic of Echinococcus)
        │  │  ┌──────────────────┐  │  │
        │  │  │  ENDOCYST /      │  │  │  ← Inner: germinal (nucleated) layer
        │  │  │  GERMINAL LAYER  │  │  │     produces brood capsules, protoscolices,
        │  │  │  ┌────────────┐  │  │  │     daughter cysts, hydatid fluid
        │  │  │  │  BROOD     │  │  │  │
        │  │  │  │  CAPSULES  │  │  │  │
        │  │  │  │ + SCOLICES │  │  │  │
        │  │  │  └────────────┘  │  │  │
        │  │  │  Hydatid sand    │  │  │
        │  │  │  Daughter cysts  │  │  │
        │  │  └──────────────────┘  │  │
        │  └────────────────────────┘  │
        └──────────────────────────────┘

1. Pericyst — outermost; fibrous; host-derived (compressed liver/lung tissue)
2. Ectocyst (Laminated layer) — middle; acellular, white, laminated; unique to Echinococcus
3. Endocyst (Germinal/Germinal epithelium layer) — innermost; nucleated; produces:
   • Brood capsules → contain protoscolices (invaginated scolices — infective stage)
   • Daughter cysts (secondary cysts)
   • Hydatid fluid (clear, "water-white"; contains hydatid sand = protoscolices + hooklets)

Clinical Features

• Liver (most common, 60–70%): Slowly growing cystic mass, RUQ pain
• Lung (20–30%): Cough, haemoptysis; Camelogram sign (CXR: air between layers after rupture)
• Rupture: Anaphylaxis (life-threatening); dissemination → seeding of new cysts
• Casoni's test (intradermal): Historical; now replaced by serology

Diagnosis

• Imaging: USG (Gharbi/WHO classification), CT scan
• Serology: ELISA, IHA (indirect haemagglutination), Western blot for Echinococcus Ag
• Microscopy: Scolices/hooklets in aspirate (aspirate only in controlled PAIR procedure)
• Casoni test: Intradermal antigen test (historical)
• ⚠ Do NOT aspirate blindly — risk of anaphylaxis and spillage

Treatment

• PAIR (Puncture-Aspiration-Injection-Re-aspiration) with albendazole cover
• Surgery for complicated cysts
• Albendazole (drug of choice for medical management)

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SN 4: Waterborne Hepatitis

Hepatitis A Virus (HAV)

Hepatitis E Virus (HEV)

Comparison Table

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SN 5: Visceral Larva Migrans (VLM)

Definition

Causative Agents

• Toxocara canis (dog roundworm) — most common
• Toxocara cati (cat roundworm)
• Baylisascaris procyonis (raccoon roundworm — rare, severe neurological disease)

Transmission

• Ingestion of embryonated eggs from soil contaminated with dog/cat faeces
• Common in children (geophagia, pica, sandpits)
• Eggs hatch in intestine → L2 larvae penetrate intestinal wall → enter circulation → migrate to liver, lungs, brain, eyes, muscles (but cannot complete development in human — migrate aimlessly)

Clinical Features

• Classic VLM: Liver involvement — hepatomegaly, fever, hypereosinophilia (pathognomonic feature), hypergammaglobulinaemia
• Pulmonary: Wheezing, cough, Loeffler-like syndrome
• Ocular larva migrans (OLM): Retinal granuloma, visual loss, strabismus — different syndrome from classic VLM
• Covert/common toxocariasis: Subtle — asthma, abdominal pain, eosinophilia

Diagnosis

• Peripheral blood: Marked eosinophilia (hallmark)
• Serology (method of choice): ELISA using Toxocara excretory-secretory (TES) antigens; titre ≥1:32 significant
• Liver biopsy: Granuloma with eosinophils + larvae (definitive but rarely done)
• Ocular: Ophthalmoscopy; serology (low titre in OLM — larvae not migrating systemically)
• Note: Larvae are never seen in stool (human is not definitive host)

Treatment

• Albendazole or mebendazole (anti-helminthic)
• Corticosteroids for severe cases (pulmonary, ocular, neurological)

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SN 6: Non-Tubercular Mycobacteria (NTM) / Atypical Mycobacteria

Definition

Runyon's Classification

Clinical Syndromes

1. Pulmonary disease (TB-like): M. kansasii, MAC — in COPD patients, elderly women (Lady Windermere syndrome)
2. Lymphadenitis (most common in children): M. scrofulaceum, MAC — cervical nodes
3. Skin/soft tissue: M. marinum (swimming pool/fish tank granuloma), M. ulcerans (Buruli ulcer — painless necrotic ulcer), rapid growers
4. Disseminated disease (AIDS, CD4 <50): MAC — fever, weight loss, anaemia, diarrhoea, hepatosplenomegaly
5. Catheter/device infections: Rapid growers

Diagnosis

• ZN stain / Auramine-Rhodamine stain — AFB positive (like MTB)
• Culture: LJ medium or BACTEC; slower than rapid growers
• Key differentiation from MTB:
  • Niacin test: MTB positive, NTM negative
  • Nitrate reduction: MTB positive, most NTM negative
  • Growth temperature, pigmentation (Runyon)
  • HPLC, molecular methods (PCR, line probe assay) — gold standard
• NTM are NOT transmitted person-to-person (environmental source)

Treatment

• MAC in AIDS: Azithromycin + Ethambutol ± Rifabutin
• M. kansasii: Rifampicin-based regimen
• Prophylaxis in AIDS (CD4 <50): Azithromycin weekly

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SN 7: Bacterial Lobar Pneumonia — Organisms & Lab Diagnosis

Causative Organisms

Lab Diagnosis of Lobar Pneumonia (S. pneumoniae)

1. Sputum Examination

• Gram stain: Gram-positive lancet-shaped diplococci in pairs, surrounded by a capsule halo; abundant PMNs; >25 WBCs/LPF and <10 epithelial cells = adequate sample (Bartlett criteria)
• Culture: Blood agar (5% CO₂) — alpha-haemolytic (green haemolysis), small, mucoid "draughtsman/ring" colonies (central depression)
• Identification:
  • Optochin sensitivity (P-disc) — S. pneumoniae sensitive (zone ≥14 mm); viridans streptococci resistant
  • Bile solubility test — S. pneumoniae soluble (lysis in bile/deoxycholate)
  • Quellung (Neufeld) reaction — capsular swelling with specific antisera (serotyping)
  • Inulin fermentation — positive

2. Blood Culture

• Positive in ~25% bacteraemic cases (2 sets, aerobic + anaerobic)
• Bacteraemia = worse prognosis

3. Antigen Detection

• Urinary pneumococcal antigen test (Binax NOW) — rapid, sensitive (>70%), specific; useful in partially treated cases

4. Molecular

• PCR on sputum/BAL — high sensitivity

5. Serology

• Quellung reaction for serotyping
• Cold agglutinins (for Mycoplasma atypical pneumonia)

Klebsiella — Additional Points

• Gram stain: Gram-negative plump bacilli, capsule visible (pink halo)
• Culture: Mucoid, string-like colonies on MacConkey (pink/lactose-fermenting); Friedländer bacillus
• Quellung test not applicable; capsule staining done

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SN 8: Diphtheria

Causative Agent

Morphology

• Club-shaped (one end swollen) — Coryne = club
• Metachromatic granules (Volutin/Babes-Ernst granules) — intracellular stored polyphosphate, appear reddish-purple when stained with blue stain → "Chinese letter"/"Cuneiform" arrangement
• Stains: Albert's stain (granules stain dark green-blue, body light green); Neisser's stain (granules dark brown, body yellow)

Pathogenesis

• Exotoxin — encoded by β-prophage (tox gene); produced only by lysogenic strains
• Toxin structure: Fragment B (binds receptor — HB-EGF) + Fragment A (enzymatically active)
• Mechanism: Fragment A ADP-ribosylates EF-2 (Elongation Factor-2) → irreversible inhibition of protein synthesis → cell death

Clinical Features

• Faucial/pharyngeal diphtheria (most common): Sore throat, low fever, tough grey-white pseudomembrane on tonsils/pharynx that bleeds on removal → "Bull neck" (cervical lymphadenopathy + soft tissue oedema)
• Laryngeal: Hoarseness, croup, asphyxia (most dangerous)
• Nasal: Serosanguinous discharge
• Complications (due to exotoxin):
  • Myocarditis (1–2 weeks; most common cause of death)
  • Neuropathy — palatal palsy (week 3), oculomotor palsy (week 5), peripheral polyneuritis

Lab Diagnosis

Prevention

• DPT vaccine (toxoid — inactivated exotoxin) at 6, 10, 14 weeks, booster at 18 months and 5 years
• Schick test (historical): Intradermal injection of toxin — positive reaction = susceptible (no antitoxin), negative = immune

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SN 9: Opportunistic Parasitic & Fungal Respiratory Infections in HIV

A. Fungal Infections

1. Pneumocystis jirovecii Pneumonia (PCP) — Most Important

• Previously classified as a protozoon; now a fungus (atypical — lacks ergosterol)
• CD4 threshold: <200 cells/µL
• Clinical: Progressive dyspnoea, dry cough, fever; hypoxia out of proportion to X-ray findings
• CXR: Bilateral symmetrical "ground-glass" interstitial infiltrates (butterfly pattern); may be normal early
• Diagnosis:
  • Bronchoalveolar lavage (BAL) — best specimen
  • Gomori Methenamine Silver (GMS) stain — black cysts against green background (gold standard)
  • Toluidine blue O stain, Giemsa (trophic forms), immunofluorescence
  • PCR — most sensitive
  • LDH elevated (non-specific but supports diagnosis)
• Treatment: Co-trimoxazole (TMP-SMX) — drug of choice; Pentamidine (alternative); corticosteroids if PaO₂ <70 mmHg
• Prophylaxis: TMP-SMX when CD4 <200

2. Cryptococcus neoformans — Pulmonary Cryptococcosis

• CD4 threshold: <100 cells/µL
• Clinical: Cough, fever, dyspnoea; often asymptomatic pulmonary nodule; meningitis is main concern
• Diagnosis: India ink (CSF), CrAg (serum/CSF), culture on Sabouraud's agar (mucoid colonies), Urease positive
• Treatment: Fluconazole (mild pulmonary); Amphotericin B + Flucytosine (severe/meningitis)

3. Histoplasma capsulatum / Coccidioides immitis

• Disseminated histoplasmosis / coccidioidomycosis in AIDS; endemic areas

B. Parasitic Respiratory Infections

1. Toxoplasma gondii — Pulmonary Toxoplasmosis

• CD4 <50–100; bilateral interstitial pneumonia (rare vs. CNS toxoplasmosis)
• Diagnosis: BAL, PCR; serology (IgG reactivation)

2. Strongyloides stercoralis — Hyperinfection Syndrome

• Accelerated autoinfection in immunosuppressed → larvae penetrate gut → carry gut bacteria → gram-negative sepsis + pulmonary infiltrates, haemoptysis
• Diagnosis: Rhabditiform/filariform larvae in stool, sputum, BAL
• Treatment: Ivermectin (drug of choice)

3. Cryptosporidium — Pulmonary Cryptosporidiosis (rare)

• Biliary and pulmonary spread in severe AIDS

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SN 10: Rabies Virus — PEP & Diagram

The Virus

Diagram of Rabies Virus

     ___________________________
    /  BULLET-SHAPED VIRION    \
   |  (75 × 180 nm)            |
   |                            |
   |  ┌──────────────────────┐  |
   |  │  ENVELOPE             │  |  ← Derived from host cell membrane
   |  │  (with G-protein      │  |  ← G protein (surface spikes) — induces
   |  │   spikes)             │  |     neutralising antibodies; key for vaccine
   |  │  ┌────────────────┐   │  |
   |  │  │ M protein layer │   │  |  ← Matrix (M) protein — links envelope to RNP
   |  │  │ ┌────────────┐ │   │  |
   |  │  │ │ NUCLEOCAPSID│ │   │  |  ← Helical symmetry
   |  │  │ │ (N-P-L-RNP) │ │   │  |  ← N (nucleoprotein): group-specific Ag for diagnosis
   |  │  │ │  ssRNA(–)   │ │   │  |  ← L (RNA-dependent RNA polymerase)
   |  │  │ └────────────┘ │   │  |
   |  │  └────────────────┘   │  |
   |  └──────────────────────┘  |
    \____________________________/

• G protein — surface glycoprotein; virus attachment to nicotinic ACh receptor on nerve cells; target of virus-neutralising antibodies (VNA); basis of vaccines
• N protein — nucleoprotein; group-specific antigen; used in DFA diagnosis; basis of Negri body formation
• M protein — matrix protein; bridges nucleocapsid and envelope
• RNA: Single-stranded, negative-sense, non-segmented

Pathogenesis

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Post-Exposure Prophylaxis (PEP)

WHO Wound Categories

Steps in PEP

• Thorough washing with soap and water for ≥15 minutes
• Apply iodine-based antiseptic or 70% alcohol
• Do NOT suture immediately (if unavoidable, RIG infiltrated first, then minimal suturing)

• Human RIG (HRIG): 20 IU/kg
• Equine RIG (ERIG): 40 IU/kg (skin test before use)
• All possible RIG dose infiltrated into and around wound site (passive immunisation — immediate protection)
• Remaining volume given IM at distant site
• Given only once; must be given on Day 0 (with 1st vaccine dose)

• Day 0, 3, 7, 14, 28 — 5 doses IM in deltoid
• Alternatively: Zagreb regimen (2-1-1): Day 0 (2 doses), Day 7 (1 dose), Day 21 (1 dose)

• PCECV — Purified Chick Embryo Cell Vaccine
• PVRV — Purified Vero cell Rabies Vaccine (Rabipur, Verorab)
• HDCV — Human Diploid Cell Vaccine (gold standard, expensive)
• Intra-dermal (ID) route: 0.1 mL ID (Thai Red Cross method) — cost-saving

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SN 11: Cryptococcal Meningitis

Aetiology

Morphology

• Yeast, 5–10 µm, thick polysaccharide capsule (key virulence factor)
• Reproduce by narrow-based budding
• Capsule functions: Anti-phagocytic; inhibits migration of leukocytes; impairs antigen presentation

Epidemiology

• Primary habitat: Pigeon droppings (C. neoformans); eucalyptus trees (C. gattii)
• Most important opportunistic fungal CNS infection in AIDS (CD4 <100)
• Also seen in organ transplant recipients

Clinical Features

• Subacute/chronic meningitis: Headache, fever, meningismus (may be minimal)
• Raised ICP: Nausea, vomiting, visual changes, papilloedema
• CSF: Lymphocytic pleocytosis, elevated protein, low glucose
• Cryptococcomas in brain parenchyma ("soap bubble lesions" on MRI)

Lab Diagnosis

Treatment

• Induction (2 weeks): Amphotericin B + Flucytosine (5-FC) — reduces fungal burden rapidly
• Consolidation (8 weeks): Fluconazole 400 mg/day
• Maintenance/Suppression: Fluconazole 200 mg/day (lifelong or until CD4 >200 on ART)
• Raised ICP management: Serial LPs (primary treatment — no diuretics); VP shunt if refractory

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SN 12: Tetanus

Causative Agent

• Spores: Terminal (drumstick/tennis racket appearance) — highly resistant to heat, chemicals
• Habitat: Soil, intestines of animals and humans; spores survive for years

Pathogenesis

1. Spores inoculated via wound (especially puncture wounds, rusty nail, contaminated wound, neonatal umbilical stump)
2. Spores germinate in anaerobic conditions → vegetative bacilli produce tetanospasmin (exotoxin)
3. Tetanospasmin travels by retrograde axonal transport along motor neurons to spinal cord and brainstem
4. Mechanism: Toxin cleaves VAMP (synaptobrevin) → blocks release of GABA and glycine (inhibitory neurotransmitters) from Renshaw cells in spinal cord → unopposed excitation of motor neurons → spastic paralysis

Clinical Features

• Incubation: 3–21 days (shorter = more severe)
• Trismus (lockjaw) — earliest sign; masseter spasm
• Risus sardonicus — spasm of facial muscles → sardonic smile
• Opisthotonos — severe arching of back
• Tetanic seizures — generalised muscle spasms triggered by noise/touch
• Autonomic instability (tachycardia, hypertension — in severe cases)

Types

1. Generalised (most common)
2. Localised — confined to area near wound
3. Cephalic — cranial nerve involvement (facial nerve palsy); poor prognosis
4. Neonatal — tetanus neonatorum; umbilical infection; "stiff baby" (cannot suck)

Lab Diagnosis

• Primarily clinical diagnosis — no reliable lab test
• Mouse neutralisation test: Serum from patient + tetanospasmin injected into mice; protected if antibody present
• Culture: Anaerobic culture on blood agar — drumstick spores; swarming growth
• Gram stain: Gram-positive bacilli with terminal round spores (drumstick)
• Serology generally not helpful acutely

Treatment

• Wound debridement (remove source of toxin)
• Passive immunisation: Human Tetanus Immunoglobulin (HTIG) — 3000–6000 IU IM (neutralises unbound toxin)
• Active immunisation: Tetanus toxoid simultaneously (different site)
• Metronidazole (antibiotic of choice) or penicillin
• Muscle relaxants: Diazepam (GABA-A agonist — counteracts toxin); baclofen, midazolam
• Airway management/ICU

Prevention

• DPT vaccine: Primary series at 6, 10, 14 weeks; boosters at 18 months, 5 years
• TT in pregnancy: 2 doses (TT1, TT2) — protects mother and neonate
• Post-exposure: Clean minor wound + immunised → TT booster; unimmunised/dirty wound → TT + HTIG

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SN 13: Free-Living Amoebae (FLA)

Important Genera

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1. Naegleria fowleri — PAM

• CSF: Haemorrhagic; high pressure; PMN pleocytosis; amoebae on wet mount of CSF (motile trophozoites with characteristic eruptive (eruptive pseudopodal) motility)
• Trophozoite: 10–30 µm; single large karyosome (nucleus)
• Culture on non-nutrient agar overlaid with E. coli (NNA-E. coli) — tracks on agar

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2. Acanthamoeba — GAE & Keratitis

• CNS: Haematogenous spread from skin/lung; enters via broken skin or lung
• Keratitis: Contact lens wearers (contaminated lens solution/water); corneal trauma

• GAE: Subacute/chronic meningoencephalitis in immunocompromised; focal neurological deficits
• Keratitis: Severe pain, photophobia, ring infiltrate on cornea; misdiagnosed as herpes keratitis

• Brain biopsy: Cysts and trophozoites with acanthopodia in perivascular spaces
• Corneal scraping: Double-walled cysts on wet mount, Giemsa, calcofluor white (fluorescent)
• Culture on NNA-E. coli
• PCR (most sensitive)

• GAE: Combination (azoles + miltefosine + pentamidine)
• Keratitis: Topical PHMB (polyhexamethylene biguanide) + propamidine isethionate (Brolene)

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3. Balamuthia mandrillaris — GAE

• No flagellate stage
• Similar to Acanthamoeba GAE but affects both immunocompromised and normal hosts
• Diagnosis: Brain biopsy, PCR, serology

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SN 14: Non-Gonococcal Urethritis (NGU)

Definition

Aetiology

Chlamydia trachomatis — Key Points

• Obligate intracellular bacteria; lacks cell wall peptidoglycan (outer membrane complex instead)
• Two forms:
  • Elementary body (EB): Extracellular, infectious, compact, spore-like; 0.3 µm
  • Reticulate body (RB): Intracellular, replicative, metabolically active; 0.5–1 µm
• Replication in intracytoplasmic inclusions

Clinical Features

• Men: Urethral discharge (mucoid/mucopurulent — less profuse than GC), dysuria, urethral itching; often asymptomatic
• Women: Mucopurulent cervicitis, urethral syndrome; often asymptomatic → ascending infection → PID, infertility, ectopic pregnancy
• Complications: Epididymo-orchitis, Reiter's syndrome (reactive arthritis: urethritis + conjunctivitis + arthritis + skin lesions — "can't see, can't pee, can't climb a tree")

Lab Diagnosis

Treatment

• First line: Doxycycline 100 mg BD × 7 days (chlamydia)
• Alternatives: Azithromycin 1 g single dose; Ofloxacin; Erythromycin
• M. genitalium: Azithromycin or moxifloxacin (doxycycline less effective)
• Partner treatment is essential
• Test-of-cure if symptoms persist (recurrent NGU → exclude M. genitalium, T. vaginalis, HSV)

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Quick Reference Summary

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