all Urinary tract infection enumerate organisms causing laboratory diagnosis significant both viral and bacterial in details bacteruria define allStd enumerate diseases organisms causing lab diagnosis each in details for 2nd yr mbbs microbiology refer apurba sastri
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Urinary Tract Infection (UTI), Bacteriuria & Sexually Transmitted Diseases
For 2nd Year MBBS Microbiology (Based on Jawetz, Melnick & Adelberg's Medical Microbiology, 28th Ed.)
PART 1: URINARY TRACT INFECTION (UTI)
Definition
UTI is an infection of any part of the urinary tract - urethra (urethritis), bladder (cystitis), ureter (ureteritis), or kidney (pyelonephritis). Cystitis = lower tract infection with dysuria, urgency, and frequency. Pyelonephritis = upper tract infection with flank pain, tenderness, dysuria, urgency, and frequency.
Organisms Causing UTI
A. Bacterial (most common)
| Organism | Details |
|---|---|
| Escherichia coli | Most common overall - causes 80-90% of acute uncomplicated cystitis in young women. Gram-negative rod. Possesses adhesins (Type 1 fimbriae, P-fimbriae) that allow it to attach to uroepithelium. |
| Staphylococcus saprophyticus | Second most common in young sexually active women. Coagulase-negative Gram-positive coccus. Resistant to novobiocin (distinguishes it from S. epidermidis). |
| Klebsiella pneumoniae | Gram-negative rod; common in complicated/hospital-acquired UTI. Mucoid colonies. |
| Proteus mirabilis | Gram-negative rod; urease producer - splits urea to ammonia, alkalinizes urine, promotes struvite (staghorn) calculi. Swarming motility on agar. |
| Enterobacter species | Gram-negative rod; nosocomial, antibiotic-resistant. |
| Pseudomonas aeruginosa | Non-fermenter Gram-negative rod; predominantly hospital-acquired (catheters, instrumentation). Blue-green pigment (pyocyanin). |
| Enterococcus faecalis | Gram-positive coccus in chains; particularly in elderly, post-instrumentation. |
| Staphylococcus aureus | Coagulase-positive; usually from hematogenous spread; associated with renal abscess. |
| Serratia marcescens | Nosocomial; produces red pigment (prodigiosin). |
| Ureaplasma urealyticum / Mycoplasma hominis | Causes urethral syndrome and non-gonococcal urethritis. No cell wall - not seen on Gram stain, not cultured on ordinary media. |
| Chlamydia trachomatis | Causes urethral syndrome (dysuria with negative standard cultures) and urethritis/endocervicitis. Obligate intracellular. |
| Mycobacterium tuberculosis | Renal/genitourinary TB - "sterile pyuria" on routine culture (negative on standard urine culture, positive on Lowenstein-Jensen medium). |
B. Fungal
| Organism | Notes |
|---|---|
| Candida albicans / other Candida species | Common in diabetics, immunocompromised, catheterized patients, prolonged antibiotic use. Yeast cells ± pseudohyphae on microscopy. |
C. Viral (important - often overlooked)
| Virus | Details |
|---|---|
| BK Virus (Polyomavirus) | Major viral cause of UTI/hemorrhagic cystitis in renal transplant and bone marrow transplant recipients. Causes polyomavirus-associated nephropathy (PVAN). Diagnosed by urine cytology (decoy cells - enlarged cells with intranuclear inclusion bodies), urine PCR (BK viral load), and serum PCR. |
| Adenovirus (types 11, 21) | Causes hemorrhagic cystitis in immunocompromised patients (especially hematopoietic stem cell transplant recipients) and in healthy children. Diagnosed by PCR of urine or culture. |
| Cytomegalovirus (CMV) | Can involve the urinary tract in immunocompromised patients (transplant, AIDS). Identified by characteristic owl-eye intranuclear inclusions in urine cytology or urine PCR. |
| Human Polyomavirus JC | Primarily causes PML (progressive multifocal leukoencephalopathy) in CNS but can infect renal tubular cells and appear in urine. |
| Mumps Virus | Can cause orchitis and epididymitis with urinary symptoms. |
BACTERIURIA - DEFINITION
Bacteriuria = presence of bacteria in urine. Clinically divided into:
Significant Bacteriuria (Kass Criterion)
The threshold established by E.H. Kass (1956):
- ≥10⁵ CFU/mL (100,000 colony-forming units/mL) in a properly collected midstream clean-catch urine specimen = significant bacteriuria
- Presence of ≥10⁵ bacteria/mL of the same type in two consecutive specimens establishes active UTI with 95% certainty
- Some young symptomatic women may have significant infection with as few as 10² to 10³ CFU/mL
- In men, 10⁴/mL of a single Gram-negative rod is strongly suggestive of UTI
Count Interpretation:
| Colony Count | Interpretation |
|---|---|
| ≥ 10⁵ CFU/mL | Significant bacteriuria - active UTI |
| 10⁴ CFU/mL (single Gram-negative rod, in men) | Strongly suggestive of UTI |
| 10² - 10³ CFU/mL | May be significant in symptomatic young women |
| < 10⁴ CFU/mL (mixed flora) | Contamination / improper collection |
Asymptomatic Bacteriuria
- Bacteriuria without symptoms
- Prevalence: 1-2% in school-age girls, 1-3% in non-pregnant women, 3-8% in pregnancy
- Treatment is indicated in: pregnant women, pre-urological procedure patients
- Must be screened in first trimester of pregnancy
(Source: Jawetz Melnick & Adelbergs Medical Microbiology 28E, pp. 808-809)
LABORATORY DIAGNOSIS OF UTI
Step 1: Proper Specimen Collection
- Midstream clean-catch is the gold standard for most patients
- Female: Labia spread, clean front-to-back with non-bacteriostatic saline swabs x3, collect midstream
- Male: Retract foreskin, clean glans, collect midstream
- Catheter specimen: Aspirate from catheter port with needle/syringe (NOT from collection bag)
- Suprapubic aspiration: Gold standard (any organism is significant), done in infants and diagnostic dilemmas
- Urine must reach lab within 30 min OR be refrigerated (bacteria multiply rapidly at body temp)
Step 2: Microscopic Examination
| Finding | Significance |
|---|---|
| ≥10⁵ organisms/mL on wet mount | Strong evidence of active UTI |
| Gram-negative rods on Gram stain of uncentrifuged urine | Indicates ≥10⁵ bacteria/mL; indicative of UTI |
| Pyuria (WBCs ≥5-10/hpf) | Highly suggestive of infection (not specific) |
| WBCs + bacteria | Bacterial UTI |
| WBCs without bacteria ("sterile pyuria") | TB, chlamydia, fungal, viral, urethral syndrome |
| Squamous epithelial cells, mixed flora | Contamination - repeat specimen |
| Yeast cells / pseudohyphae | Candida UTI |
| Decoy cells (enlarged cells, intranuclear inclusions) | BK virus nephropathy |
Step 3: Dipstick Tests
| Test | What it Detects | Significance |
|---|---|---|
| Leukocyte esterase | PMN (pyuria) | Positive = suggests bacterial UTI |
| Nitrite | Nitrate-reducing bacteria (E. coli, Klebsiella, etc.) | Positive = Gram-negative bacteriuria |
| Both positive | High positive predictive value for bacterial UTI | |
| Both negative | Low likelihood of UTI (except neonates, immunocompromised) |
Note: Nitrite test is negative with Enterococcus, Pseudomonas, Staphylococcus (don't reduce nitrates)
Step 4: Quantitative Culture (Definitive)
- Medium used: Blood agar + MacConkey agar (or CLED - Cystine Lactose Electrolyte-Deficient agar, preferred for urine culture - inhibits swarming of Proteus)
- Loop method: Calibrated bacteriologic loop (0.001-0.01 mL) is used to inoculate; colonies counted after overnight incubation at 37°C
- Dip-slide method: Slide coated with agar dipped into urine - used in field settings
- Identification of organism + antibiotic sensitivity testing (AST) reported
Step 5: Special Tests for Specific Organisms
| Organism | Special Test |
|---|---|
| Mycobacterium tuberculosis | Ziehl-Neelsen stain; Lowenstein-Jensen culture (6-8 weeks); urine PCR |
| BK Virus | Urine PCR (viral load), urine cytology (decoy cells), serum BK PCR |
| Adenovirus | Urine PCR, shell vial culture |
| CMV | Urine PCR, urine cytology (owl-eye inclusion cells) |
| Chlamydia trachomatis | NAAT (nucleic acid amplification test) - most sensitive |
| Candida | Wet mount (pseudohyphae), fungal culture on Sabouraud's dextrose agar |
| N. gonorrhoeae | NAAT or culture on Thayer-Martin medium |
PART 2: SEXUALLY TRANSMITTED DISEASES (STDs)
Classification with Organisms and Lab Diagnosis
1. GONORRHEA
Organism: Neisseria gonorrhoeae (Gonococcus)
- Gram-negative diplococcus (kidney-bean shaped pairs), intracellular in PMNs
- Fastidious aerobe; oxidase positive
- Piliated strains - virulent (anti-phagocytic pili)
Clinical features: Urethritis (men) - purulent discharge, dysuria; Endocervicitis (women) - mucopurulent cervical discharge; also pharyngitis, proctitis, PID
Laboratory Diagnosis:
| Method | Details |
|---|---|
| Gram stain of discharge | Intracellular Gram-negative diplococci in PMNs; sensitivity ~90% men, ~50% women |
| Culture | Gold standard - Thayer-Martin medium (chocolate agar + antibiotics: vancomycin, colistin, nystatin, trimethoprim = VCNT). Candle-jar incubation (5% CO₂). Oxidase-positive, Gram-negative diplococci, ferments glucose only |
| NAAT (PCR/TMA) | Most sensitive (>99%); detects N. gonorrhoeae DNA in urethral/cervical exudate or urine; preferred for women and pharyngeal/rectal specimens |
| Serology | Not useful for acute diagnosis |
2. CHLAMYDIAL GENITAL INFECTION
Organism: Chlamydia trachomatis serovars D-K (genital tract)
- Obligate intracellular parasite; Gram-negative but cannot be Gram-stained meaningfully
- Exists as elementary body (EB, infectious) and reticulate body (RB, replicating)
Clinical features: Non-gonococcal urethritis (NGU) in men; endocervicitis, PID in women; "silent" infections common; neonatal conjunctivitis + pneumonia
Laboratory Diagnosis:
| Method | Details |
|---|---|
| NAAT (PCR/SDA/TMA) | Method of choice - sensitivity > 90%, can use cervical swab, urethral swab, or first-void urine |
| Cell culture | McCoy cells (treated with cycloheximide); iodine stain shows inclusion bodies (glycogen-containing inclusions stain brown with iodine); definitive but insensitive, mainly research |
| Direct Fluorescent Antibody (DFA) | Monoclonal antibodies against MOMP; detects EBs in smears |
| Enzyme Immunoassay (EIA) | Antigen detection; less sensitive than NAAT |
| Serology (MIF) | Microimmunofluorescence - useful for LGV and pneumonia, not routine genital infections |
3. SYPHILIS
Organism: Treponema pallidum subsp. pallidum
- Motile spirochete; too thin to see on Gram stain or light microscopy
- Cannot be cultured in vitro
Stages: Primary (chancre - painless ulcer), Secondary (rash - palms/soles, condylomata lata, mucous patches), Latent, Tertiary (gumma, cardiovascular, neurosyphilis)
Laboratory Diagnosis:
| Method | Stage/Details |
|---|---|
| Dark-field microscopy | Primary/secondary - visualize T. pallidum in fresh tissue fluid from chancre base; corkscrew morphology + rotational motility |
| Direct Fluorescent Antibody (DFA-TP) | Fluorescein-labeled anti-T. pallidum antibody on exudate smear |
| VDRL (Venereal Disease Research Laboratory) | Non-treponemal; detects anticardiolipin-lecithin-cholesterol antibody; screening test; titer correlates with disease activity, used to monitor treatment; becomes positive 3-6 weeks post-infection |
| RPR (Rapid Plasma Reagin) | Non-treponemal; same principle as VDRL; more convenient for screening |
| FTA-ABS (Fluorescent Treponemal Antibody-Absorbed) | Treponemal confirmatory test; uses patient serum absorbed with Reiter's treponemes; highly specific; remains positive for life |
| TPHA / MHA-TP | Treponemal agglutination test; confirmatory |
| TPPA (T. pallidum Particle Agglutination) | Confirmatory treponemal test; gelatin particles coated with T. pallidum antigens |
| NAAT (PCR) | Available in some reference labs; useful for primary lesions |
| CSF-VDRL | Neurosyphilis diagnosis (CSF examination) |
Serologic Algorithm: Positive RPR/VDRL (non-treponemal) → Confirm with FTA-ABS or TPPA (treponemal). Treponemal tests remain positive even after treatment. Non-treponemal titers fall with successful treatment.
4. GENITAL HERPES
Organism: Herpes Simplex Virus type 2 (HSV-2, primarily genital); HSV-1 (increasingly causes genital herpes)
Clinical features: Painful vesicles and ulcers on genitals; primary episode most severe; recurrences common (latent in sacral ganglia)
Laboratory Diagnosis:
| Method | Details |
|---|---|
| Tzanck smear | Scraping from base of fresh vesicle stained with Giemsa or Wright stain; shows multinucleated giant cells with intranuclear inclusions - suggestive (not specific - cannot distinguish HSV-1 from HSV-2 or VZV) |
| Viral culture | Gold standard for active lesions - inoculate on Vero cells or MRC-5 cells; cytopathic effect (CPE): cell rounding, ballooning; confirm with immunofluorescence. Sensitivity highest in vesicular stage |
| NAAT (PCR) | Most sensitive and specific; preferred test; can type HSV-1 vs HSV-2; also useful for CSF in HSV encephalitis |
| Direct Fluorescent Antibody (DFA) | Lesion scraping with type-specific fluorescent antibody |
| Serology (type-specific) | gG-based ELISA; IgG remains positive for life; IgM indicates recent primary infection; useful when no active lesions |
| Electron microscopy | Rapid but non-specific (shows herpesviridae family) |
5. CHANCROID
Organism: Haemophilus ducreyi
- Gram-negative coccobacillus; streptobacillary chains ("school of fish" / "railroad track" pattern on Gram stain)
- Fastidious; requires enriched media
Clinical features: Painful soft chancre (unlike syphilis painless); undermined ragged edges; inguinal lymphadenopathy (bubo) - painful and tender
Laboratory Diagnosis:
| Method | Details |
|---|---|
| Gram stain of exudate | "School of fish" / "railroad track" - chains of Gram-negative coccobacilli |
| Culture | Most sensitive but difficult; specimen from ulcer base or bubo aspirate; special media: GC agar base + hemoglobin + IsoVitaleX + vancomycin; incubate at 33°C, 5% CO₂, high humidity; small yellow-gray translucent colonies; "brick-like" cohesive colonies that can be pushed intact across agar |
| NAAT (PCR) | Available in reference labs; most sensitive and specific |
| Serology | Not reliable for routine diagnosis |
Diagnosis is often clinical after excluding syphilis (dark-field, serology) and HSV.
6. LYMPHOGRANULOMA VENEREUM (LGV)
Organism: Chlamydia trachomatis serovars L1, L2, L3
- More invasive than D-K serovars; infects lymphoid tissue
Clinical features: 3 stages - primary (small painless papule/ulcer, heals quickly), secondary (inguinal buboes - "groove sign" - enlarged nodes above and below inguinal ligament = pathognomonic), tertiary (elephantiasis of genitalia, rectal strictures)
Laboratory Diagnosis:
| Method | Details |
|---|---|
| NAAT (PCR) | Preferred; can type serovars (L1, L2, L3); specimen from ulcer, bubo aspirate, rectal swab |
| Frei test | Historical only - intradermal skin test with chlamydial antigen; no longer used |
| Complement Fixation (CF) test | Titer ≥1:64 is diagnostic of LGV; genus-specific, cross-reacts with all Chlamydiae |
| Microimmunofluorescence (MIF) | Type-specific antibody; titer ≥1:512 suggests LGV |
| Cell culture | McCoy cells; difficult |
7. GRANULOMA INGUINALE (DONOVANOSIS)
Organism: Klebsiella granulomatis (formerly Calymmatobacterium granulomatis)
- Gram-negative rod; cannot be cultured on ordinary media
Clinical features: Painless, beefy-red, friable granulomatous ulcer of genitalia; no inguinal lymphadenopathy (distinguishes from LGV); progressive, slowly spreading lesion
Laboratory Diagnosis:
| Method | Details |
|---|---|
| Tissue biopsy | Most important; crush preparation of biopsy tissue |
| Donovan bodies | Bipolar-staining (safety-pin appearance), encapsulated bacilli within large mononuclear cells (macrophages); stain with Wright-Giemsa or Leishman stain - this is the hallmark diagnostic finding |
| Culture | Very difficult; rarely attempted (Hep-2 cells or yolk sac); not clinically useful |
| NAAT (PCR) | Available in reference/research labs; most sensitive |
| Serology | Not helpful |
8. GENITAL WARTS (CONDYLOMATA ACUMINATA)
Organism: Human Papillomavirus (HPV) - types 6 and 11 (anogenital warts); types 16, 18, 31, 33 (high-risk, oncogenic - cervical/anal carcinoma)
Laboratory Diagnosis:
| Method | Details |
|---|---|
| Clinical inspection | Cauliflower-like warts in perianal/genital area |
| Colposcopy + acetic acid test | Acetic acid (5%) application whitens HPV-infected cells (acetowhite areas) - used in cervical evaluation |
| PAP smear / cervical cytology | Koilocytes (perinuclear halo, wrinkled nucleus) are cytopathic effect of HPV |
| Histology (biopsy) | Koilocytosis, parakeratosis, acanthosis |
| HPV DNA detection (NAAT) | Identifies specific HPV type; used in cervical cancer screening (high-risk HPV testing) |
| Southern blot / In situ hybridization | Research; detects HPV DNA in tissue |
9. TRICHOMONIASIS
Organism: Trichomonas vaginalis
- Flagellated protozoan (pear-shaped); 4 anterior flagella + undulating membrane; NOT a bacterium
Clinical features: Frothy, yellow-green, malodorous vaginal discharge; "strawberry cervix" (punctate hemorrhages); vulvovaginitis; often asymptomatic in men (urethral carriage)
Laboratory Diagnosis:
| Method | Details |
|---|---|
| Wet mount | Fresh vaginal discharge in saline; motile pear-shaped trichomonads with characteristic tumbling motility; sensitivity ~50-70% |
| Culture | Diamonds medium or InPouch TV system; most sensitive traditional method; incubate 37°C, 5-7 days |
| NAAT (PCR/TMA) | Most sensitive and specific (>95%); APTIMA Trichomonas vaginalis assay |
| Pap smear | May detect T. vaginalis but sensitivity low (~60%), false positives occur |
| Rapid antigen tests | e.g., OSOM Trichomonas Rapid Test |
10. BACTERIAL VAGINOSIS (BV)
Organism: Gardnerella vaginalis + anaerobes (Mobiluncus, Prevotella, Bacteroides, Peptostreptococcus, Mycoplasma hominis)
- Polymicrobial disruption of normal Lactobacillus-dominant vaginal flora
Laboratory Diagnosis (Amsel's Criteria - 3 of 4 required):
| Criterion | Finding |
|---|---|
| 1. Vaginal discharge | Thin, grayish-white, homogeneous, adherent discharge |
| 2. Vaginal pH | >4.5 (normal <4.5) |
| 3. Whiff test (KOH test) | "Fishy" amine odor when 10% KOH added to discharge |
| 4. Clue cells | Vaginal epithelial cells covered with Gram-variable coccobacilli (Gardnerella) giving a stippled "ground-glass" appearance; >20% of epithelial cells = clue cells |
Additional:
- Nugent score: Gram stain scoring system (0-10) based on morphotypes - score ≥7 = BV
- Culture: Not recommended (Gardnerella found in normal women too)
11. GENITAL MOLLUSCUM CONTAGIOSUM
Organism: Molluscum contagiosum virus (MCV) - Poxvirus
- Largest of human viruses; brick-shaped; DNA virus
Clinical features: Umbilicated, pearly white papules in genital area; sexually transmitted in adults; self-limited
Laboratory Diagnosis:
| Method | Details |
|---|---|
| Clinical inspection | Umbilicated papules - pathognomonic appearance |
| Histology (Giemsa/H&E) | Large cytoplasmic Henderson-Patterson (molluscum) bodies in keratinocytes |
| Electron microscopy | Brick-shaped poxvirus particles |
SUMMARY TABLE: STD Organisms & Key Lab Tests
| STD | Organism | Key Lab Test |
|---|---|---|
| Gonorrhea | N. gonorrhoeae | Gram stain (intracellular GNDs), Thayer-Martin culture, NAAT |
| Chlamydia | C. trachomatis D-K | NAAT (first-void urine or swab) |
| Syphilis | T. pallidum | Dark-field, VDRL/RPR (screening), FTA-ABS/TPPA (confirmatory) |
| Genital herpes | HSV-1 / HSV-2 | NAAT (PCR), viral culture, Tzanck smear |
| Chancroid | H. ducreyi | Gram stain ("school of fish"), culture on special media |
| LGV | C. trachomatis L1-L3 | NAAT (PCR), CF test titer ≥1:64, MIF titer ≥1:512 |
| Granuloma inguinale | K. granulomatis | Biopsy - Donovan bodies (Wright-Giemsa) |
| Genital warts | HPV 6, 11 (warts); 16, 18 (cancer) | Colposcopy, Pap smear (koilocytes), HPV DNA NAAT |
| Trichomoniasis | T. vaginalis | Wet mount (motile trophozoites), NAAT |
| Bacterial vaginosis | G. vaginalis + anaerobes | Amsel's criteria (clue cells, pH, whiff test), Nugent score |
| Molluscum contagiosum | MCV (Poxvirus) | Clinical + Henderson-Patterson bodies on histology |
Reference: Jawetz, Melnick & Adelberg's Medical Microbiology, 28th Edition (equivalent to Apurba Sastri's approach for 2nd year MBBS - both cover the same organisms, lab methods, and clinical correlates). Note: Apurba Sastri's "Essentials of Medical Microbiology" was not available in this library, but Jawetz is the international equivalent and covers all 2nd year MBBS syllabus topics at the same depth.
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