Urinary Tract Infection

Anatomy of the Urinary Tract

  • Kidneys → Ureters → Bladder → Urethra (downward flow)

  • Infection classification often mirrors this anatomic path: upper (kidney, ureter) vs. lower (bladder, urethra)

Classification of UTI

• By EPISODES

  • Sporadic (single-episode): \leq 1\text{ UTI}/6\text{ months}

  • Recurrent: \geq 1\text{ UTI}/6\text{ months}
    • By CLINICAL CONTEXT

  • Uncomplicated: infection with no structural/functional abnormality (e.g. healthy, non-pregnant females)

  • Complicated: infection with metabolic, anatomic or functional abnormality (pregnancy, catheter, diabetes, stones…)
    • By ANATOMIC SITE

  • Upper: Pyelonephritis, Ureteritis

  • Lower: Cystitis, Urethritis

Major Etiological Agents

1. Bacteria in Lower vs. Upper UTI

  • Lower UTI: Escherichia coli, Staphylococcus saprophyticus, Klebsiella spp., Proteus mirabilis

  • Upper UTI: E. coli, Klebsiella spp., Proteus mirabilis, other Enterobacteriaceae, Staphylococcus aureus

2. Enterobacteriaceae – Key Biochemical Traits

  • Gram-negative, Catalase +ve, Oxidase –ve, Nitrate +ve, ferment glucose

  • Genera: E. coli, Klebsiella, Salmonella, Shigella, Proteus, Yersinia, Citrobacter, Enterobacter

  • Lactose fermenters (pink on MacConkey): E. coli, Klebsiella; non-fermenters (colorless): Proteus, Salmonella, Shigella, Serratia (late LF)…

  • Selected differentiators: Indole +ve (E. coli, Proteus vulgaris), Urease +ve (Proteus, Klebsiella), H$_2$S +ve (Salmonella, Proteus)

3. Escherichia coli

  • Accounts for ≈ 80 % of UTIs; gut commensal

  • Virulence factors:

    • Fimbriae → adherence to uroepithelium

    • O & K antigens → evade phagocytosis

    • Hemolysin → tubular epithelial damage → invasive infection

  • Lab ID: Gram-negative rod, pink LF colonies on MacConkey; Indole +ve

4. Proteus mirabilis

  • Gram-negative rod; swarming motility on blood agar

  • Non-lactose fermenter; Urease +ve; H2S +ve

  • Pathogenesis hallmark: stone formation
    Urease: Urea → NH3 + CO2↑ ⇒ pH↑ ⇒ struvite (MgNH4PO4) & CaPO4​

5. Pseudomonas aeruginosa

  • Gram-negative bacillus, non-lactose fermenter, Oxidase +ve

  • Produces pyocyanin (blue-green pigment) → ROS → biofilm (eDNA matrix)

  • Classical hospital-acquired UTI pathogen; grows at 42\ ^\circ \text C

6. Staphylococcus saprophyticus

  • Gram-positive cocci in clusters; Catalase +ve, coagulase –ve, novobiocin-resistant

  • Epidemiology: sexually active young women; 2nd most common community lower UTI

7. Candida albicans (Fungus)

  • Most prominent opportunistic fungal UTI (especially nosocomial, catheterized)

  • Normal flora of mouth, gut, vagina

  • Morphology: yeast, pseudohyphae, or true septate hyphae

Antimicrobial Susceptibility Highlights (Indian studies)

  • Most effective: Meropenem, Gentamicin, Nitrofurantoin, Cotrimoxazole

  • High resistance: Fluoroquinolones (Ciprofloxacin), Amoxicillin, 3rd-gen Cephalosporins (Cefotaxime)

  • Emphasizes need for local antibiogram-guided therapy rather than empirical fluoroquinolones

Pathogenesis of UTI

  1. Initial colonization: peri-urethral bacteria (usually gut flora) adhere via fimbriae

  2. Ascending route (most common): Urethra → Bladder (cystitis) → Ureters/Kidney (pyelonephritis)

    • Facilitated by sexual activity, catheters, vesicoureteral reflux, pregnancy

  3. Hematogenous (descending) route: bloodstream seeding of kidneys; classically Staph aureus bacteremia

  4. Host response: inflammatory cytokines → pyuria, dysuria, urgency

  5. Potential complications: sepsis, renal scarring, chronic kidney disease if untreated

Clinical Features

  • LOWER UTI: Dysuria, frequency, urgency, suprapubic pain, ± hematuria

  • UPPER UTI: Fever, chills, flank pain, costovertebral angle tenderness, ± lower symptoms

Laboratory Diagnosis Workflow

A. Urine Collection

  1. Midstream clean-catch (MSU) – ideal; cleanse–void–collect (≈½ cup)

  2. Catheterized urine – aspirate from sampling port, never from bag/tip

  3. Suprapubic aspirate – needle tap; mainly infants/urgent sterile sample

  4. Bag urine – infants; use adhesive collection bag then transfer to cup

B. Specimen Handling

  • Label; biohazard bag

  • Deliver to lab within 1–2 h; if delayed: refrigerate (≤ 24 h) or add preservatives (boric acid, barium salts)

  • Rejection: > 2 h at RT, leaky container, urine from catheter bag, Foley tips, 24-h pooled urine

C. Urine Analysis (FEME)

  1. Physical: color, clarity, odor, foam

    • Normal: pale-amber, clear, aromatic

    • Abnormal colors: red (hematuria), orange (bilirubin/drugs), blue-green (drugs), cloudy (infection/stones)

  2. Dipstick Biochemical (60-120 s readings)

    • Nitrite + ⇒ gram-negative convert nitrate

    • Leukocyte esterase + ⇒ pyuria

    • Protein, blood, pH, glucose, ketone, bilirubin, urobilinogen, SG

  3. Microscopy (centrifuged sediment)

    • WBC > 5/HPF ⇒ pyuria

    • Bacteria, yeast, casts, crystals, epithelial cells

  4. Reporting: degrees of pyuria + organism presence within 2 h to clinician

D. Culture & Sensitivity (C&S)

  1. Primary media

    • CLED agar (cystine lactose electrolyte-deficient): differential, ↓Proteus swarming.
      • LF (yellow) = E. coli, Klebsiella, S. saprophyticus; alkaline dark-blue = Proteus (cystine decarboxylation)

    • MacConkey agar – confirms LF vs NLF among Gram-negatives

  2. Enumeration (Significant bacteriuria)

    • Threshold: \ge 10^5\;\text{CFU ml}^{-1} (105) in MSU = diagnostic; lower counts may still be significant in catheter or suprapubic samples

    • Standard loop method: 0.01 ml inoculum ⇒ each colony ≈ 100 CFU / ml; thus 105 CFU/ml ⇒ ≥ 1000 colonies

    • Filter paper/uristrip: colony ranges interpret (e.g. > 25 colonies for gram-pos or > 30 for gram-neg ≈ > 10⁵ CFU/ml)

  3. Interpretation guide

    • MSU, > 105 CFU/ml with ≤ 2 species ⇒ report & perform full ID/S

    • Mixed flora (> 2 species) ⇒ likely contamination

  4. Further identification

    • Gram stain; rapid tests (catalase, coagulase, oxidase, indole, urease); API, VITEK, serotyping

  5. Antibiotic susceptibility: disk diffusion, MIC; guide therapy per local resistance patterns

E. Integrated Report Example

  • Provides SG, pH, dipstick, microscopy counts (e.g. RBC 105/µL, WBC 98/µL) to correlate with culture

Practical / Laboratory Exercises (Teaching Session)

Day 1

  • 3 volunteers per PBL group collect MSU

  • Perform physical exam & microscopy; inoculate culture using uristrip
    Day 2

  • Read plates, document growth, Gram stain isolates; solve 3 clinical case studies

Ethical / Practical Implications

  • Over-use of empirical fluoroquinolones drives resistance; lab confirmation critical

  • Catheter care & prompt removal essential to cut nosocomial UTIs (esp. Candida, Pseudomonas)

  • Rejection criteria & correct collection protect patients from mis-diagnosis & over-treatment

Summary (Mnemonic: "PCP – Pathogen, Collection, Processing")

  • Pathogen spectrum: Gram-negatives dominate; recognize Gram-positives & fungi

  • Collection integrity determines diagnostic accuracy

  • Processing: quick analysis, quantitative culture, targeted susceptibility = best patient outcomes