GC101 Diagnosis Of Infections
Diagnosis of infections is the systematic process of identifying causative pathogens through clinical assessment, microbiological techniques (culture, microscopy, serology, molecular methods), and laboratory markers to guide appropriate antimicrobial therapy.
Diagnosis of Infections: Collection & Handling of Clinical Specimens for Microbiological Tests
Lecture Map
This lecture is fundamentally about how to correctly diagnose infections in the laboratory — not just what tests to order, but why specimen quality determines whether you get a meaningful answer or misleading garbage. The lecture walks through a real clinical case (Legionella pneumonia in a CAPD patient), then systematically covers every major specimen type, what tests apply to each, and common pitfalls.
"The usefulness of microbiological tests is directly related to the quality of specimens." — This is the single most important principle of the entire lecture. [1]
- Understand the clinical approach to a patient with suspected infection (6-step framework)
- Know the two broad categories of laboratory diagnosis: detecting the microbe vs. detecting the host response
- Learn general principles of specimen collection, transport, and labelling
- Know specimen-specific requirements for blood, CSF, urine, sputum, stool, genital, wound, and other body fluids
- Recognize specimens of dubious significance and avoid ordering tests that produce misleading results
- Understand when and why to consult a microbiologist
Past papers consistently test: blood culture indications/technique, sputum quality assessment, urine collection methods, CSF workup for meningitis/encephalitis, stool investigations, and the concept of contamination vs. true infection. The 2024 SAQ directly tested transmission modes and common pathogens in hospital settings. [2]
The 6-step clinical approach from the lecture handout is the backbone of how HKU teaches infection management: [1]
| Step | Action | Why It Matters |
|---|---|---|
| 1 | History, PE, preliminary Ix → formulate clinical diagnosis | You must suspect infection before you can diagnose it |
| 2 | Localize the focus of infection (clinical + radiological) | Determines which specimens to collect |
| 3 | Collect & transport relevant specimens for microbiology | The quality here determines everything downstream |
| 4 | Start empirical antimicrobial therapy if indicated | Don't wait for culture results in serious infection |
| 5 | Modify therapy when rapid tests (Gram stain) or final C/ST come back | De-escalation or targeted therapy |
| 6 | Monitor therapy — further specimens, drug levels | Ensure response; catch resistance or complications |
Critical Sequence
Specimens should ideally be collected BEFORE antibiotics are started — but empirical antibiotics must NOT be delayed for specimen collection in sepsis. The 1-hour sepsis bundle mandates antibiotics within 1 hour. [3]
The Case: Legionella Pneumonia in a CAPD Patient
This case is used throughout the lecture to illustrate diagnostic principles. Understanding it helps you see how the framework works in practice.
- Patient: Elderly male, extensive comorbidities (HT ×30yr, DM ×15yr on insulin, mild CAD, hyperlipidaemia, gout, CKD on CAPD)
- Presentation: Acute fever + SOB ×1 day. Given ciprofloxacin 250mg q12h by GP → worsened → admitted QMH
- On admission: Tachycardic (120/min, irregular), febrile (39°C), desaturating (SpO₂ 70% on RA, 95% on CPAP), slow mentation, bilateral ankle oedema, decreased air entry left posterior chest, coarse inspiratory crepitus
- Labs: Hb 7.5 (dropped from 11), WBC 8.6, N 7.4, Cr 1299, K 5.1 — uraemic patient in acute LHF
Key history elicited on retrospective questioning: Travel to a hotel and zoo in Guangzhou 6 days before admission [1] — This completely changed the differential diagnosis.
| Investigation | Result | Teaching Point |
|---|---|---|
| Blood culture | Negative | Blood cultures are often negative in atypical pneumonia — doesn't rule out serious infection |
| Cold agglutinin | Negative | Rules against Mycoplasma (though sensitivity is low) |
| NPA viral IF | Negative | Direct fluorescent antibody for respiratory viruses |
| Resplex II RT-PCR (16 viruses) | Negative | Comprehensive viral panel — important to systematically exclude |
| Urine antigen (Binax) for Legionella SG1 & S. pneumoniae | Negative | Binax detects only serogroup 1 — other serogroups missed; also timing matters |
| Stool C/ST & C. difficile toxin | Negative | Patient had diarrhoea — must investigate |
| PD fluid | Normal cell count, culture negative | Rules out PD-related peritonitis |
| RT-PCR for Legionella pneumophila | POSITIVE (NPA Day 1 and sputum Day 4) | This was the definitive diagnosis |
The urine antigen for Legionella was negative because it detects only serogroup 1. The RT-PCR detected the organism. This illustrates why relying on a single test modality is dangerous. [1]
- Stop meropenem and zanamivir
- Continue levofloxacin alone (fluoroquinolones are the treatment of choice for Legionella)
- Notify CHP (Centre for Health Protection) — Legionella is a notifiable disease
- 13/38 water samples from a newly commissioned Government Office were positive for Legionella
- High count in the patient's private office shower room → This confirmed the source
Exam Pearl
Legionella is acquired from environmental water sources (cooling towers, showers, hot tubs) — NOT person-to-person. Travel history and environmental exposure history are critical. [1]
Laboratory Diagnosis of Infection: The Two Pillars
The lecture divides laboratory diagnosis into two fundamental approaches: [1]
| Method | What It Detects | Examples |
|---|---|---|
| Visualization | Morphology of organisms | Gram stain (bacteria), ZN stain (AFB/TB), electron microscopy (viruses), wet mount (parasites/amoeba) |
| Culture | Growth of living organisms | Blood culture broth, agar plates, viral culture in cell lines |
| Detection of microbial components | ||
| — Proteins | Antigen by EIA/LA | SARS-CoV-2 RAT, Cryptococcal antigen, Dengue NS1 |
| — Polysaccharides | Antigen by EIA/LA | Pneumococcal urinary antigen, Legionella urinary antigen |
| — Lipids | Chromatography | Gas-liquid chromatography for anaerobes |
| Nucleic acid detection | Specific DNA/RNA | PCR, probe hybridization, RT-PCR, next-generation sequencing (NGS) |
| Method | What It Detects | Examples |
|---|---|---|
| Antibody response | IgM (acute), IgG (past/rising titre) | Brucella, Rickettsia, VDRL, Toxoplasma IgM; 4× rise in IgG titre between acute and convalescent sera |
| Cellular immune response | T-cell activation | Mantoux/TST (tuberculin skin test), IGRA (IFN-γ release assay) — detecting activated CD4/CD8 lymphocytes expressing IFN-γ, TNF-α after stimulation by specific antigens |
Why Two Approaches?
Direct detection (PCR, culture, antigen) gives you the causative organism itself — high specificity, often faster. Host response (serology, cellular immunity) tells you the body has encountered the organism — useful when the bug is hard to grow or has been cleared, but can have issues with timing (IgM takes days to appear, need paired sera for IgG rise). Both approaches are complementary.
"Garbage In, Garbage Out" — Improperly collected specimens → Misleading test results [1]
This is a deliberately provocative slide to emphasize that the entire diagnostic chain fails if the specimen is poor. The three determinants of specimen quality are:
- Representative of the pathophysiological process — Is the specimen actually from the site of infection?
- Manner of collection — Was aseptic technique used? Was the right container chosen?
- Manner of transportation — Was it delivered promptly? Were transport conditions appropriate?
These principles appear repeatedly in the lecture and handout: [1]
| Principle | Explanation |
|---|---|
| Relevant specimens with clinical indication | Don't send random swabs without clinical suspicion |
| Correct containers | Prevent leakage and contamination |
| Expedient transport | Preserve microbial viability; prevent overgrowth of contaminants |
| Proper request form entry | Clinical information guides the lab — wrong info = wrong tests |
| Biohazard / Universal precaution | Protect yourself and lab staff |
| Known hazards — inform lab | If you suspect high-risk pathogens (TB, SARS, avian flu), TELL the lab |
| Unusual infections — consult microbiologist | Don't just send specimens blindly for rare organisms |
Common Exam Trap
"Fill the entries in computer form properly!!!" — The lecture specifically emphasizes that clinicians often fail to provide adequate clinical information on request forms. Without clinical context, the lab cannot select appropriate tests. A sputum sent "for C/ST" without mentioning immunosuppression will not be tested for fungi or Nocardia. [1]
Specimen-by-Specimen Guide
Blood culture collection has specific rules regarding indication, timing, number, site, and technique: [1]
| Parameter | Details | Why |
|---|---|---|
| Indications | Fever, sepsis, suspected endocarditis, suspected bacteraemia, PUO | Blood cultures are positive in ~10-30% of sepsis cases — still essential |
| Timing | Ideally before antibiotics; for endocarditis: ≥3 sets over ≥1 hour | Persistent bacteraemia is a Duke criterion |
| Number | At least 2 sets (aerobic + anaerobic per set) from different sites | Single set has high false-positive rate from contamination |
| Site | Peripheral veins, different sites; NOT through existing IV lines (high contamination) | Minimizes skin flora contamination |
| Broth | Contains antibiotic-absorbing resins | If patient already on antibiotics, resins absorb residual drug to allow organism growth |
| Aseptic technique | Skin antisepsis (chlorhexidine/alcohol), no-touch technique | Reduces contamination with coagulase-negative staphylococci (CoNS) |
For culture-negative endocarditis, consider PCR & antibody tests for: Coxiella, Bartonella, Tropheryma (Whipple's), Brucella, Leptospira, Mycoplasma, Chlamydia [1]
Differential Time to Positivity (DTP)
In patients with central venous catheters, blood cultures drawn simultaneously from the catheter and a peripheral vein can help diagnose catheter-related bloodstream infection (CRBSI). If the catheter culture turns positive ≥2 hours before the peripheral culture, it suggests the catheter is the source. [3]
CSF collection and testing is a critical exam topic: [1]
Pre-requisites:
- CT brain first to rule out space-occupying lesions (risk of herniation with LP if raised ICP)
- Use non-reused bottles (from lumbar puncture set) — reused bottles may be contaminated
Tests to order on CSF:
| Test | Target | Why |
|---|---|---|
| Gram stain | Bacteria (pyogenic meningitis) | Rapid — guides empirical therapy within hours |
| ZN smear | AFB (TB meningitis) | Low sensitivity (~10-20%) but highly specific |
| Wet mount | Free-living amoeba (primary amoebic meningoencephalitis) | Rare but rapidly fatal — must consider if freshwater exposure |
| Bacterial culture | Standard pathogens | Gold standard but takes 24-48h |
| PCR + AFB culture for TB | M. tuberculosis | PCR faster than culture (which takes weeks) |
| Cryptococcal antigen (latex agglutination) + fungal culture | Cryptococcus neoformans | Especially in HIV/immunocompromised — cryptococcal antigen is highly sensitive |
| PCR for HSV1, HSV2, VZV | Herpes encephalitis | PCR is the single most important method for diagnosing CNS viral infections [4] |
| RT-PCR for enterovirus | Acute encephalitis | Common viral cause of meningitis |
| CSF IgM for Japanese encephalitis & Mycoplasma pneumoniae | Specific causes of encephalitis | JE is important in Asia — IgM in CSF indicates intrathecal production |
Semiquantitative culture of catheter tips (roll-plate method) is indicated when: [1]
- Local signs of phlebitis at the insertion site
- Persistent fever without other localizing signs
Threshold: ≥15 CFU of bacteria on roll-plate culture = significant (Maki technique)
Why this matters: Catheters are foreign bodies that become colonized. Differentiating colonization from true catheter-related infection requires quantitative/semiquantitative methods, not just qualitative culture.
There is a critical hierarchy of specimen quality for skin/soft tissue infections: [1]
| Specimen Type | Representation | Contamination Risk | Comment |
|---|---|---|---|
| Tissue biopsy | Excellent — directly from infected site | Low | Best specimen for deep infections |
| Sterile aspirate / Abscess fluid | Excellent | Low | Use needle aspiration, not swabs |
| Drain fluid | Variable | Moderate-High | Long-term drains become colonized |
| Wound swab | Poor | High — picks up superficial colonizing flora | Degree of representation low, degree of contamination high |
For normally sterile body fluids (joint, pleural, peritoneal, pericardial): inoculate ALSO into blood culture broth to maximize yield [1]
This is a practical pearl — blood culture broth contains enrichment media and antibiotic-neutralizing resins that improve recovery of fastidious organisms.
Actinomycosis
The lecture includes an image of actinomycosis — a chronic bacterial infection caused by Actinomyces israelii (anaerobic, Gram-positive filamentous bacterium). Diagnosis requires tissue biopsy showing "sulfur granules." Swabs are inadequate — you need deep tissue. [1]
Stool specimens have unique challenges: [1]
| Challenge | Explanation | Solution |
|---|---|---|
| Overgrowth of commensal flora | Normal gut has 10¹¹ bacteria/g — pathogens easily overgrown | Selective media (e.g., MacConkey, XLD agar) |
| Death/loss of architecture of parasites | Trophozoites of amoeba die quickly at room temperature | Examine fresh stool within 30 min; fix specimens for ova & cysts |
| Antibiotic-related diarrhoea | C. difficile — toxin-mediated, not just culture | Tissue culture assay, EIA for antigen, PCR for toxin gene |
Standard stool workup: Bacterial culture (Salmonella, Shigella, Campylobacter, Vibrio), ova & cysts, C. difficile testing
Viral gastroenteritis workup:
- Rotavirus: EIA for antigen detection
- Norovirus, sapovirus, astrovirus, enteric adenovirus 40/41: faeces in viral transport medium for RT-PCR
Special requests (must specify clinically): Mycobacteria, Cryptosporidium, Isospora, Cyclospora, Microsporidia, Yersinia enterocolitica, Bacillus anthracis [1]
Three collection methods with decreasing contamination risk: [1]
| Method | Contamination Risk | Indication |
|---|---|---|
| Mid-stream urine (MSU) | Moderate — requires proper instruction | Standard for ambulatory patients |
| Catheterized urine | Low | Patients who cannot provide MSU |
| Suprapubic aspirate (SPA) | Lowest — gold standard | Neonates, ambiguous results, anaerobic culture needed |
Urine can be used for:
- Bacterial culture (UTI)
- Yeast (Candida)
- PCR for N. gonorrhoeae & C. trachomatis (first-void urine)
- Antigenuria: Pneumococcal & Legionella urinary antigen [1]
The lecture specifically covers the approach to suspected gonococcal infection: [1]
| Specimen | Test | Purpose |
|---|---|---|
| Urethral discharge | Gram smear (intracellular Gram-negative diplococci) + gonococcal culture | Direct visualization is rapid and specific for gonorrhoea in males |
| First-void urine | PCR for N. gonorrhoeae / C. trachomatis | Non-invasive, high sensitivity |
| Urethral scrapings | Cell-based tests | Chlamydia is an intracellular pathogen — need cells, not just discharge |
| Triple swabs (if gonococcal infection suspected with risk factors) | Urethral + Throat + Anal | Gonorrhoea can colonize multiple mucosal sites — must sample all |
Two main specimen types with different pathogen targets: [1]
| Specimen | Pathogens Detected | Key Points |
|---|---|---|
| Nasopharyngeal swab/aspirate (NPA) | Bordetella pertussis, Mycoplasma pneumoniae, all respiratory viruses (Rhinovirus, RSV, metapneumovirus, Adenovirus, Influenza A/B, PIV 1-4, Coronaviruses) | NPA is more sensitive than throat swab for most respiratory viruses |
| Throat swab | Streptococcus pyogenes, Neisseria gonorrhoeae, Corynebacterium diphtheriae, respiratory viruses | Generally not as sensitive as NP specimens except in patients with pneumonia |
All samples for RT-PCR must be in unreused, gamma-irradiated bottles [1] — This prevents contamination with residual nucleic acid from previous use.
Transport medium: Viral transport medium (VTM) is essential — it maintains viral viability during transport. The lecture shows the VTM tube specifically.
Rapid antigen testing (RAT): Uses immunochromatographic EIA (as with SARS-CoV-2 rapid tests). Lower sensitivity than RT-PCR but provides point-of-care results.
The lecture presents a hierarchy of specimens from lowest to highest invasiveness and yield: [1]
| Specimen | Indication | Quality |
|---|---|---|
| Expectorated sputum | Unusual chest infections (instructed/assisted by physiotherapist) | Oropharyngeal / saliva contamination is the main problem |
| Endotracheal aspirate | Intubated patients | Better than sputum |
| Bronchoscopic aspirate | As above | Better access to lower airways |
| Bronchoalveolar lavage (BAL) | Severe/persistent/undetermined pneumonia | Predominant pathogens — high yield |
| Protected catheter brush | As above | Minimizes upper airway contamination |
| Transbronchial lung biopsy | Immunocompromised with undetermined pneumonia | Tissue diagnosis |
| Open lung biopsy | Last resort | Highest yield but most invasive |
Sputum Quality
A sputum sample contaminated with saliva is USELESS — the lecture shows a slide of a sputum Gram stain with squamous epithelial cells (indicating oropharyngeal contamination). A good sputum sample has >25 WBC and < 10 squamous epithelial cells per low-power field. The patient in the case didn't produce sputum until Day 4 — this is common and you may need to use other specimen types. [1]
Causes of Febrile Respiratory Illness
The lecture provides a comprehensive list of bacterial, viral, fungal, and parasitic causes. This is HIGH YIELD: [1]
| Organism | Key Association / Notes |
|---|---|
| Streptococcus pneumoniae | Most common CAP pathogen; urinary antigen available |
| Staphylococcus aureus / Streptococcus pyogenes | Post-influenza pneumonia, skin/wound source |
| Haemophilus influenzae / Neisseria meningitidis | Common in COPD; meningococcal pneumonia rare |
| Klebsiella pneumoniae | Ill health, > 65 years — thick, bloody "red currant jelly" sputum |
| Oral aerobes/anaerobes | Aspiration pneumonia |
| Acinetobacter baumannii | Hospital-acquired, multidrug-resistant |
| Pseudomonas aeruginosa | Hospital-acquired, structural lung disease, ICU |
| Burkholderia pseudomallei | Melioidosis — SE Asia, travel history, DM |
| Legionella pneumophila | Urinary antigen EIA (but only SG1); travel/water exposure |
| Mycoplasma pneumoniae | RT-PCR or Ab — atypical pneumonia |
| Chlamydophila pneumoniae/psittaci | Atypical pneumonia; psittaci = bird contact |
| Coxiella burnetii | Q fever — animal/farm exposure |
| Mycobacterium tuberculosis | Sputum for AFB smear/culture |
| Virus | Notes |
|---|---|
| Influenza A (H3N2, H1N1, avian H5N1/H9N2/H7N9), B, C | Most important respiratory virus |
| Adenovirus | Can cause severe pneumonia in immunocompromised |
| RSV, Metapneumovirus | Important in children and elderly |
| Parainfluenza 1-4 | Croup in children |
| Rhinovirus Clade A, B, C | Most common cause of common cold; can cause pneumonia |
| Coronavirus: MERS, SARS-CoV-1/2, OC43, HKU1, 229E | Pandemic potential; HKU1 discovered in HK |
| Enterovirus, Bocavirus | Less common respiratory pathogens |
| Organism | Notes |
|---|---|
| Cryptococcus | HIV/AIDS, cryptococcal meningitis |
| Aspergillus | Invasive aspergillosis in neutropenic patients |
| Dimorphic fungi: Penicillium, Histoplasma, Coccidioides | Geographic distribution matters |
| Zygomycetes | Diabetic ketoacidosis, iron overload |
| Pneumocystis | PCP in HIV (CD4 < 200) or other immunosuppression |
| Organism | Notes |
|---|---|
| Paragonimus westermanii | Lung fluke — raw crabs/crayfish |
| Ascaris lumbricoides | Löffler syndrome (pulmonary eosinophilia) |
| Strongyloides stercoralis | Hyperinfection in immunosuppressed |
Beyond blood cultures, serum/blood provides three categories of diagnostic information: [1]
| Category | Tests | Examples |
|---|---|---|
| Therapeutic drug monitoring | Drug levels, serum bactericidal titre | Aminoglycosides, vancomycin — narrow therapeutic index, need peak/trough levels |
| Serum antibody detection | Acute + convalescent sera; IgM for viruses; 4× rise in IgG titre | Brucella, Rickettsia/Orientia, ASO titre, VDRL, Toxoplasma, Aspergillus IgG |
| Serum/blood antigen detection | Direct antigen assays | Cryptococcal antigen, Aspergillus galactomannan, 1,3-beta-D-glucan (pan-fungal), Dengue NS1, CMV pp65 antigen in WBC |
The 4× Rise Rule
A 4-fold rise in IgG titre between acute and convalescent sera (taken 2-4 weeks apart) is the serological gold standard for confirming recent infection. A single IgG titre is often meaningless — it could represent past exposure. IgM is useful for acute infection but can have false positives (rheumatoid factor interference) and false negatives (early in disease). [1]
This is a critical concept the lecture emphasizes — ordering the wrong test wastes resources and produces misleading results: [1]
| Dubious Specimen | Why It's Problematic |
|---|---|
| Bedsore / superficial wound swabs | Colonized by multiple organisms — culture reflects flora, not the pathogen causing deep infection |
| Routine culture of penile/perineal/nasal swabs | Same problem — surface colonization ≠ infection |
| Long-term drain fluids (e.g., PTBD) | Drains become colonized over time — culture grows colonizers, not pathogens |
| Urine from chronic catheterized patients | All chronically catheterized patients have bacteriuria — treating it is usually inappropriate (asymptomatic bacteriuria) |
| Colonic biopsy for routine bacterial culture (without clinical info) | Without context, the lab cannot interpret results — need histological confirmation of infection |
The lecture shows images of clinical scenarios asking "Does this need Rx?" — with wound cultures growing MRSA + Candida, or Morganella + Group B Strep + Bacteroides + Clostridium. The answer is: clinical correlation is essential. Growth of organisms from a superficial swab doesn't automatically mean treatment is needed. [1]
The Teaching Slide With Three Organisms
A wound swab growing WBC+, Enterococcus, Acinetobacter, and Stenotrophomonas — this is almost certainly colonization of a chronic wound, not an infection requiring antibiotics. Treat the patient, not the culture result. [1]
This is a deliberate clinical scenario testing whether you understand the significance of a positive AFB smear: [1]
- M/56, old TB, occasional dry cough
- CBP: Hb 11, WBC 6.8, ESR 30
- LFT/RFT: normal
- Sputum AFB smear/culture ×3 → 1 specimen: AFB smear +++, culture: M. tuberculosis
This patient has active TB — despite appearing relatively well. A sputum smear +++ means highly infectious (open TB). This requires:
- Notification
- Contact tracing
- Anti-TB treatment (RIPE regimen)
- Respiratory isolation
The lecture specifically highlights that blood cultures, pleural fluid cultures, and BAL cultures are often neglected but critical: [1]
- Blood cultures in pneumonia: positive in ~10-25% of bacteraemic pneumonia — identifies the organism when sputum is unavailable
- Pleural fluid: if parapneumonic effusion/empyema, MUST sample — inoculate into blood culture broth
- BAL: for immunocompromised patients or when sputum is non-diagnostic
Integration with Related Lectures
- MSU collection technique matters — contamination with periurethral flora causes false-positive cultures
- Pyuria + bacteriuria = true UTI; bacteriuria alone in catheterized patient = colonization
- Empirical therapy should be narrowed once C/ST results return
- TDM for aminoglycosides and vancomycin — lecture mentions these specifically
- CSF specimen handling directly feeds into this lecture's content
- PCR for HSV is the single most important test for viral encephalitis
- Blood cultures are part of the septic workup
- The 6-step approach applies to all febrile patients
- The Legionella case demonstrates travel-associated infection
- Travel history changes the differential and specimen requirements
- Most common MDR Gram-positive (contact): MRSA
- Most common MDR Gram-negative (contact): ESBL-producing Enterobacteriaceae (or Acinetobacter baumannii)
- Most common MDR yeast (contact): Candida auris
- Most common bacterial cause of infectious diarrhoea (contact, hospital): Clostridioides difficile
- Airborne: TB, measles, varicella (chickenpox)
- Blood-borne: HBV, HCV, HIV
Likely Exam Questions
- Which specimen type is the gold standard for urine culture? → SPA
- Which urinary antigen test detects only serogroup 1? → Legionella
- What threshold defines significant catheter tip culture? → ≥15 CFU on roll-plate
- In culture-negative endocarditis, which organisms should be tested by PCR? → Coxiella, Bartonella, Tropheryma, Brucella
- A sputum sample with >10 squamous epithelial cells per LPF indicates → oropharyngeal contamination (poor quality)
-
"A 65-year-old diabetic man on CAPD presents with fever and SOB. Recent travel to Guangzhou. CXR shows left lower lobe consolidation. List 5 microbiological investigations you would order."
- Blood culture ×2, sputum for Gram stain/C/ST/AFB, NPA for respiratory virus RT-PCR, urine for Legionella and pneumococcal antigen, PD fluid for cell count and culture
-
"A catheterized elderly patient has bacteriuria. When should you treat?"
- Only if symptomatic UTI — asymptomatic bacteriuria in catheterized patients should NOT be treated
-
"Name 3 organisms that cause culture-negative endocarditis and the test used to diagnose them."
- Coxiella burnetii (serology), Bartonella spp (serology/PCR), Tropheryma whipplei (PCR)
"A wound swab from a chronic bedsore grows MRSA and Candida. The patient is afebrile and the wound appears clean. Should you treat?" → No — this represents colonization. Superficial wound swabs have high contamination rates. Clinical correlation is essential. Treatment should be based on signs of infection (erythema, warmth, purulent discharge, systemic signs), not culture results alone.
High Yield Summary
1. Clinical approach: 6 steps — suspect → localize → collect specimens → empirical Rx → modify with results → monitor
2. GIGO: Specimen quality determines result quality. Three pillars: representative of disease, proper collection, proper transport.
3. Blood cultures: ≥2 sets, different sites, before antibiotics, aseptic technique, use resin-containing broth if on antibiotics. Culture-negative endocarditis → PCR/serology for Coxiella, Bartonella, Tropheryma.
4. CSF: CT first, non-reused bottles. Gram/ZN/wet mount/culture/cryptococcal antigen/PCR for HSV/VZV/enterovirus/CSF IgM for JE.
5. Sputum quality: >25 WBC, < 10 squamous epithelial cells/LPF. BAL is superior for immunocompromised.
6. Urine: MSU (standard), SPA (gold standard). Urine antigenuria for Legionella (SG1 only) and Pneumococcus.
7. Stool: Fresh for parasites, VTM for viral PCR, specify special organisms if suspected. C. difficile: toxin EIA/PCR.
8. Genital: Triple swabs (urethral/throat/anal) for suspected gonorrhoea. First-void urine PCR for GC/CT.
9. Dubious specimens: Bedsore swabs, long-term drain cultures, catheterized urine — treat the patient, not the culture.
10. Serology: 4× rise in IgG titre = confirmed recent infection. IgM = acute. Antigen detection: Cryptococcal Ag, Aspergillus galactomannan, 1,3-beta-D-glucan, Dengue NS1.
11. Legionella case: Environmental water source, travel history critical, urine antigen detects only SG1, PCR was diagnostic.
Active Recall - Diagnosis of Infections
[1] Lecture slides: GC 101. Diagnosis of infections.pdf; GC 101. Diagnosis of infections [Handouts].pdf [2] Past papers: 2024 Fourth Summative SAQ.pdf (Q12) [3] Senior notes: Maksim Medicine Notes.pdf (Infectious diseases, p186) [4] Senior notes: MBBS Final MB (Pediatrics) (Felix PY Lai).pdf (p508) [5] Lecture slides: GC 210. Urinary tract infection.pdf [6] Lecture slides: GC 106. Practical issues in antibiotic use.pdf [7] Lecture slides: GC 051. Fever and confusion_meningitis and encephalitis; suppurative brain infection.pdf [8] Lecture slides: GC 048. Fever.pdf [9] Lecture slides: GC 103. Fever after travelling.pdf
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