Microbiology
High-yield MBBS Microbiology question bank — bacteriology, immunology, virology, mycology and parasitology, with laboratory diagnosis, at Ananthanarayan & Paniker / Jawetz depth.
12chapters144questions82High-Yield
Definition
Correct collection and transport of specimens is the first and most critical step in laboratory diagnosis — a poor specimen gives a worthless result.
General Principles
- Collect before starting antibiotics
- Take from the actual site of infection, avoiding commensal contamination
- Adequate quantity, sterile leak-proof container
- Label properly with patient details, site, date and time
- Transport promptly; use transport medium if delayed
Specimen-Specific Points
- Blood culture — during fever spike, before antibiotics, aseptic skin preparation
- Urine — clean-catch midstream, early morning; refrigerate if delayed
- Sputum — early morning, deep cough, not saliva
- CSF — never refrigerate (meningococcus dies); process immediately
- Swabs — Stuart’s or Amies transport medium; stool — Cary-Blair
Every step from bedside to bench affects the validity of the report. Specimen Key point Blood Before antibiotics CSF Never refrigerate Urine Midstream, refrigerate Applied
- ‘Garbage in, garbage out’ — poor specimens mislead treatment
- Reject improperly labelled or delayed specimens
🔑KEY POINTS TO REMEMBER- Collect before antibiotics, from the true site, in sterile containers.
- Transport promptly or use appropriate transport medium.
- CSF must never be refrigerated; urine should be midstream.
📚SOURCES: Textbook of Microbiology (Ananthanarayan & Paniker); Jawetz, Melnick & Adelberg’s Medical Microbiology; Textbook of Microbiology (Baveja).Definition
Antimicrobial susceptibility testing (AST) determines which antibiotics inhibit a given isolate, guiding rational therapy.
Methods
- Kirby-Bauer disc diffusion — commonest; zone of inhibition measured and compared with CLSI standards
- Broth/agar dilution — gives MIC (minimum inhibitory concentration)
- E-test — gradient strip, gives MIC directly
- Automated systems — VITEK, BacT/ALERT
Key Concepts
- MIC — lowest concentration inhibiting visible growth
- MBC — lowest concentration killing the organism
- Reported as sensitive, intermediate or resistant
- Standardised inoculum, medium (Mueller-Hinton agar) and incubation are essential
- Special tests: cefoxitin disc for MRSA, ESBL and carbapenemase detection
Standardisation at every step makes the zone diameter meaningful. Method Gives Disc diffusion S / I / R E-test MIC Dilution MIC / MBC Applied
- Guides de-escalation from empirical to targeted therapy
- Feeds hospital antibiograms and stewardship policy
🔑KEY POINTS TO REMEMBER- Kirby-Bauer disc diffusion is the standard method (Mueller-Hinton agar).
- MIC = lowest inhibitory concentration; MBC = lowest bactericidal.
- Results reported as sensitive, intermediate or resistant.
📚SOURCES: Textbook of Microbiology (Ananthanarayan & Paniker); Jawetz, Melnick & Adelberg’s Medical Microbiology; Textbook of Microbiology (Baveja).Definition
Hospital-acquired (nosocomial) infections are infections acquired in a healthcare setting, appearing 48 hours or more after admission.
Common Types & Organisms
- Catheter-associated urinary tract infection — commonest
- Surgical site infection, ventilator-associated pneumonia, bloodstream infection
- Organisms: E. coli, MRSA, Pseudomonas, Klebsiella (ESBL), Acinetobacter, C. difficile, Candida
- Typically multidrug-resistant
Risk Factors & Prevention
- Invasive devices, prolonged stay, ICU care, immunosuppression, broad-spectrum antibiotics
- Hand hygiene is the single most effective measure
- Aseptic technique, early device removal, isolation of resistant cases
- Surveillance, infection control committee, antibiotic stewardship
Devices and hospital flora combine to produce infection after admission. Infection Device UTI Urinary catheter Pneumonia Ventilator Bloodstream Central line Applied
- Bundles of care markedly reduce device-associated infection
- Increases cost, stay and mortality
🔑KEY POINTS TO REMEMBER- Nosocomial infection appears ≥48 hours after admission.
- Catheter-associated UTI is commonest; organisms are often multidrug-resistant.
- Hand hygiene is the single most effective preventive measure.
📚SOURCES: Textbook of Microbiology (Ananthanarayan & Paniker); Jawetz, Melnick & Adelberg’s Medical Microbiology; Textbook of Microbiology (Baveja).Definition
Blood culture is the definitive investigation for bacteraemia and septicaemia, and remains the gold standard for bloodstream infection.
Technique
- Collect before antibiotics, during a fever spike or rigor
- Strict asepsis — skin disinfection with alcohol and chlorhexidine/iodine
- Two to three sets from different sites within 24 hours
- Adequate volume (adults 8–10 mL per bottle) — volume is the key determinant of yield
- Blood-to-broth ratio 1:10; aerobic and anaerobic bottles
Processing & Interpretation
- Automated systems (BACTEC, BacT/ALERT) detect growth continuously
- Positive bottle → Gram stain, subculture, identification, susceptibility testing
- Single positive for skin commensal (CoNS, diphtheroids) usually means contamination
- Same organism in multiple sets indicates true infection
Multiple adequately filled sets distinguish true infection from contamination. Factor Requirement Timing Before antibiotics Sets 2–3 Ratio 1:10 blood to broth Applied
- Essential in enteric fever (positive in week 1) and endocarditis
- Take three sets over 24 hours in suspected endocarditis
🔑KEY POINTS TO REMEMBER- Blood culture is the gold standard for bloodstream infection.
- Collect 2–3 sets aseptically before antibiotics, 1:10 blood-to-broth ratio.
- A single positive skin commensal usually indicates contamination.
📚SOURCES: Textbook of Microbiology (Ananthanarayan & Paniker); Jawetz, Melnick & Adelberg’s Medical Microbiology; Textbook of Microbiology (Baveja).Definition
Biomedical waste management is the safe segregation, handling, treatment and disposal of waste generated during healthcare, governed by statutory rules.
Colour-Coded Segregation (India)
- Yellow — human/animal anatomical waste, soiled waste, expired medicines → incineration
- Red — contaminated recyclable plastics (tubing, syringes without needles, catheters) → autoclave then recycle
- White (translucent puncture-proof) — sharps, needles → autoclave/disinfect then shred
- Blue — broken/discarded glass, metallic implants → disinfect then recycle
Principles
- Segregate at the point of generation — the most important step
- Never recap needles; use puncture-proof containers
- Labelled bags, barcoding, trained staff, personal protective equipment
- Treatment: incineration, autoclaving, microwaving, chemical disinfection, deep burial
Segregation at the point of generation determines the whole disposal chain. Colour Waste Treatment Yellow Anatomical Incineration Red Plastics Autoclave, recycle White Sharps Shred Applied
- Improper disposal spreads hepatitis B, C and HIV
- Governed by Biomedical Waste Management Rules
🔑KEY POINTS TO REMEMBER- Segregation at source into colour-coded bins is the key step.
- Yellow = anatomical (incinerate); red = plastics; white = sharps; blue = glass.
- Improper disposal transmits hepatitis B, C and HIV.
📚SOURCES: Textbook of Microbiology (Ananthanarayan & Paniker); Jawetz, Melnick & Adelberg’s Medical Microbiology; Textbook of Microbiology (Baveja).Definition
Antimicrobial resistance (AMR) is the ability of microorganisms to withstand antimicrobial agents that previously killed or inhibited them.
Mechanisms
- Enzymatic inactivation — β-lactamase, ESBL, carbapenemase
- Altered target — PBP2a in MRSA, altered ribosome or gyrase
- Reduced permeability / efflux pumps
- Bypass pathway — alternative metabolic route
- Genetic basis: mutation or transfer (conjugation, transduction, transformation)
Drivers & Control
- Irrational prescribing, incomplete courses, over-the-counter sale, agricultural use
- Antibiotic stewardship, culture-guided therapy, full courses
- Infection control, hand hygiene, surveillance, vaccination
- ‘Superbugs’: MRSA, VRE, ESBL, MDR/XDR tuberculosis
Selection pressure plus gene transfer spreads resistance rapidly. Mechanism Example Enzyme β-lactamase Altered target MRSA Efflux Tetracycline Applied
- AMR is declared a global health emergency by the WHO
- Conjugation is the main route of resistance spread
🔑KEY POINTS TO REMEMBER- Mechanisms: enzymes, altered targets, efflux, bypass pathways.
- Driven by irrational antibiotic use in humans and agriculture.
- Controlled by stewardship, infection control and surveillance.
📚SOURCES: Textbook of Microbiology (Ananthanarayan & Paniker); Jawetz, Melnick & Adelberg’s Medical Microbiology; Textbook of Microbiology (Baveja).Definition
Hand hygiene is the single most effective measure to prevent healthcare-associated infection; standard precautions apply to all patients regardless of diagnosis.
WHO ‘Five Moments’ for Hand Hygiene
- Before touching a patient
- Before a clean/aseptic procedure
- After body-fluid exposure risk
- After touching a patient
- After touching patient surroundings
Methods & Standard Precautions
- Alcohol-based hand rub — 20–30 seconds; preferred when hands are not soiled
- Soap and water — 40–60 seconds; required for visibly soiled hands and C. difficile (spores resist alcohol)
- Standard precautions: gloves, mask, gown, eye protection as needed; safe sharps handling; safe waste disposal; respiratory hygiene
- Treat all blood and body fluids as potentially infectious
Consistent hand hygiene breaks the commonest route of cross-infection. Situation Method Hands not soiled Alcohol rub Visibly soiled Soap and water C. difficile Soap and water Applied
- Compliance monitoring improves adherence
- Cheapest and most effective infection-control intervention
🔑KEY POINTS TO REMEMBER- Hand hygiene is the most effective infection-control measure.
- WHO five moments guide when to perform it.
- Alcohol rub usually; soap and water for soiled hands and C. difficile.
📚SOURCES: Textbook of Microbiology (Ananthanarayan & Paniker); Jawetz, Melnick & Adelberg’s Medical Microbiology; Textbook of Microbiology (Baveja).Definition
Automated and molecular methods provide rapid, sensitive and standardised microbiological diagnosis, increasingly replacing conventional culture.
Automated Systems
- BACTEC / BacT/ALERT — continuous-monitoring blood culture
- VITEK, MicroScan — automated identification and MIC
- MALDI-TOF mass spectrometry — identification within minutes by protein profile
- MGIT — rapid liquid culture for mycobacteria
Molecular Methods
- PCR / real-time PCR — rapid, highly sensitive; detects non-cultivable organisms
- CBNAAT (GeneXpert) — tuberculosis + rifampicin resistance in ~2 hours
- Line probe assay — drug-resistant tuberculosis
- Sequencing, microarrays, viral load quantification
- Limitations: cost, infrastructure, cannot give full susceptibility profile
Rapid results allow targeted therapy far sooner than conventional culture. Method Advantage MALDI-TOF Identification in minutes CBNAAT TB + rifampicin resistance Real-time PCR Viral load Applied
- CBNAAT has transformed tuberculosis diagnosis under the national programme
- Molecular tests may detect dead organisms — interpret with clinical context
🔑KEY POINTS TO REMEMBER- Automated systems: BACTEC, VITEK, MALDI-TOF for rapid identification.
- Molecular: PCR, CBNAAT (GeneXpert) for TB with rifampicin resistance.
- Rapid and sensitive but costly; cannot fully replace culture.
📚SOURCES: Textbook of Microbiology (Ananthanarayan & Paniker); Jawetz, Melnick & Adelberg’s Medical Microbiology; Textbook of Microbiology (Baveja).Definition
Antibiotic stewardship is a coordinated programme promoting the appropriate use of antimicrobials to improve outcomes and limit resistance.
Core Strategies
- Right drug, right dose, right route, right duration
- De-escalation — narrow the spectrum once culture results are available
- Prospective audit and feedback; formulary restriction and pre-authorisation of reserve drugs
- Local antibiogram-based empirical guidelines
- Intravenous-to-oral switch; avoid unnecessary prophylaxis
Implementation & Benefits
- Multidisciplinary team: physician, microbiologist, clinical pharmacist, nurse, infection control
- WHO AWaRe classification — Access, Watch, Reserve
- Benefits: less resistance, fewer adverse effects and C. difficile infection, lower cost
- Requires surveillance data and continuous education
Regular review converts broad empirical cover into targeted therapy. Element Action De-escalation Narrow spectrum Duration Shortest effective AWaRe Reserve last-line drugs Applied
- Reduces multidrug resistance and C. difficile colitis
- Every hospital should have a stewardship programme
🔑KEY POINTS TO REMEMBER- Stewardship ensures right drug, dose, route and duration.
- De-escalation and 48–72 hour review are central practices.
- WHO AWaRe classification protects reserve antibiotics.
📚SOURCES: Textbook of Microbiology (Ananthanarayan & Paniker); Jawetz, Melnick & Adelberg’s Medical Microbiology; Textbook of Microbiology (Baveja).Definition
A needle-stick injury is percutaneous exposure to blood or body fluids, carrying risk of hepatitis B, hepatitis C and HIV transmission.
Immediate Management
- Wash with soap and running water; do not squeeze, scrub or apply caustics
- Report immediately and document the incident
- Test the source and the exposed person for HBsAg, anti-HCV, HIV
- Assess the risk (type of needle, depth, fluid, source status)
Prophylaxis by Virus
- HIV — risk ~0.3%; start antiretroviral PEP within 2 hours (ideally), continue 28 days
- Hepatitis B — risk highest (up to 30%); if unvaccinated give hepatitis B immunoglobulin + vaccine
- Hepatitis C — risk ~3%; no prophylaxis; monitor and treat early infection
- Follow-up testing at 6 weeks, 3 and 6 months
Speed matters most — prophylaxis works best within the first hours. Virus Risk Prophylaxis Hepatitis B Highest HBIG + vaccine Hepatitis C ~3% None HIV ~0.3% ART 28 days Applied
- Prevention: never recap needles, use puncture-proof containers
- All healthcare workers should be hepatitis B vaccinated
🔑KEY POINTS TO REMEMBER- Wash with soap and water, report, and test source immediately.
- Hepatitis B carries the highest risk — give HBIG plus vaccine.
- HIV PEP: start within hours, continue 28 days; no PEP for hepatitis C.
📚SOURCES: Textbook of Microbiology (Ananthanarayan & Paniker); Jawetz, Melnick & Adelberg’s Medical Microbiology; Textbook of Microbiology (Baveja).Definition
Catheter-associated urinary tract infection (CAUTI) is infection arising in a catheterised patient — the commonest hospital-acquired infection.
Pathogenesis & Organisms
- Organisms ascend extraluminally (along the catheter surface) or intraluminally
- Biofilm forms on the catheter → protects organisms from antibiotics
- Risk rises about 5% per day of catheterisation
- Organisms: E. coli, Klebsiella, Pseudomonas, Proteus, Enterococcus, Candida
Diagnosis & Prevention
- Fever, suprapubic or flank pain; symptoms often subtle in the elderly
- Significant growth from a freshly placed catheter or midstream sample
- Asymptomatic bacteriuria should not be treated (except pregnancy or before urological surgery)
- Prevention: avoid unnecessary catheterisation, aseptic insertion, closed drainage system, bag below bladder level, early removal
Biofilm on the catheter makes eradication impossible while it stays in. Measure Effect Early removal Most effective Closed drainage ↓ Entry of organisms Antibiotic prophylaxis Not recommended Applied
- Removing or changing the catheter is essential for cure
- Do not send routine urine cultures from asymptomatic catheterised patients
🔑KEY POINTS TO REMEMBER- CAUTI is the commonest nosocomial infection; biofilm protects organisms.
- Risk increases about 5% per catheter day.
- Prevent by avoiding catheters, closed drainage and early removal.
📚SOURCES: Textbook of Microbiology (Ananthanarayan & Paniker); Jawetz, Melnick & Adelberg’s Medical Microbiology; Textbook of Microbiology (Baveja).Definition
Serological diagnosis detects antibodies or antigens in serum to identify infection, particularly when the organism is difficult to culture.
Principles
- IgM → recent or acute infection
- IgG → past infection or immunity
- Fourfold rise in titre between paired acute and convalescent sera confirms recent infection
- Antigen detection useful in the window period (e.g. p24, NS1, HBsAg)
Common Tests & Limitations
- Agglutination — Widal, Weil-Felix; precipitation — VDRL
- ELISA — HIV, dengue, hepatitis; immunofluorescence; rapid card tests
- Limitations: window period, false positives, cross-reactions, persisting antibody after cure
- Poor in immunocompromised patients (impaired antibody response)
Antibody appears only after a lag, so timing decides the test chosen. Marker Interpretation IgM Recent infection IgG Past / immunity Fourfold rise Confirms recent Applied
- Essential for HIV, syphilis, hepatitis, dengue and enteric fever
- Interpret alongside clinical picture and stage of illness
🔑KEY POINTS TO REMEMBER- IgM indicates recent infection; IgG past infection or immunity.
- A fourfold rise in paired sera confirms recent infection.
- Window period and cross-reactions limit serology.
📚SOURCES: Textbook of Microbiology (Ananthanarayan & Paniker); Jawetz, Melnick & Adelberg’s Medical Microbiology; Textbook of Microbiology (Baveja).