Bedside interpretation: ECG, CXR, CT and labs

Cultures and microbiology interpretation

Reviewed Nov 2026·5 references
New· views rounded down, updated weekly

Blood culture technique, contaminants vs true pathogens, respiratory and urine samples, rapid diagnostics and reading an antibiogram.

Definition
Microbiology results are only as good as the sample: take cultures before antibiotics when this causes no meaningful delay, use correct volume and technique, and interpret the organism in the clinical context.

At the bedside

Timed steps
  1. 1

    Blood cultures

    Before antibiotics

    At least 2 sets (aerobic + anaerobic bottles) from separate venepunctures, 20 mL per set in adults; before antibiotics if no significant delay.

  2. 2

    Suspected line infection

    Paired cultures from the catheter and a peripheral vein; catheter culture positive ≥ 2 h earlier than peripheral (differential time to positivity) suggests catheter-related bacteraemia.

  3. 3

    Contaminants vs pathogens

    Coagulase-negative staphylococci, Corynebacterium, Bacillus (non-anthracis) or Cutibacterium in a single set usually = contamination; S. aureus, Gram-negative bacilli, Candida or S. pneumoniae in any bottle = true bacteraemia.

  4. 4

    Respiratory samples

    Endotracheal aspirate (semi-quantitative) or BAL; Candida in respiratory samples is almost always colonisation.

  5. 5

    Urine

    Culture only with symptoms or sepsis without another source; from the sampling port of a freshly replaced catheter if in situ > 2 weeks.

  6. 6

    Rapid diagnostics

    Rapid identification/resistance tests on positive blood cultures (e.g. multiplex PCR, carbapenemase detection) speed targeted therapy; interpret with stewardship input.

  7. 7

    Antibiogram

    Read MICs against breakpoints (S, I/SDD, R); use the local unit antibiogram for empirical choices and the isolate report for targeted therapy.

Positive blood culture: first response

OrganismUsual meaningAction
S. aureusTrue bacteraemia alwaysTreat; repeat cultures; echo; ID consult; source control
Candida spp.True candidaemiaEchinocandin; remove CVC; ophthalmology review
Gram-negative bacilliTrue bacteraemiaReview empirical cover against local resistance; source control
CoNS in 1 of 2 setsUsually contaminantRepeat cultures if prosthetic material or line infection suspected
Red flag · call your senior now
S. aureus or Candida in a blood culture is never a contaminant - start appropriate therapy and look for a source.
Pitfall
A single blood culture set - lower sensitivity and impossible to judge contaminants.
Pitfall
Treating Candida in sputum or asymptomatic bacteriuria.
Pearl
Underfilled bottles are the commonest reason for false-negative blood cultures - blood volume matters more than timing with fever spikes.

References

  1. 1

    Miller JM, Binnicker MJ, Campbell S, et al. Guide to utilization of the microbiology laboratory for diagnosis of infectious diseases: 2024 update by the IDSA and ASM. Clin Infect Dis 2024.

  2. 2

    Prescott HC, Antonelli M, Alhazzani W, et al. Surviving Sepsis Campaign: international guidelines for management of sepsis and septic shock 2026. Intensive Care Med. 2026;52(5):863-936. Co-published in Crit Care Med. 2026 (doi:10.1097/CCM.0000000000007075)

  3. 3

    Patel PK, Advani SD, Kofman AD, et al. Strategies to prevent catheter-associated urinary tract infections in acute-care hospitals: 2022 update. Infect Control Hosp Epidemiol 2023;44:1209-31.

  4. 4

    Indian Council of Medical Research. Annual Report: Antimicrobial Resistance Research and Surveillance Network, January 2023-December 2023. New Delhi: ICMR; 2024.

  5. 5

    Farkas J. The Internet Book of Critical Care (IBCC). EMCrit Project; continuously updated.

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