Laboratory tests - microbiology

Role

Microbiological culture (blood, urine, sputum, CSF, tissue, and other specimen types) remains the reference standard for identifying a causative organism and its antimicrobial susceptibility, directly enabling targeted (rather than empirical) antimicrobial therapy
Central to essentially all infectious diseases practice, though increasingly complemented (and in some contexts superseded) by faster molecular/PCR-based methods for specific organisms

Specimen quality and timing substantially affect yield - blood cultures collected before antimicrobial administration, adequate volume, and correct collection technique (minimising contamination) all improve diagnostic sensitivity, while culture after antibiotics have started can produce false-negative results
Culture turnaround time (typically 24-72 hours for identification, longer for susceptibility and for slow-growing organisms like mycobacteria) means empirical therapy is usually started before results return, then rationalised once results are available

Positive culture with growth of a recognised pathogen at a sterile site (blood, CSF, joint fluid) is generally treated as clinically significant; growth from a non-sterile site (sputum, wound swab, urine in some contexts) requires clinical correlation to distinguish true infection from colonisation
Antimicrobial susceptibility results should prompt de-escalation to the narrowest effective agent once available, a core antimicrobial stewardship principle

Culture-guided de-escalation from broad empirical therapy to a targeted narrow-spectrum agent once susceptibilities are known - reduces resistance selection pressure and adverse effects without compromising efficacy
Persistently positive cultures despite treatment (e.g. persistent bacteraemia) should prompt search for an undrained source or endovascular focus (endocarditis)

Blood culture contamination vs true bacteraemia, sterile vs non-sterile site interpretation, antimicrobial stewardship de-escalation, persistent bacteraemia as a red flag for endocarditis/undrained source

Collecting blood cultures before starting antibiotics, wherever feasible without meaningfully delaying treatment in a critically unwell patient, substantially improves diagnostic yield and should not be skipped even when empirical treatment feels urgent - a missed organism identification removes the ability to de-escalate or confirm the diagnosis later

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