01Purpose and principlesWhat the assessment is for and the core concepts behind it.
Microbiology is a diagnostic intervention with pre-analytical, analytical and interpretive stages. The best test collects an adequate sample from the involved compartment before treatment, using technique that prevents contamination and preserves organism viability. Poor sampling creates two harms: missed pathogens and false diagnoses that prolong unnecessary antibiotics.
Blood cultures are particularly dependent on blood volume and asepsis. Separate peripheral collections help distinguish continuous bacteraemia from contamination; device and peripheral paired samples may answer a catheter question when planned correctly. A single bottle growing common skin flora has a different meaning from repeated concordant growth in a patient with prosthetic material.
Laboratory dialogue is essential for endocarditis, mycobacteria, fungi, parasites, molecular testing and tissue. Some specimens need special containers, rapid transport or separate allocation for histology and culture. Results are probabilities integrated with syndrome and treatment exposure, not autonomous instructions to prescribe.
Key points
- Define the question before collecting: bloodstream infection, source pathogen, colonisation, resistance or treatment failure require different specimens.
- National adult default: obtain at least two blood-culture sets—two aerobic and two anaerobic bottles—using aseptic peripheral venepuncture, place 8–10 mL in each bottle and send them immediately so incubation can begin within 4 hours; verify the current local bottle system.
- Obtain cultures before antimicrobials when this causes no harmful delay, and record prior doses because partial treatment changes sensitivity and interpretation.
- Sample the actual site whenever safe: deep tissue or aspirate is usually more informative than a superficial swab from colonised skin.
- Label anatomical site, time and clinical context accurately, transport promptly and discuss unusual, hazardous or time-dependent organisms with microbiology before collection.
- Interpret results using organism identity, number and timing of positive bottles, source concordance, devices and host phenotype; not every isolate is a pathogen and not every negative sample excludes infection.
02Indications, selection and cautionsWhen it is useful, when urgency changes and important limitations.
A correctly obtained specimen from the infected compartment before antimicrobials offers the best chance of organism identification and susceptibility-guided narrowing.
Single-set growth of typical skin flora with poor collection technique and no compatible device or syndrome suggests contamination, but host and repeat cultures decide.
Continued growth of a significant organism despite treatment suggests endovascular infection, uncontrolled source, ineffective exposure or retained infected material and requires urgent review.
Suspected tuberculosis, viral haemorrhagic fever, brucellosis or other laboratory hazard requires advance communication so collection, packaging and processing protect staff.
03Method and interpretationA systematic approach to the test and its findings.
Read from the initial assessment onwards. Tests may run in parallel in urgent care; first-line, preferred, confirmatory, definitive and gold-standard labels appear only when the chapter explicitly states them.
- 01
Peripheral blood-culture setsFirst step - Why
- Detect bacteraemia and provide identification and susceptibility results.
- Interpretation and limitations
- For the national adult default, collect at least two sets from aseptic peripheral venepunctures: two aerobic and two anaerobic bottles, each filled with 8–10 mL, sent immediately for incubation within 4 hours. Use syndrome-specific microbiology instructions for suspected endocarditis, line-associated infection, candidaemia, paediatrics and organism-specific clearance cultures.
- 02
Urine microscopy and culture - Why
- Confirm symptomatic urinary infection and guide therapy when culture is indicated.
- Interpretation and limitations
- Midstream clean-catch technique reduces contamination. Pyuria or bacteriuria without compatible symptoms may represent asymptomatic bacteriuria and usually does not prove the cause of illness.
- 03
Respiratory sampling - Why
- Investigate lower-respiratory pathogens using sputum, induced samples, aspirates or lavage according to severity and host.
- Interpretation and limitations
- Quality microscopy may reveal salivary contamination. Upper-airway PCR can diagnose viruses but does not necessarily establish the cause of lower-airway infiltrates.
- 04
Deep tissue, aspirate or sterile fluid - Why
- Identify organisms within abscess, joint, pleura, cerebrospinal fluid or operative tissue.
- Interpretation and limitations
- Send adequate material in the correct sterile container and allocate tissue before formalin. Cell count, microscopy, culture and molecular tests answer different questions.
- 05
Molecular and antigen tests - Why
- Detect pathogen nucleic acid or antigen when culture is slow, hazardous or affected by treatment.
- Interpretation and limitations
- A detected target may represent non-viable organism, colonisation or prolonged shedding. Interpret cycle and platform limitations with microbiology rather than equating detection with active disease.
04Clinical next stepsHow the result changes management or prompts escalation.
01Suspected bloodstream infectionCollect high-quality cultures without delaying careFirst stepSystemic infection, endovascular features or severe focal infection makes bacteraemia clinically plausible.+
- 1Prepare the correct bottles, perform hand hygiene and skin antisepsis, then collect the adult default of at least two sets from separate peripheral venepunctures, filling every bottle with 8–10 mL and labelling exact times and sites; follow a syndrome-specific protocol when indicated.
- 2Obtain source samples in parallel, start indicated antimicrobials within the syndrome-specific timeframe and record every pretreatment dose.
- 3Review preliminary Gram stain immediately, adjust treatment only in clinical context and repeat cultures when organism or focus requires proof of clearance.
02Focal infectionSample the infected compartmentA collection, wound, joint, device, respiratory or urinary syndrome requires organism identification.+
- 1Choose the deepest safe representative specimen and arrange imaging or procedural help when aspiration or tissue is preferable to a superficial swab.
- 2Agree requested microscopy, culture, susceptibility and molecular tests with the laboratory, including special containers and transport.
- 3Correlate results with cell response, imaging and prior treatment; disregard colonising growth only after a documented clinical review.
03Unexpected resultSeparate pathogen from contaminantCulture or molecular result conflicts with the patient's phenotype or appears to show skin or environmental flora.+
- 1Verify patient, site, collection technique, bottle pattern, time to positivity and whether the same organism appears in another specimen.
- 2Re-examine for prosthetic material, intravascular devices and immune suppression, repeat cultures before new antibiotics when safe and contact microbiology.
- 3Document the interpretation and action so a contaminant is not repeatedly treated and a genuine device or endovascular infection is not dismissed.
05Risks, monitoring and follow-upComplications, safety checks and further assessment.
- Track every submitted specimen, collection time, prior antimicrobial exposure and pending result with a named clinician responsible for review.
- Act promptly on positive blood-culture Gram stain, unexpected resistance, critical cerebrospinal-fluid findings and public-health-significant organisms.
- Audit contamination rate, bottle fill and rejected specimens because sampling quality is a patient-safety and stewardship outcome.
- Review final negative results in context; decide explicitly whether treatment can stop, whether sampling was adequate or whether another compartment requires investigation.
- Repeat cultures only for a clinical purpose such as persistent fever, endovascular infection, selected pathogens or documented clearance rather than as a daily ritual.
06Special situationsVariants, exceptions and circumstances that change the usual approach.
Volume matters most
For adult blood cultures, adequate blood volume generally improves sensitivity more than drawing from a fever spike or extending collection over many hours.
Deep beats superficial
Aspirated pus or operative tissue better represents invasive organisms than a wound-surface swab that collects colonising flora.
Formalin closes a door
Tissue placed entirely in fixative cannot undergo routine culture, so microbiology and histology allocations must be planned before biopsy.
Negative is conditional
Prior antibiotics, small sample volume, intermittent bacteraemia, fastidious organisms and the wrong anatomical compartment all reduce sensitivity.
07Common pitfallsFrequent interpretation and management errors.
- 01
Drawing all blood cultures through an existing line without a specific catheter question.
- 02
Underfilling bottles and then treating a negative result as exclusion.
- 03
Sending a superficial swab when deep tissue or aspirate is safely obtainable.
- 04
Failing to tell the laboratory about a suspected hazardous or fastidious organism.
- 05
Treating colonisation or contamination without correlating syndrome and repeated results.