Sterility, Contamination and Specimen Interpretation

Isolation of an organism from a specimen does not automatically mean that organism is causing disease. Correct interpretation requires knowing which body site the specimen came from and what growth is expected there normally.

• Sites with no resident microbiota in health: blood, CSF, deep tissues, joint fluid, pleural fluid, peritoneal fluid, and (traditionally) the lower respiratory tract and bladder urine.
• Any organism isolated from a properly collected specimen from one of these sites is presumed clinically significant until proven otherwise, since there is no normal flora to explain its presence.

• Sites with an established resident microbiota: skin, mouth, upper respiratory tract, gastrointestinal tract, distal urethra, and vagina.
• Growth from these sites requires careful interpretation, since isolation of an organism may simply reflect normal colonisation rather than infection.

• Introduction of organisms into a specimen during collection or handling, not present in the patient at the sampled site, most commonly skin flora entering a blood culture during venepuncture, or environmental organisms introduced during specimen processing.
• Suggested by growth of typical skin organisms (Staphylococcus epidermidis, diphtheroids, Cutibacterium acnes) in only one of several blood culture bottles/sets, by growth after prolonged incubation, or by growth that is inconsistent with the clinical picture.

• Presence and multiplication of an organism at a nonsterile site without invasion or disease, an expected and often normal finding.
• A positive culture from a nonsterile site (sputum, skin swab, urine with low colony counts) may represent colonisation rather than the cause of the patient's current illness.

• Growth of an organism that is genuinely responsible for the patient's clinical presentation, supported by isolation from a sterile site, isolation in high quantity or pure/predominant growth from a nonsterile site consistent with the clinical picture, or isolation of an organism not normally found at that site at all.
• Correlating the microbiology result with the clinical presentation (fever, localising symptoms, inflammatory markers, imaging) is essential; the organism and the illness must fit together.

• Growth of multiple different organism types from a single specimen, typical of nonsterile sites and of specimens contaminated by normal flora during collection (for example, a poorly collected sputum sample heavily contaminated by oral flora).
• A report of "mixed flora" or "mixed growth consistent with contamination" generally indicates the specimen is not interpretable as showing a single significant pathogen, and, where clinically indicated, prompts repeat sampling with more careful technique.

• The single governing principle of specimen interpretation: a laboratory result must always be interpreted in the context of the patient's clinical presentation, not read in isolation.
• The same organism, at the same site, in the same quantity, can represent either harmless colonisation or true infection depending entirely on whether the patient has a clinical picture consistent with infection at that site.
• This principle is the reason microbiology results are reported with an interpretive comment by laboratory staff in many cases, and why clinicians are expected to actively question an apparently positive result that does not fit the clinical picture, rather than treating every positive culture automatically.