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Specimen Collection – General Guidance

Bacteriology Specimens

 The objective of laboratory testing for bacterial and fungal infection is to isolate viable organisms therefore proper specimen collection and prompt transport arrangements are required.


Specimens should be collected from patients with care to minimize the possibility of introducing extraneous or contaminating microorganisms. This precaution is needed to distinguish commensal or ‘normal flora’ from organisms causing infection. The presence of commensal flora at site of infection will mask the true aetiological agent making isolation more difficult.

The list below gives common sites of contamination from specimen sites which are adjacent to body sites having more resident normal flora than others.

Site of Infection  Source of contamination
Middle Ear External ear canal
Nasal Sinus Nasopharynx
Lower respiratory tract Oropharynx
Endometrium Vagina
Superficial wounds/Subcutaneous infection Skin and mucous membranes
Abdominal fistulae Gastrointestinal tract
Bladder Urethra and external genitalia

To help us to optimise organism recovery


Details of specimen collection procedures for specific sample types/tests can be found on the test pages on this website – click here to search.


Virology & Molecular (PCR) Specimens

Please read this guidance on Biotin Interference prior to taking samples for serological testing – Biotin Alert (Potential Assay Interference)

Requirements for specimen containers for collection of blood for Serology and Molecular (PCR) testing can be found on the test pages on this website – click here to search.

Please click here for a poster that gives guidance on blood collection and order of draw for collection tubes:




Once collected, blood samples must be transported to Microbiology ASAP.

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