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HSL Microbiology specimens

See the main Tests section for general information on ordering tests, and specimen collection, packaging and transport.



The specimen must be labelled with the patient details as on the request form. Please ensure that electronically created barcodes are placed down the length of the specimen container and do not obscure any pre-existing barcodes.

Unlabelled samples or samples with insufficient unique identifiers cannot be processed and will be discarded.


Clinical details

Clinical details are essential for to ensure that specimens are processed appropriately. For example:

  • Include travel history if submitting an enteric specimen to ensure that specific agar plates necessary for detecting travel-related organisms such as Vibrio sp. are set up.
  • Specify whether prosthetic material is present when submitting joint specimens to ensure that cultures have the prolonged incubation and enrichment conditions required to identify PJI- related organisms such as Cutibacterium acnes.



All samples must be collected in the specified sterile containers.


Factors that significantly affect the performance of the examination or interpretation of results

General factors

  • Specimens must be sent in sterile containers.
  • Always use aseptic technique for collection of specimens.
  • Specimens can easily be contaminated with surface and mucosal flora, so the specimen should be collected using methods to minimise contamination. For example, take mid-stream clean catch urine samples to minimize contamination from urethral flora.
  • False-negative results may occur in patients taking antibiotics.
  • The time that a specimen is collected can impact on the diagnostic yield e.g. early morning urine (EMU) sample for TB investigation.
  • Delays in transport and/or incorrectly stored samples may lead to loss of viability of some organisms and/or overgrowth of other flora.
  • Always send separate samples if requesting multiple tests from different departments. Failure to adhere to this may result in the testing being missed or delayed.
  • Storage conditions of the samples prior to testing are important.

Blood cultures

  • Hospital procedures for optimal blood culture technique should be followed to minimise contamination with skin flora.
  • Incorrectly collected blood cultures (under/overfilled) may affect organism growth and recovery.
  • Never refrigerate blood culture samples.
  • Blood cultures should be delivered to the laboratory promptly to ensure rapid incubation for maximal diagnostic yield.
  • The time and date of blood culture collection should be clearly stated on the blood culture bottle labels.

Urine specimens

  • The optimal non-invasive urine specimen is a mid-stream clean catch urine.
  • Urine for culture should be sent in a container with boric acid preservative to preserve specimen quality and minimise overgrowth of contaminating flora.
  • Urine culture specimens should be stored in a fridge prior to transportation to reduce the rate of multiplication of microorganisms.

Therapeutic drug monitoring (TDM)

  • Clinical details should include the name of the antimicrobial given, dose, date and time of dose, and date and time of sample.
  • Avoid the use of gel tubes for TDM as they may impact analysis.

Serology testing

  • Haemolysed, lipaemic and icteric blood samples are not suitable for serological investigations.

Molecular testing

  • Swabs with additives (such as charcoal or gel) cannot be used for PCR tests. A specific NAAT swab or dry swab should be used.

Dermatology specimens

  • Do not refrigerate Dermapak specimens (nail, skin, hair) as this will lead to loss in viability of Dermatophytes.

Sterile fluid microscopy analysis

  • Sterile fluid is prone to clotting which makes accurate cell count impossible. If sending sterile fluid for the investigation of infection please send an additional aliquot of fluid in an EDTA vial for an accurate cell count.

Swabs for Neisseria gonorrhoeae culture

  • As this organism dies rapidly, these should be transported to the laboratory as soon as possible after collection to ensure maximal yield.

Pre-inoculated culture plates

  • Where possible pre-inoculated plates for Neisseria gonorrhoeae culture should be pre-incubated for a minimum of 18 hours in appropriate CO2 gas packs prior to referral to the laboratory.
  • All other pre-inoculated plates should be transported to the laboratory urgently to prevent plate dehydration, which will reduce recovery of organisms.