This information is to assist staff in institutions or treating medical officers how to manage specimen collection in the event of an
outbreak of gastroenteritis.


Advice can be sought from the laboratory or Public Health Unit (PHU) about the collection and transportation of specimens for testing, along with how many samples to collect and what tests should be requested.

Specimen collection for bacterial, viral and parasitic pathogen detection should begin immediately an outbreak of gastroenteritis
is suspected. This is important as the aetiology (microbiological cause) can guide the response.

Specimen collection

In outbreaks, the PHU may organise for specimens to be collected and sent to a particular laboratory. In other circumstances, treating doctors may collect and send specimens to their normal laboratory.

The following guidance applies to collecting specimens during outbreaks:
  • Faecal specimens are preferable for detecting viruses and other causes of gastroenteritis. Vomit samples should only be collected after consultation with the laboratory or PHU. (Collection and storage of vomit specimens are the same as those for faecal specimens).
  • Specimens should be collected in an appropriate sterile laboratory container. If one is not available, then cases should be advised to use a clean disposable container. Collect approximately 10–20 ml of faeces in a jar.
  • To collect faecal specimens:
    • Place a disposable container inside the toilet before use by the patient.
    • Use a disposable spoon or spatula to collect faeces from linen, incontinence pads or bedpans.
  • It is preferable that specimens are collected while the person has diarrhoea, as maximal virus shedding usually occurs 24–72 hours after exposure.
  • Where possible, give the laboratory prior notice if an increased number of specimens will be submitted from cases of gastroenteritis that are part of an outbreak.
  • Collect specimens from at least six ill people or consult with the PHU and laboratory as to the number of samples required.
  • Staff collecting specimens should wear personal protective equipment where possible, particularly gloves and possibly masks and gowns. It is important that staff wash their hands thoroughly after collecting specimens.
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Storage and transportation

  • Store specimens in the refrigerator at 4˚C. If a fridge is not available a chilled ice chest can be used. Do not use a food refrigerator for storing specimens.
  • Specimens should be transported to the laboratory as soon as possible. During transportation specimens should remain bagged and sealed and kept on ice or in a refrigerated container.
  • Ensure that each specimen is accompanied by a specimen request form. It should be noted on the form that the specimens are from patients in an outbreak. Each request form and specimen should be marked URGENT and clearly labelled with all patient details, including a brief description of the outbreak in the clinical notes field and a reference number for the outbreak.

Specimen testing

In general, all specimens should undergo standard bacterial testing and testing for viral pathogens, particularly norovirus. The following tests should be requested for faecal specimens:
  • microscopy, culture and sensitivity (MC&S)
  • viruses, particularly norovirus
  • parasites.
If the outbreak has occurred in a setting where norovirus outbreaks are common, it may be appropriate to test specimens only for norovirus in the first instance.