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Enteric samples (faeces)

The isolation and correct identification of faecal pathogens is an important aid in the diagnosis and management of infected patients. A wide range of pathogens is capable of producing diarrhoea.

Specimen requirements

Routine culture requires 1-2 g of specimen.

Specimens should be tested as soon as possible after onset of symptoms, as a number of pathogens such as Shigella species may not survive the pH changes that occur in faeces specimens which are not promptly delivered to the laboratory, even if refrigerated.

Only one sample per patient taken per day will be processed (if multiple specimens dated the same day are received the specimens will be pooled).

All stool specimens received from GPs are processed if they are not 'formed stool' while the 'three day rule' is used as selective criteria for the culture of non-formed specimens from hospital inpatients.

Focused testing

Stool appearance is checked prior to processing of the sample to ensure that formed stools are NOT processed unless the sample is to check for clearance of a previous pathogen, part of an outbreak or the patient has eosinophilia. Requests for parasites are decided on a case-by-case basis. For more information see the Oxfordshire Clinical Commisioning Group guidance for the management of acute diarrhoea in primary care.

Guidance for the management of acute diarrhoea in primary care -

Laboratory turnaround time

Please see Turnaround times

Laboratory method

Faeces samples are tested in the laboratory using one of four methods.

  1. All samples are tested using the molecular platform, the BD MAX™, for the presence of Salmonella spp, Campylobacter spp, Shigella spp, Enteroinvasive E. coli (EIEC) and Shiga toxin producing E. coli (STEC). Any pathogens detected are confirmed using culture. Samples are also inoculated in parallel into a selective broth and later cultured on to chromogenic media for isolation of any Salmonella spp. in very low numbers.
  2. Samples that are not suitable for processing on the BD MAX (e.g. those with a previous high risk pathogen (S.typhi, S.paratyphi, Shigella sp, E.coli O157) are processed by inoculating a sample of the faecal material into a selective broth and then onto various selective plate media. The media used is highly selective and is specific for the target pathogenic bacteria that cause enteric infection.
    Such bacteria include:
    E. coli O157
    Samples are also processed for the examination of parasites either by ELISA in the case of Cryptosporidium and Giardia, BD MAX (e.g. Entamoeba histolytica) or by microscopy for other parasites.
  3. Samples requesting Norovirus, usually from a suspected outbreak, are tested using the Cephid® GeneXpert®, a simplified molecular platform.
  4. Samples requesting Clostridium diffficile are tested daily using the Dynex DS2® an automated workstation used to run microplate assays.

Samples are also processed for examination of parasites either by ELISA in the case of Cryptosporidium and Giardia, or by microscopy for other parasites such as Entamoeba hystolytica.

Where to find results of these tests

  • All results are returned electronically where possible (EPR, SunquestICE).
  • Some results may be phoned to clinicians and GPs.
  • Results are never given directly to patients by the laboratory staff.

Further information and contact details

For further information please email:

Confidential patient information should only be sent from accounts.

Microbiology Laboratory Users Manual (pdf, 684 KB)