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Stool Samples


The stool sample should be collected in a clean, dry screw-top container.

When to send a stool sample to the laboratory

Most diarrhoea episodes due to infection are self-limiting. Microbiological diagnosis of infected diarrhoea might be useful in some cases in order to manage the patient or reduce risk to others. Therefore, sending stool samples to the laboratory might be useful in the following circumstances:

Clinical Indications

Blood and/or pus in the stool.

  • Children with acute painful, or bloody diarrhoea.
  • History of foreign travel (also need ova, cysts and parasites)
  • After antibiotics treatment. The primary request should be for Clostridium difficile (Cdiff). Other tests will be carried out if Cdiff is negative.
  • Systemically unwell.
  • Prolonged diarrhoea (> 14 days) where amoeba, Giardia or cryptosporidium might be the cause.
  • Worsening symptoms in a patient with chronic bowel disease such as irritable bowel syndrome or inflammatory bowel disease.Public Health IndicationsFor public health indications, stool collection may be required even in those patients who do not have diarrhoea or no longer have diarrhoea. In these cases, requests to collect stool sample will normally come from the local Health Protection Unit (HPU) and the request form must make it clear that the sample is part of an outbreak investigation.
  • Suspected food poisoning
  • Diarrhoea in high risk patients such as food handlers, health or child care workers, children at nurseries or after farm visits.
  • Contact with other affected individuals in a diarrhoea outbreak such as norovirus.Virology should be requested but it is essential to state that this is part of an outbreak and that testing is requested by HPU as there is otherwise a risk that the sample will be rejected as funding is not available for community viral gastroenteritis in those > 5 years).
  • Close household contacts of giardia cases.
  • Other cases as directed by HPU.Managing suspected infectious diarrhoea:

Stool Samples Required Information

Patient and sender identifiers

Patient immune status, e.g. immunosuppressed.

Travel history or E.Coli 0157 in case of holiday on farms in the UK.

Antibiotic history-recent use of antibiotics

Association with other patients with diarrhoea.


Campylobacter, Salmonella (excluding S.typhi and paratyphi). Most common cause of food poisoning, normally self-limiting condition. Treatment may be required in severe infection or in immunocompromised patient.

  • Cryptosporidium. Self-limiting.
  • Shigella. Self-limiting condition but treatment may be required in severe infection or in immunocompromised patients.

E.coli 0157. Can be associated with bloody diarrhoea. There is a potential complication of haemolytic uraemic syndrome (HUS) which can potentially be fatal. Antibiotics are contra-indicated as there is a theoretical risk of triggering HUS.

Choice of antibiotics

Most infective causes of diarrhoea do not require antibiotic treatment.


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