When should I consider stool testing for a patient with acute diarrhoea, and what pathogens should I specifically test for?

Guideline-aligned answer with reasoning, red flags and references. Clinically reviewed by Dr Kola Tytler MBBS CertHE MBA MRCGP.

Posted: 16 August 2025 Guideline-Aligned (High Confidence) Clinically Reviewed
Dr Kola Tytler MBBS CertHE MBA MRCGPClinical Lead • iatroX

You should consider stool testing for a patient presenting with acute diarrhoea in several specific circumstances:

  • Clinical Indications:
    • If the person is systemically unwell, requires hospital admission, or needs antibiotics .
    • If there is blood or pus in the stool .
    • If the person is immunocompromised .
    • If the person has recently received antibiotics, a proton pump inhibitor (PPI), or been in hospital .
    • If diarrhoea occurs after foreign travel .
    • If amoebae, Giardia, or Cryptosporidium are suspected, particularly if diarrhoea is persistent (2 weeks or more) or the person has travelled to an at-risk area .
    • If there is a need to exclude infectious diarrhoea (e.g., severe abdominal pain, exacerbation of inflammatory bowel disease, or irritable bowel syndrome) .
    • If diarrhoea is recurrent or prolonged .
  • Public Health Indications:
    • For high-risk individuals such as food handlers, healthcare workers, or elderly residents in care homes .
    • If food poisoning is suspected (e.g., after a barbeque, restaurant meal, or eating eggs, chicken, or shellfish) .
    • During outbreaks of diarrhoea in the family or community, where isolating the organism may help pinpoint the source .

When sending a stool sample, ensure it is a loose stool, as laboratories will not examine formed stools . A quarter-full specimen pot is the minimum needed for routine microbiology investigation . For ova, cysts, and parasites, send three specimens a minimum of 2 days apart .

The request form should include details such as clinical features (e.g., fever, bloody stool, severe abdominal pain), history of immunosuppression, food intake (e.g., shellfish), recent foreign travel (specify countries), recent antibiotic therapy, proton pump inhibitor therapy, or hospitalisation (suggestive of Clostridioides difficile infection), exposure to untreated water (suggestive of protozoa), and contact with other affected people or an outbreak .

Regarding specific pathogens to test for:

  • Routine microbiology investigation should be requested when indicated .
  • Clostridioides difficile should be specifically tested for if the person has recently received antibiotics, a proton pump inhibitor, or been in hospital .
  • Ova, cysts, and parasites should be requested if diarrhoea occurs after foreign travel, is recurrent, or prolonged . This includes testing for organisms like amoebae, Giardia, and Cryptosporidium, especially if suspected or if the person has travelled to an at-risk area .
  • Consideration for organisms like Escherichia coli O157 may be relevant where there may be serious clinical sequelae .

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Educational content only. Always verify information and use clinical judgement.