When should I consider testing for specific pathogens in a patient with gastroenteritis?

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

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

When a patient presents with gastroenteritis, you should consider testing for specific pathogens in several circumstances, depending on their age, symptoms, and risk factors.

  • For Adults:
    • Consider sending a faecal specimen for routine microbiology investigation if the person is systemically unwell, needs hospital admission, or requires antibiotics .
    • Testing is indicated if there is blood or pus in the stool .
    • If the person is immunocompromised, a stool sample should be sent .
    • For individuals who have recently received antibiotics, a proton pump inhibitor (PPI), or been in hospital, specifically request testing for Clostridioides difficile .
    • If diarrhoea occurs after foreign travel, or is recurrent or prolonged, request tests for ova, cysts, and parasites, and specify the countries visited on the form . This may involve sending three specimens a minimum of 2 days apart .
    • Consider testing 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 .
    • Testing may be needed to exclude infectious diarrhoea, for example, in cases of severe abdominal pain or exacerbation of inflammatory bowel disease .
    • Public Health Indications for Adults:
      • Test if the patient is in a high-risk group, such as food handlers, healthcare workers, or elderly residents in care homes .
      • Consider testing in cases of suspected food poisoning (e.g., after a barbeque or restaurant meal, or eating eggs, chicken, or shellfish) .
      • Testing is important during outbreaks of diarrhoea in the family or community, as isolating the organism can help pinpoint the source .
      • Consider testing contacts of people infected with organisms like Escherichia coli O157 or C. difficile, or close household contacts of a person with a Giardia infection, due to potential serious clinical sequelae .
  • For Children (under 5s):
    • Consider performing stool microbiological investigations if the child has recently been abroad .
    • Testing is also considered if the diarrhoea has not improved by day 7 .
    • If there is uncertainty about the diagnosis of gastroenteritis, microbiological investigations may be considered .
    • Perform stool microbiological investigations if you suspect septicaemia .
    • Testing is required if there is blood and/or mucus in the stool .
    • If the child is immunocompromised, stool microbiological investigations should be performed .
    • When stool microbiology is performed, ensure relevant clinical information is provided to the laboratory .

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