Pathology Handbook

Faeces microbiology

Test Includes


Culture for Salmonella, Shigella, Campylobacter and Ecoli 0157

Children less than 5 years

Routine plus Adenovirus, Rotavirus and Cryptosporidium detection if appropriate.

Traveller (Tropical, Mediterranean and certain other countries)

Routine plus culture for Vibrio species and related organisms; concentrated examination for parasites and culture for E. coli 0157.

Patients over 65 years

Clostridium difficile toxins A and B detection

Liquid, gassy, blood stained or mucoid stools

Routine plus microscopy 

Also available on request (or when clinically indicated):

  • Vibrios associated with shellfish and epidemic diarrhoea

  • Clostridium difficile toxin in cases of antibiotic associated diarrhoea

  • Virus culture for Enteroviruses in cases of rash, pyrexia and myocarditis

  • Examination for Enterobius vermicularis ova (see "Specimen" section - stool sample NOT appropriate)

  • Electron microscopy or PCR for virus detection
    Outbreak investigation, including food poisoning organisms, norovirus detection, C. difficile toxin A + B detection

Request Form

ICE request


On request during normal working hours

Specific Criteria

Please give detailed clinical information including:

  • date of onset/ contact with the suspected infection; 
  • details of any recent travel (especially outside the UK), with dates; 
  • details of any possible food poisoning, or diarrhoea and vomiting, outbreak contacts, with dates; 
  • details of any recent, current, or intended, antibiotic therapy

Turnaround Time

Microscopy - same day
Cultures - Up to 72 hours

Rotavirus and Adenovirus - same day
Cryptosporidium - next routine working day after receipt
Clostridium difficile toxin - next normal working day after receipt
Viral PCR - 5 days


Faeces (Up to three separate specimens may be submitted). If multiple samples are sent together they must be labelled with the time of collection to indicate that they were collected at different times (see "Causes for Rejection" below)

Sellotape slide for patients with suspected Enterobius vermicularis infection


A walnut sized portion should be submitted in a faeces container


 Large white capped universal container

Large white top universal


Samples should be transported to laboratory as soon as possible

Causes for Rejection

Unlabelled / inadequately labelled sample
Delay in sample reaching laboratory 
If multiple samples are received without any indication that they were collected at different times only one sample will be tested

Lab Handling

Samples should be processed on day of receipt, store at 4oC if delay in processing