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Faecal Culture & Microscopy


Test Usage

All samples are tested for:

Salmonella / Shigella / Campylobacter / E. coli O157 / Giardia and Cryptosporidium as standard. In addition:

  • Requests mentioning consumption of seafood or contact with salt-water will be cultured for Vibrio sp.
  • Requests mentioning foreign travel are also cultured for Vibrio sp. (including V. cholerae and V. parahaemolyticus) and examined for ova, cysts & parasites by microscopy (OCP only performed for foreign travel outside of Europe.)
  • Requests with clinical details including mesenteric adenitis are also cultured for Yersinia enterocolitica.
  • Requests for patients who have diarrhoea and are on antibiotics will be tested for C. difficile.

Samples from inpatients will NOT be cultured if they have been in hospital for >3 days, unless bacterial gastroenteritis is suspected (please state in request.)

Please click here for details on viral testing.

Please click here for details on Helicobacter pylori testing.


Stool Sample

Specimen container

Fecon pot

Specimens received in toilet paper, nappies, margarine tubs, etc., or rectal swabs are not acceptable.

Please ensure that stool sample pots are filled between 1/3 to 1/2 full. This is sufficient sample volume for all stool tests. Under-filling or over-filling stool sample pots may lead to samples being unsuitable for analysis.

To Request On EPIC

For electronic requesting using EPIC (RDUH ONLY):

Search for: ‘Faeces MC&S‘ or test code ‘LAB9265

Special Instructions

Please state all relevant clinical details on the request as the range of tests set up will be determined by the clinical information provided.

This should include (but not limited to):

  • Details of any recent foreign travel (within the last 6 months)
    • Include dates of travel and the countries/regions visited
  • If any of the following are suspected:
    • Food poisoning
    • Parasites
    • Mesenteric adenitis
    • HUS (Haemolytic Uremic Syndrome)
  • If the patient has eosinophilia
  • Details about any recent consumption of seafood or contact with salt-water (e.g. Swimming.)
  • Details of the patients profession (if relevant):
    • e.g. Food handler, Sewage worker, works with farm animals
  • If the patient has had recent contact with any farm animals
  • Details of any immunocompromise
  • If the patient is on antimicrobial therapy
  • If sample is being sent as part of an outbreak
    • Please also include the outbreak number
  • If this is a clearance test (e.g. previous positive E.coli O157 etc.)

Specimen Collection Procedure

1. DO NOT mix urine with the stool. If you need to pass water, do so first.

2. Place a wide mouth container (potty, empty plastic food container e.g. 1 litre ice cream carton) in the bowl, or put clean newspaper or plastic wrap over the toilet seat opening (this prevents the faecal specimen from falling into the toilet bowl. (Collection container does not have to be sterile, but must be clean).

3. Pass stool onto the potty, plastic container, newspaper or plastic wrap.

4. Using the spoon built into the lid of the collection tube (or the wooden sticks, if supplied), place small scoopfuls of stool from areas which appear bloody, slimy or watery into the tube. DO NOT OVERFILL. Try not to spill stool on the outside of the tube.

5. Replace the collection tube lid and screw on tightly.

6. Dispose of remaining stools in your potty, plastic container or newspaper down the toilet. Clean potty with soapy water. Wrap plastic container, newspaper or plastic wrap in newspaper and dispose of in normal refuse in a plastic bag.

7. Label the collection tube with your name, date of birth, and the date of collection.

8. Place the container in the plastic bag attached to the specimen request form.

9. Wash your hands thoroughly in hot running water with soap.

10. Deliver to the surgery/laboratory as soon as possible.

11. If specimen cannot be delivered immediately, refrigerate in surgery fridge until delivery.


Primary testing performed locally in Microbiology at RDUH

Positive samples/cultures may be sent to UKHSA for epidemiological typing/confirmation.

Processing Time

48 -72 hours for negatives/ provisional positives. Confirmation of positives may take longer than this.

Useful Links

For Patients:

Stool Culture – Lab Tests Online UK

For Healthcare Professionals:

Gastrointestinal infections: guidance, data and analysis – UKHSA

Gastrointestinal bacteria reference unit (GBRU), UKHSA Colindale


Specimen Labelling Procedure
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