Faeces are essential for all enteric examinations. Specimens in toilet paper, nappies, margarine tubs, etc., or rectal swabs are not acceptable. Please state if the patient has been abroad, or is on antimicrobial therapy as the range of tests set up will be determined by the clinical information provided. Also state if the patient is a food handler. Formed stool samples and repeat samples from inpatients are not routinely examined.

Sample Container:

60 ml sterile container - wide necked clear plastic container with yellow cap

Collection Process:

  • Do not mix urine with the stool sample; patient should be encouraged to urinate first.
  • 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 bowl (to prevent the specimen from falling into the toilet bowl).
  • Pass the stool onto the potty, plastic container, newspaper or plastic wrap.
  • Using a spatula, half-fill a faeces container. Do not fill more than a third full if the specimen is liquid. (Minimum sample volume is approx. 2ml).
  • Flush the remainder of the stool sample down the toilet.

Routine Analysis:

Fluid and/or unformed stool samples are routinely examined for the following:

  • Salmonella spp.
  • Shigella spp.
  • Campylobacter spp.
  • E. Coli 0157 – cause of haemorrhagic colitis/Haemolytic Uraemic Syndrome ( HUS )
  • C.difficile

The above list is not exclusive: other pathogens such as Yersinia and Cryptosporidium oocysts may be looked for depending on clinical details.


Foreign Travel

If there is an appropriate history of foreign travel, culture for Vibrio (including V. cholerae and V. parahaemolyticus) will be performed.
A concentrate for ova, cysts and parasites will also be performed where there is history of foreign travel to Central or South America, Africa or Asia.


Clostridium difficile

Testing for C. difficile toxin is performed daily; on weekdays on specimens received before 15:00hrs, on weekends and Bank Holidays – on specimens received before 10:00hrs. Specimens received after these times will be tested the following day.
C. difficile testing: samples should be refrigerated unless they are tested within 2 hours of collection.
C. difficile will be tested on fluid/mucoid/ bloodstained stools from inpatients and community patients >2 yrs old.
C. difficile will not be tested:

  • On non- fluid stools
  • On patients <2 years old
  • If two samples have been sent in the previous 10 days
  • If positive within the last 28 days; if still symptomatic, discuss with the Consultant Medical Microbiologist

Samples tested early in a C difficile infection may test as toxin negative. If symptoms continue, and C. difficile remains a clinical possibility, please repeat after 48 hours.


Rotavirus & Adenovirus
Rotavirus and Adenovirus testing is routinely performed on all stools from Caroline Thorpe, and fluid stools from in patients, those in nursing homes, and food handlers.


Ova, Cysts & Parasites
Investigations for Ova, Cysts & Parasites A concentrate for ova, cysts and parasites is performed routinely on the following stool samples:  Patients with persistent / intermittent GI symptoms for > 2 weeks.

  • Patients with eosinophilia
  • Patients who have returned from Central / South America, Africa or Asia.
  • Query worms seen in sample.

In other circumstances, please request on form and provide appropriate clinical details.


Helicobacter pylori Testing

This is a stool antigen test which is currently performed daily and confirmation tests are done weekly. It is a non-invasive enzyme immunoassay (EIA) test that has shown high sensitivity and specificity and the ability to confirm eradication. It detects the presence of H pylori and cannot be performed within 2 weeks of taking a PPI (Protein Pump Inhibitor) or within 4 weeks of antibiotics as both these suppress bacteria and can cause false negatives. A pea sized stool is required in a universal container.
Details of when to test and how to treat H pylori infection are provided by Public Health England.


Sellotape slides

“Sellotape” slides are used in the diagnosis of threadworm and the procedure should be carried out first thing in the morning. The laboratory provides a glass slide and transport container. Cut a 4″ strip of sellotape, press the sticky middle 1-2″ firmly against the perianal skin. Stick the sellotape on to the microscope slide lengthways, tucking the ends over. The slide should then be labelled and placed in the plastic slide container and sent to the laboratory with a completed microbiology form in a plastic transport bag.

Last updated: August 30, 2022