Stool culture

You do not need to do anything special before collecting your sample. Your GP or laboratory will give you a sterile container with instructions. 

Collect a fresh stool (poo) sample into the container provided. Do not let the sample touch the inside of a toilet bowl, and do not allow it to be contaminated with urine or water. Label the container clearly with your full name, date of birth, and the date and time of collection — the laboratory needs this to process the sample correctly. 

Send the sample to the laboratory as soon as possible after collection. If there will be a delay, keep it in the fridge. Bacteria in the stool continue to grow after collection, so a fresh sample gives the most accurate result. If your infant uses a nappy, take care to collect the sample without touching the inside of the nappy, as nappies often contain substances that can interfere with bacterial growth.

What the test measures 

The stool culture looks for harmful (pathogenic) bacteria in your stool. In the laboratory, a small amount of your sample is spread onto special growth media — thin, jelly-like surfaces in sealed dishes. Each type of medium encourages certain bacteria to grow while suppressing others. The dishes are placed in an incubator and checked regularly over 24 to 48 hours. 

Bacteria grow into visible colonies on the surface of the medium. Each type of bacteria produces colonies with distinctive characteristics — shape, colour, and chemical properties — that allow laboratory scientists to identify them. If a harmful bacterium is found, further tests (called susceptibility testing) may be done to find out which antibiotics will be effective against it. 

Standard UK stool cultures routinely test for the four most common causes of bacterial diarrhoea: 

• Campylobacter — the most common cause of bacterial diarrhoea in the UK. Usually caught from raw or undercooked poultry. 
• Salmonella — often linked to raw eggs, raw poultry, or reptiles kept as pets. Some people become long-term carriers after infection. 
• Shigella — spread through contaminated food and water, or person-to-person contact when hygiene is poor. 
• Escherichia coli O157 (and other STEC strains) — found in undercooked beef or unpasteurised products. Can cause bloody diarrhoea and, rarely, serious kidney complications. 

If your clinical history suggests other bacteria — such as Yersinia, Vibrio, or Clostridioides difficile — the laboratory may test for these too. Tell your doctor about any recent travel, unusual food, or relevant medical history so the right tests can be requested. 

What your results mean 

If bacteria are found (positive result) 

A positive result — sometimes reported as ​‘isolated’ — means a harmful bacterium was detected in your stool. The report will name the bacterium found, for example ​‘Salmonella enteritidis isolated’ or ​‘Campylobacter isolated’. This is most likely the cause of your illness. 

Your doctor will work with you on next steps. Most bacterial gut infections in otherwise healthy people will clear up on their own within a week, with rest and plenty of fluids. Antibiotics are not always needed or appropriate — for some infections, such as E. coli O157, they can increase the risk of complications and are generally avoided. Your doctor will advise you on whether any treatment is needed. 

A positive result must also be reported to the local public health team. This is a legal requirement. The team may contact you to gather information about where you may have caught the infection, to prevent it spreading further in the community. 

If no bacteria are found (negative result) 

A negative result — sometimes reported as ​‘not isolated’ — means no harmful bacteria were detected in this sample. This is reassuring, but it does not always rule out a bacterial infection. It is possible for bacteria to be present in the gut but not found in a single stool sample. 

If your symptoms continue, your doctor may request another culture. They may also consider other causes of your diarrhoea, such as a viral infection, a parasitic infection, food intolerance, or a bowel condition such as inflammatory bowel disease. An OCP test may be arranged to check for parasites. 

Most bacterial gut infections clear up on their own within a week. The most important things are to rest and drink plenty of fluids to avoid dehydration. Dehydration can be dangerous, especially in young children and older adults. Signs include feeling very thirsty, having dark urine, or urinating less than usual. 

Do not take anti-diarrhoeal medicines such as loperamide unless your doctor specifically advises you to. These can slow the removal of bacteria from your gut and may prolong your illness. If you or a child develop bloody diarrhoea, severe stomach pain, or feel very unwell, contact your GP or call NHS 111 straight away. 

Stay away from work or school until at least 48 hours after your symptoms have stopped. If you work in food handling, healthcare, or with vulnerable people, or if your child is under 5, speak to your GP or the public health team about when it is safe to return. 

The freshness of the sample is the most important factor. Bacteria in the stool continue to grow after collection, which can change the balance of organisms present and make it harder to detect pathogens. Always send your sample to the laboratory as soon as possible after collection. 

If the sample is contaminated with urine, toilet water, or the inside surface of a nappy, this can inhibit bacterial growth and affect the result. Follow the collection instructions carefully to get the most reliable result. 

Some medicines can suppress bacterial growth and reduce the chance of detecting an infection. These include antibiotics. If you have recently taken antibiotics, tell your doctor before the test, as this may affect how your results are interpreted.

A stool culture is often requested alongside an OCP test, which checks for parasites such as Giardia and Cryptosporidium. Both tests use the same stool sample, and your doctor may request them together if the cause of your diarrhoea is unclear. If faecal specimens for ova, cysts and parasites testing are requested and microscopy is performed (rather than more sensitive molecular or EIA assays), three specimens should be sent at least two days apart as OCP are shed intermittently. 

If STEC (Shiga toxin-producing E. coli) is suspected — for example, if you have bloody diarrhoea — a specific STEC test may be arranged alongside, or instead of, a standard culture. Many UK laboratories now use PCR testing to screen for STEC first, with culture used to confirm a positive result. 

If Clostridioides difficile (C. diff) is suspected — especially after recent antibiotic use or a hospital stay — a separate C. difficile toxin test will be arranged, as C. diff requires different testing methods.

Bacterial gut infections (gastroenteritis) are caused by harmful bacteria entering the digestive system, usually through contaminated food or water. Common causes in the UK include Campylobacter, Salmonella, Shigella, and E. coli O157. Most people recover fully within a week. For more information, visit NHS: Food poisoning.