Formal Name
Enteric Pathogens Culture, stool
This article was last reviewed on
This article waslast modified on 29 May 2019.
At a Glance
Why Get Tested?

To determine whether you have pathogenic bacteria in your gastrointestinal tract.

When To Get Tested?

When you have diarrhoea that lasts more than a few days and/or have blood or mucous in your loose stools.

Sample Required?

A fresh stool sample in a container provided by your healthcare professional

Test Preparation Needed?


On average it takes 7 working days for the blood test results to come back from the hospital, depending on the exact tests requested. Some specialist test results may take longer, if samples have to be sent to a reference (specialist) laboratory. The X-ray & scan results may take longer. If you are registered to use the online services of your local practice, you may be able to access your results online. Your GP practice will be able to provide specific details.

If the doctor wants to see you about the result(s), you will be offered an appointment. If you are concerned about your test results, you will need to arrange an appointment with your doctor so that all relevant information including age, ethnicity, health history, signs and symptoms, laboratory and other procedures (radiology, endoscopy, etc.), can be considered.

Lab Tests Online-UK is an educational website designed to provide patients and carers with information on laboratory tests used in medical care. We are not a laboratory and are unable to comment on an individual's health and treatment.

Reference ranges are dependent on many factors, including patient age, sex, sample population, and test method, and numeric test results can have different meanings in different laboratories.

For these reasons, you will not find reference ranges for the majority of tests described on this web site. The lab report containing your test results should include the relevant reference range for your test(s). Please consult your doctor or the laboratory that performed the test(s) to obtain the reference range if you do not have the lab report.

For more information on reference ranges, please read Reference Ranges and What They Mean.

What is being tested?

The stool culture is a test that allows the detection and identification of pathogenic (harmful) bacteria in the stool. In the laboratory, a small amount of a fresh faecal sample is applied to a variety of nutrient media (thin layers of gelatin like material in sterile covered plastic dishes). These media are selective, each encourages the growth of some bacteria and discourages the growth of others. Once inoculated, the media are incubated and checked daily for bacterial growth. Bacteria that are present in the stool grow as colonies that look like dots on the surface of the gel. The physical characteristics of the colonies - their shape, colour, and some of their chemical properties are unique to each type of bacteria and allow them to be differentiated.

The bacteria in the stool are representative of the bacteria that are present in the gastrointestinal tract and it is a far from sterile environment. Bacteria and fungi called “normal flora” inhabit the gastrointestinal tract. They play an important role in the digestion of food and they form a protective barrier against the growth of other pathogenic bacteria. Normal flora are usually in balance but sometimes one, such as Clostridium difficile, will become pathogenic by overgrowing. This upsets the balance of the normal flora and may lead to the production of toxins that can irritate and damage the intestinal tract. Bacterial overgrowth is usually a side effect of the administration of broad-spectrum antibiotics (which depresses the growth of the other normal flora) but it may also be seen in patients who are immunocompromised.

Other pathogenic bacteria are usually brought into the body when someone eats food or drinks water that has been contaminated. This may include raw or undercooked eggs, poultry or beef, unpasteurised milk, and contaminated water from lakes, streams, and (occasionally) from community water supplies. Those that travel outside the U.K., especially to developing nations, may face a greater risk of being exposed to pathogenic bacteria. Some of these bacteria may be “true pathogens” while others are strains of gastrointestinal bacteria that are normal flora for the locals, but cause gastrointestinal distress to the tourist. Visitors may become infected by eating or drinking anything that has been contaminated with the bacteria (things as simple as tap water, ice cubes in a drink, a fresh salad etc).

The most common symptoms of a pathogenic bacterial infection are prolonged, bloody diarrhoea, mucous in stool, abdominal pain, and nausea. This is usually a self-limiting illness and doesn’t require antibiotics. If diarrhoea lasts more than a few days, it may lead to dehydration and electrolyte imbalance - dangerous conditions in children and the elderly. Dehydration can cause symptoms such as: thirst, dry skin, fatigue, light-headedness, and fever. Severely affected patients may require hospitalization to replace lost fluids and replace lost electrolytes. A serious complication that may occasionally arise is haemolytic uraemic syndrome. It is most frequently seen in children infected with Eschericia coli 0157:H7 and may lead to the destruction of red blood cells and to kidney failure.

The most common pathogenic bacteria and their most frequently encountered sources include:

  • Salmonella, often found in raw eggs (even intact disinfected eggs), raw poultry and in reptiles. Pets, such as lizards and turtles, may carry salmonella in their intestines without being ill themselves. Some humans may become carriers of salmonella.
  • Shigella, from faecally contaminated food and water, and from infected-person to person when careful sanitation is not observed. For instance, it can be a challenge to prevent the spread of shigella within a family, and in a day care or nursing home setting.
  • Campylobacter, from raw or undercooked poultry. It is the most common cause of bacterial diarrhoea in the U.K. It may become especially serious if it spreads to the bloodstream and occasionally causes long-term complications such as arthritis, and Guillain-Barré syndrome (an autoimmune condition affecting the nervous system), however this is rare.
  • Escherichia coli 0157:H7 (other strains of E. coli are normal flora). Found in raw or undercooked hamburger / beef or unpasteurised cider. Causes bloody diarrhoea and may lead to haemolytic uraemic syndrome.

Others include: Staphylococcus aureus, Clostridium difficile and strains of Yersinia and Vibrio.

How is the sample collected for testing?

A fresh stool sample is collected in a sterile universal container. The stool sample should not be contaminated with urine or water. Once it has been collected the stool should be sent to the laboratory as soon as possible. The container should be labelled with the patient’s forename, surname, date of birth (as a minimum) and the date and time of the stool collection.

Special measures will need to be taken with infants wearing a nappy, both to prevent urine contamination of the sample and to prevent the samples from touching the inside surface of disposable nappies. The nappies often contain a bacteriostatic agent that will inhibit the growth of the bacteria in the sample and interfere with the results of the stool culture.

Accordion Title
Common Questions
  • How is it used?

    A stool culture is used, often along with other tests such as microscopy (to look for parasites), to help determine the cause of your prolonged diarrhoea.

  • When is it requested?

    Stool cultures may be requested when you have had diarrhoea for several days and when you have blood and/or mucous in your loose stools. This is especially true when you have eaten food or drunk fluids that you or your doctor suspect may have been contaminated with a pathogenic bacteria, such as undercooked meat or raw eggs, or the same food that has made others ill. Recent travel outside the United Kingdom may also suggest possible food contamination.

    If you have had a previous pathogenic bacterial infection of your gastrointestinal tract and have been treated for it or recovered on your own, your doctor may request one or more stool cultures to verify that the pathogenic bacteria are no longer detectable. This can be important because in some cases people can become carriers of the bacteria. For instance, people with Salmonella typhi may become carriers (like "typhoid Mary") - they are not ill themselves any more but they can infect other people.

  • What does the test result mean?

    Results are frequently reported out as “isolated” – which means the particular pathogen was found in your stool sample, or “not isolated” - which means that bacteria was not found. Negative results usually reflect the fact that the stool culture was checked for pathogens at several intervals and none were found (not isolated). A report may say something like: “no Campylobacter isolated in 24 or 48 hours,” “no Salmonella or Shigella isolated in 24 or 48 hours,” etc. If the culture is negative for the major pathogens, then it is likely that your diarrhoea is due to another cause. It is also possible that the pathogenic bacteria are present in the gastrointestinal tract but were not found in this particular stool sample. If your doctor suspects this is the case and your symptoms continue, he may occasionally request another stool culture.

    If your stool culture is positive for pathogenic bacteria, then that is the most likely cause of your prolonged diarrhoea. The stool culture report may say something like, “Salmonella isolated, species to follow” (which means the doctor is still trying to identify the particular type of salmonella), or “Salmonella enteritidis isolated” (which means that you have an infection caused by this particular pathogenic bacterium). Usually it will be a single type of bacteria causing your infection, but it is possible to have more than one present.

  • Is there anything else I should know?

    Severe pathogenic bacterial infections of the gastrointestinal tract, and those causing complications, may be treated with antibiotics but many uncomplicated cases are left to run their course. Those patients with competent immune systems will usually get better on their own within a week or so. Patients are instructed in how to prevent the spread of the infection and are treated and monitored for symptoms such as dehydration.

    Pathogenic bacterial infections are monitored on a community level. Other than travel related cases, health officials want to try to determine where your infection came from so that they can address any potential public health concerns. For instance if your salmonella or shigella is due to eating food from a particular restaurant, the Communicables Diseases section of the local Health Board will want to investigate whether or not other people have also become ill from their food, and visit the restaurant to determine the source of the infection, taking steps to ensure that the spread of the infection is stopped.

  • What can be done to prevent a bacterial infection?

    The best way is not to drink water or eat food that may be contaminated and to be careful with sanitation measures such as hand washing. Food that might be contaminated, such as raw meats and eggs should be cooked thoroughly. Cooked foods and foods that are served raw should not touch any surfaces that may have been contaminated. When you are travelling to developing nations, it is best to only drink bottled water, carbonated drinks, and hot cooked foods. Avoid fresh fruits and vegetables, limiting yourself to those that you can peel yourself. Food from food vendors is generally not considered safe. If someone in your household has an infection that is causing diarrhoea, careful hand washing by all family members is recommended and it may be best to have the person infected not prepare food or drink for others until the infection is over.

  • Why must the stool sample be fresh?


    Bacteria in the stool will continue to multiply. If the stool is not fresh, the proportion of the different kinds of bacteria in the stool can change no longer representing the proportions present in the gastrointestinal tract. Overgrowth of normal bacteria can sometimes prevent the detection of the pathogenic bacteria as can exposing the stool sample to temperature extremes.


  • Why shouldn't I take an over the counter anti-diarrhoea medicine when I have infectious diarrhoea?

    You should only take this on the advice of your doctor. Diarrhoea is one of the methods your body uses to help rid itself of the infection, it is trying to “flush” out the pathogen. If you slow down or prevent this from happening by taking anti-diarrhoea medication you can prolong the amount of time that you are ill and sometimes make your infection worse.

  • Once I've had a pathogenic bacterial infection, can I be re-infected?

    Generally yes. You may develop immunity (for a while) against the particular strain of pathogenic bacteria that caused your infection but there are many other types and strains of pathogenic bacteria that can make you ill if you are exposed to them.

  • What else can cause diarrhoea?

    Can be due to a viral infection, parasitic infection, food intolerance, certain medications (directly causing diarrhoea or indirectly by decreasing normal flora), bowel disease or a bowel dysfunction. Diarrhoea may also be caused or exacerbated by psychological stresses.