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What is being tested?

The stool culture is a test that detects and identifies bacteria that cause infections of the lower digestive tract. The test distinguishes between the types of bacteria that cause disease (pathogenic) and the types that are normally found in the digestive tract (normal flora). The test helps to determine if pathogenic bacteria are the cause of gastrointestinal symptoms (gastroenteritis). It is important to note that viruses, such as norovirus, cause many cases of diarrhoea in the community and will not be identified on a bacterial stool culture. Viral studies on stool specimens usually need to be requested separately.


The bacteria found in stool are representative of the bacteria that are present in the gastrointestinal tract. Certain bacteria and fungi called normal flora or the microbiome inhabit everyone's gastrointestinal tract. They play an important role in the digestion of food, and their presence keeps a check on the growth of disease-causing bacteria. Sometimes, the balance of the normal flora may be affected by the administration of antibiotics; the drugs inhibit the growth of normal flora and allow bacteria resistant to the antibiotic to survive and overgrow the digestive tract. The normal flora may also be affected by anti-cancer drugs and when a person has a weakened immune system, leading to bacterial overgrowth and symptoms such as diarrhoea and abdominal pain.


Pathogenic bacteria can enter and infect the digestive tract when someone eats food or drinks water that is contaminated (food poisoning). Examples of contaminated sources include raw or undercooked eggs, poultry or beef, unpasteurised milk, and untreated water from lakes, streams, and (occasionally) from community water supplies.


People who travel outside Australia, especially to developing nations, may face a greater risk of being exposed to disease-causing bacteria. Some of these bacteria may be true pathogens while others are strains of gastrointestinal bacteria that are normal flora for the local inhabitants but cause gastrointestinal distress to the tourist. Visitors may become infected by eating or drinking anything that has been contaminated with the bacteria, even things as simple as tap water, ice cubes in a drink, a fresh salad, or food from a vendor's stall.


The most common symptoms of a pathogenic bacterial infection include prolonged diarrhoea, bloody diarrhoea, mucus in the stool, abdominal pain and cramping, and nausea. If diarrhoea lasts more than a few days, it may lead to complications such as dehydration and electrolyte imbalance - this can be dangerous, especially in children and the elderly. Dehydration can cause symptoms such as dry skin, fatigue, and light-headedness.

Severely affected people may require hospitalisation to replace lost fluids and electrolytes.


Haemolytic uraemic syndrome is a serious complication that may occasionally arise from an infection with a toxin-producing strain of the bacteria Escherichia coli (E.coli). It is characterised by the destruction of red blood cells and kidney failure. The condition is most frequently seen in children, the elderly, and those with weakened immune systems.


Some of the most common pathogenic bacteria that cause infections in Australia and their most frequently encountered sources include:

  • Salmonella - found in raw eggs (even sometimes in intact disinfected eggs), raw poultry, uncooked vegetables. Pets, such as lizards and turtles, may carry Salmonella in their intestines without being ill themselves. Some humans may become carriers of Salmonella and can transmit the bacteria to other people.
  • Shigella - found in food and water contaminated with stool, 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 daycare or nursing home setting since even a very few organisms may cause disease.
  • Campylobacter - found in raw or undercooked poultry and is a common cause of bacterial diarrhoea in Australia. It may become especially serious if it spreads to the bloodstream, and it occasionally causes long-term complications such as arthritis and Guillain-Barr√© syndrome.
  • Escherichia coli 0157:H7 and other Shiga toxin-producing E. coli (most strains of E. coli are considered normal flora and do not cause disease) - found in raw or undercooked hamburger/beef, and other products such as fresh vegetables contaminated with animal faeces; causes bloody diarrhoea and may lead to haemolytic uraemic syndrome.
  • Clostridium difficile - may be present as part of the normal flora, but use of antibiotics can result in an overgrowth of these bacteria. Toxin-producing strains can cause diarrhoea and other serious complications.


A wide variety of other bacteria may sometimes cause diarrhoea. These may include: Aeromonas species, Staphylococcus aureus, Yersinia enterocolitica, Vibrio cholerae and other Vibrio species.

How is it used?

A stool culture is used to detect the presence of disease-causing bacteria (pathogenic) and help diagnose an infection of the digestive tract. It is often used along with other tests such as an Ova, Cyst and Parasite test that detects parasites in the stool and/or Clostridium difficile toxin tests, to help determine the cause of prolonged diarrhoea. In establishing the cause, the test can help guide treatment, determining whether antibiotics or other medication may be necessary to resolve symptoms.

When is it requested?

Stool cultures may be ordered when someone has signs and symptoms of an infection of the digestive tract. This is especially true when the affected person has eaten food or drunk fluids that the doctor suspect may have been contaminated with pathogenic bacteria, such as undercooked meat or raw eggs, or the same food that has made others ill (so-called food poisoning). Recent travel  outside Australia may also suggest possible food contamination. Some signs and symptoms of infection include:

  • Diarrhoea that lasts more than a few days and may contain blood and/or mucus
  • Abdominal pain and cramping
  • Nausea, vomiting
  • Fever


Not everyone who has these symptoms will necessarily have testing done or be treated with antibiotics. In people who have healthy immune systems, these infections often resolve with supportive care and without the use of antibiotics. However, if symptoms become severe or are present in an infant, a young child, an elderly person or someone with a weakened immune system, then testing and treatment are usually warranted.


A doctor may order one or more stool cultures when someone has had a previous pathogenic bacterial infection of the gastrointestinal tract and has either been treated for it or it has resolved on its own. This may be done to verify that the pathogenic bacteria are no longer detectable because in some cases people can become carriers of the bacteria. Carriers are not ill themselves, but they can infect other people.

What does the result mean?

If a stool culture is positive for pathogenic bacteria, then they are the most likely cause of the diarrhoea and other symptoms. Results are frequently reported with the name of the pathogenic bacteria that was detected. Laboratories typically evaluate stool cultures for the most common intestinal pathogens:

  • Campylobacter species
  • Salmonella species
  • Shigella species


Depending on the affected person's medical and/or travel history, tests for other pathogens or potential pathogens may be included or be separately available. Some of these include:

  • Aeromonas
  • Plesiomonas
  • Shiga-toxin producing Escherichia coli
  • Yersinia enterocolitica
  • Vibrio species


Certain strains of Clostridium difficile can cause intestinal disease and diarrhoea. If these strains are suspected to be the cause, then separate tests that detect the toxin-producing C. difficile will be performed.

Results of stool cultures that are reported as negative usually reflect the fact that the stool culture was checked for the most common pathogens at several intervals and none were found (not isolated). A report may state: "no Campylobacter isolated," "no Salmonella or Shigella isolated," etc. If the culture is negative for the major pathogens, then it is likely that the prolonged diarrhoea is due to another cause or to a less common pathogen. In children particularly, most diarrhoea is caused by viruses, for which there is no specific treatment. Not all diarrhoea is due to an infection. It is also possible that pathogenic bacteria are present in the gastrointestinal tract, but there were too few bacteria in that particular stool sample to be detected. If a doctor suspects that this is the case and symptoms continue, he may order a stool culture on another sample and/or follow up with other tests.

Most diarrhoeal disease is caused by a single pathogen, but it is possible to have an infection with more than one.

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 best left untreated with antibiotics. Those with healthy immune systems will usually get better on their own within a week or so. People 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 and sometimes national level. Other than foreign travel-related cases, health officials try to determine where an infection came from so that they can address any potential public health concerns. Bacterial isolates causing foodborne illness are sent to Public Health Laboratories to be typed and potential outbreaks are investigated by State authorities. The typing and investigation help to identify specific foods or food products that are the source of the infection. In Australia, the OzFoodNet is a collaborative effort between the states and territories to monitor foodborne illnesses and help investigate and control any  foodborne disease outbreaks.


Travellers' diarrhoea is typically caused by toxin-producing Escherichia coli, which are the leading cause of bacterial diarrhoea infections among travellers to Africa, Asia, and Latin America. These strains of E. coli, however, are different from the strains of Shiga toxin-producing E. coli, which can cause haemolytic uraemia syndrome.

Common questions

  • What can be done to prevent a bacterial infection of the digestive tract?

The best things to do are to not drink water or eat food that may be contaminated and to be careful with sanitation measures, such as washing hands and uncooked vegetables and fruit before eating. Food that might be contaminated, such as raw meats and eggs, should be cooked thoroughly. Using separate cutting boards for meats and vegetables can prevent bacteria from raw meat contaminating salad vegetables during food preparation. Cooked foods and foods that are served raw should not touch any surfaces that may have been contaminated. When you are traveling 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 street 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 the person infected should not prepare food or drink for others until the infection is over.


  • Why must the stool sample be fresh?

If the stool is not fresh, or in a preservative, 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?

Diarrhoea is one of the methods your body uses to help rid itself of the infection. 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 a short-term immunity 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?

Diarrhoea can be due to a viral infection such as a Norovirus or rotavirus, parasites such as Giardia, food intolerance, medications (directly causing diarrhoea or indirectly by decreasing normal flora), a bowel disease or bowel dysfunction such as coeliac disease, malabsorption or inflammatory bowel disease. Persons with persistent diarrhoea should see a health professional.

Last Updated: Thursday, 1st June 2023

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