At a Glance

Why Get Tested?

To determine whether you have an infection of your digestive tract due to the presence of disease-causing (pathogenic) bacteria

When To Get Tested?

When you have diarrhea, abdominal cramps, nausea and/or vomiting that is severe or lasts more than a few days

Sample Required?

A fresh stool sample transported to the laboratory within 2 hours or one that has been placed in a transport medium (a collection vial containing a preservative)

Test Preparation Needed?


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 a person’s gastrointestinal symptoms (gastroenteritis).

The bacteria found in stool are representative of the bacteria that are present in the digestive system (gastrointestinal tract). Certain bacteria and fungi called normal flora 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 broad-spectrum antibiotics; the drugs inhibit the growth of normal flora and allow the bacteria Clostridium difficile that is resistant to the antibiotics to survive and overgrow the digestive tract, leading to symptoms such as diarrhea and abdominal pain.

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

People who travel outside the U.S., 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 are prolonged diarrhea, bloody diarrhea, mucus in the stool, abdominal pain and cramping, and nausea. If diarrhea lasts more than a few days, it may lead to complications such as dehydration and electrolyte imbalance, which can be dangerous conditions, especially for children and the elderly. Dehydration can cause symptoms such as dry skin, fatigue, and light-headedness.

Severely affected people may require hospitalization to replace lost fluids and electrolytes. Hemolytic uremic syndrome is a serious complication characterized by the destruction of red blood cells and kidney failure that may occasionally arise from an infection with a toxin-producing strain of the bacteria Escherichia coli. The condition is most frequently seen in children, the elderly, and those with weakened immune systems.

If a person’s illness is uncomplicated and goes away within a few days, a healthcare practitioner may not order testing. However, if symptoms are severe, if there is bloody diarrhea or mucus present in the stool, or if it is continuing unabated, then a stool culture may be ordered. This is especially true if the person has been outside the U.S. and/or has eaten or drunk anything that has also made someone close to them ill.

To aid diagnosis, a stool culture may be done in conjunction with or following a GI pathogens panel that simultaneously tests for multiple disease-causing bacteria, viruses, and parasites. Other tests that may be done include an ova and parasite exam or antigen tests to identify specific microbes.

How is the sample collected for testing?

A fresh stool sample is collected in a clean container. The stool sample should not be contaminated with urine or water. Once it has been collected, the stool should be taken to the laboratory within two hours after collection or should be transferred into a vial containing a preservative and taken to the lab as soon as possible. For infants, a stool sample is usually collected with a swab of the rectum.

Common Questions

How is it used?

A stool culture is used to detect the presence of disease-causing (pathogenic) bacteria and help diagnose an infection of the digestive system (gastrointestinal, GI tract). Since there are many causes of GI infections, a stool culture may be used in conjunction with other tests, such as a GI pathogens panel or an ova and parasite exam (O&P) to help establish a diagnosis.

A GI pathogens panel is performed on a stool sample to simultaneously test for the viruses, bacteria, and parasites that are common causes of GI infections. These panels are relatively new and laboratories and healthcare practitioners are still determining how to utilize them to provide the optimum patient results while being cost-effective. A stool culture and an O&P may be done if a microbe is not identified by the panel and/or there is a suspicion of bacteria or parasites other than those included in the GI panel.

Many GI infections in the U.S. resolve with no specific treatment, with only supportive care, and may not require testing. In otherwise healthy individuals, the infections are considered common illnesses that are not serious and sometimes thought of as “food poisoning” or
“stomach flu.” However, there are cases where it is useful to perform testing that identifies the cause of the GI infection – to guide its treatment, eliminate its source, and limit its spread.

Laboratories typically use stool cultures to detect and identify the most common intestinal disease-causing bacteria:

  • Campylobacter species
  • Salmonella species
  • Shigella species

Some bacteria cause illness by producing toxins. These bacteria may be cultured, but many of the tests used to detect them are dedicated to the direct detection of their toxins, either by PCR or antigen test. Examples include:

  • Escherichia coli O157:H7
  • Clostridium difficile

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
  • Yersinia enterocolitica
  • Vibrio species

When is it ordered?

A stool culture may be ordered when someone has signs and symptoms of an infection of the digestive tract, such as:

  • Diarrhea 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. In people who have healthy immune systems, these infections often resolve with supportive care and without the use of antibiotics. A stool culture is more likely to be ordered when a person:

  • Has severe symptoms, dehydration, electrolyte imbalance, and/or other complications
  • Is very young, elderly, or has a weakened immune system; according to the Centers for Disease Control and Prevention (CDC), diarrhea is a global killer. It is the second leading cause of death in children under the age of 5 worldwide, killing an estimated 2,195 children a day.
  • Has prolonged signs and symptoms and/or infections that do not resolve without treatment
  • Has an illness during and following travel outside the U.S., especially to emerging nations; the CDC estimates that 30% to 70% of those who travel outside of the U.S. will get a GI infection.
  • Has eaten food or drunk fluids that may have been contaminated with pathogenic bacteria, such as undercooked meat or raw eggs, or the same food that has made others ill
  • Is ill and a possible foodborne or waterborne outbreak prompts the medical community to investigate and identify the cause; examples include contaminated produce, contaminated food from a specific restaurant, and/or illness on a cruise ship.

A healthcare practitioner 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 test result mean?

If a stool culture is positive for pathogenic bacteria, then they are the most likely cause of the person’s diarrhea and other symptoms. Results are frequently reported out with the name of the pathogenic bacteria that was detected.

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

  • Campylobacter – found in raw or undercooked poultry and unpasteurized milk; it is one of the most common causes of bacterial diarrhea in the U.S. It may become especially serious if it spreads to the blood, and it occasionally causes long-term complications such as arthritis and Guillain-Barré syndrome.
  • Salmonella – found in raw eggs (even intact disinfected eggs), raw poultry, uncooked vegetables, 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. Salmonella may be transmitted person-to-person.
  • 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 very few organisms may cause disease.

A wide variety of other bacteria may sometimes cause GI infections and may be identified with a stool culture. Some important examples include:

  • Escherichia coli 0157:H7 and other 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, spinach, or unpasteurized cider; causes bloody diarrhea and may lead to hemolytic uremic syndrome.
  • Clostridium difficile – may be present as part of the normal flora, but use of broad-spectrum antibiotics can result in an overgrowth of these bacteria. Toxin-producing strains can cause diarrhea and other serious complications. If these strains are suspected to be the cause, then separate tests that detect the toxin-producing C. difficile will be performed.

Examples of other less common causes include:

  • Aeromonas
  • Plesiomonas
  • Yersinia enterocolitica
  • Vibrio cholerae and other Vibrio species

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 person’s signs and symptoms are due to another cause or to a less common pathogen. 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 healthcare practitioner suspects that this is the case and symptoms continue, a stool culture on another sample may be ordered and/or followed up with other tests.

Most diarrheal 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. People with healthy immune systems will usually get better on their own within a week or so. They 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 the State Public Health Laboratories to be typed by molecular methods. The results of the typing are uploaded into a national database to detect common source outbreaks across the U.S. The typing helps to identify specific foods or food products that are the source of the infection.

Travelers’ diarrhea is typically caused by toxin-producing Escherichia coli, which are the leading cause of bacterial diarrhea infections among travelers to Africa, Asia, and Latin America. These strains of E. coli, however, are different than the strains of Shiga toxin-producing E. coli (O157:H7), which can cause hemolytic uremic syndrome.

What can I do to avoid getting 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 follow good sanitation practices, such as thorough and frequent 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 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. Avoid unpasteurized dairy products. Food from street vendors is generally not considered safe. If someone in your household has an infection that is causing diarrhea, 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 resolved.

Why must the stool sample for culture 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-diarrhea medicine when I have infectious diarrhea?

Diarrhea 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-diarrhea 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 diarrhea?

Diarrhea can be due to a viral infection such as norovirus, hepatitis A, a parasitic infection such as giardiasis, food intolerance, medications (directly causing diarrhea or indirectly by decreasing normal flora), a bowel disease or bowel dysfunction such as celiac disease, malabsorption, or inflammatory bowel disease. Diarrhea may also be caused or worsened by psychological stresses.


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