Stool Culture | Definition and Patient Education

Written by Christine Case-Lo
Medically Reviewed by George Krucik, MD, MBA on June 14, 2013

Stool Culture Overview

Stool cultures are important tools for understanding and treating intestinal illness. There are many reasons why you may be experiencing uncomfortable intestinal symptoms. A stool culture examines stool (or fecal) samples for organisms that may be causing disease. 

A stool culture is the process of growing or “culturing” organisms living in feces to see if any of them cause disease. A fecal sample is smeared into dishes with various gels that encourage bacterial growth. 

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If growth is seen, the bacteria are examined under a microscope. Samples may be stained with special dyes to identify the type of bacteria. The organism may also be exposed to potential drugs that could kill it, to help determine what treatment may be effective.

Disease-causing bacteria that are looked for in a basic stool culture include:

  • Campylobacter species
  • Salmonella species
  • Shigella species

If you have recently travelled outside of the U.S. or have other risk factors, other tests may be added to search for:

  • Escherichia coli (E. coli) 0157:H7 (Shiga toxins)
  • Vibrio species
  • Yersinia entercolitica
  • Pleisomonas
  • Aeromonas

Other tests may be performed at the same time. These may include a test for Clostridium difficile (C. difficile) toxin and an ova and parasite exam to look for parasites.

Why Is a Stool Culture Performed?

Infections of the gastrointestinal tract can lead to uncomfortable, potentially dangerous symptoms. These symptoms may have a variety of causes, however. Testing the stool for harmful bacteria allows doctors to help pinpoint what may be causing symptoms. These symptoms can include:

  • severe, possibly bloody, diarrhea that lasts for several days
  • fever
  • nausea and vomiting
  • abdominal pain and cramping

A stool culture can confirm the presence of harmful bacteria. It may also show what treatments may work to kill an invasive organism. If no dangerous bacteria are present in the stool culture but symptoms still exist, other explanations like irritable bowel syndrome, a parasitic infection, or other diagnosis can be explored.

How Is a Stool Culture Performed?

A stool sample is necessary to perform a stool culture. For most patients, a stool can be collected and placed into a sample container. You may be given a sample container. This is usually a clean, dry, wide-mouth container with an airtight lid. You may have to provide your own sample container. Some labs even include a special kind of toilet paper that can be used to collect the sample.

A bedpan can be used to collect a sample. Another simple method to collect a stool sample may be to loosely place plastic wrap over the toilet seat before defecating. You can then use the plastic wrap to transfer the sample into the collection container. Try to avoid mixing urine or regular toilet paper into the sample.

The process can be more difficult with infants in diapers, or for people with active diarrhea. In some cases, a cotton swab may be used in the rectum to collect a sample. Plastic wrap placed in a diaper for an infant may also work. However, it can be difficult to keep urine away from the stool sample. 

The sample must be turned into a laboratory as soon as possible after it is collected. At the lab, smears of the stool sample are placed on special plates with a gel called a growth media. This can help the growth of bacteria that can then be identified through dye staining, microscope analysis, and other testing.

Beyond Stool Culture: A Healthy Gut

A normal, healthy person will have a variety of bacteria and other organisms that live inside their intestines and actually help maintain their health. We know disease-causing organisms can start to inhabit your intestines and kill off their “good” cousins.

Broad-spectrum antibiotics kill off all the bacteria in your intestines. This includes both disease-causing bacteria as well as the normal flora, i.e. the “good” bacteria. Sometimes, the normal flora (sometimes called the microbiome) do not reestablish themselves after the antibiotics destroy them.

Potentially harmful bacteria that are antibiotic-resistant can survive and take over the gastrointestinal tract, causing uncomfortable symptoms. C. difficile is one of these harmful bacteria. Infections with C. difficile can be very difficult to treat. They can also cause pseudomembranous colitis.

A new and exciting treatment for C. difficile is fecal bacteriotherapy or a stool substitute transplant. A stool sample from a donor is implanted into the patient via a colonoscopy. Another procedure involves a purified bacterial culture implanted in the same way. The healthy bacteria can colonize the unhealthy gut and help return normal function to someone with persistent C. difficile infection.

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