Stool Pathogen Testing

Why get tested?

To determine whether your diarrhea is caused by pathogenic bacteria, parasites, or viruses.

When to get tested?

Testing may be recommended by your gastroenterologist in cases of possible infectious colitis. Symptoms may include diarrhea, abdominal cramps, nausea/vomiting, and blood or mucus in your loose stools.

What is being tested?

We test for 22 different organisms, which are mostly a variety of viruses, bacteria and parasites that can cause infections of the digestive system.  The gastrointestinal pathogen panel simultaneously tests for the presence of multiple disease-causing microbes in a stool sample.

The GI pathogen panel detects the genetic material of many common pathogens.  It can identify co-infections (more than 1 microbe causing infection) and identify microbes that are often missed with traditional testing. Results of a GI pathogen panel may be available within a few hours, compared to a few days with some traditional testing.

GI infections are often caused by ingesting food or fluid that has been contaminated by bacteria, viruses, or more rarely, parasites.  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.

If a person has a GI infection caused by a less common bacterium, parasite or virus not included in the PCR pathogen panel, it will not be detected.  Additional tests, such as a stool culture or additional stool pathogen testing may be required to help establish a diagnosis.

How is the sample collected for testing?

Gastro Health will provide you with a sample collection kit and detailed instructions on how to collect a sample for testing.  The stool sample should not be contaminated with urine or water.  Once it has been collected, the stool should be taken to your provider’s office as soon as possible.  If your provider ordered multiple tests, they may need to be delivered to other laboratories.  You will receive instructions on how to collect those samples and where to deliver at your appointment.

Is any test preparation needed to ensure the quality of the sample?

No test preparation is needed.

What does the test result mean?

Results are typically interpreted in conjunction with a person’s signs and symptoms, medical history, and travel history. 

A positive result means that the microbe detected and identified is likely causing the signs and symptoms.  If more than one result is positive, the person may be infected with more than one pathogenic microbe (co-infection).

A negative result means that the microbes tested were not detected and the person’s signs and symptoms may be caused by a condition other than an infection or a pathogen other than those in the test panel.

If results are negative and symptoms persist and/or if suspicion of an infection remains high, other tests may be done to help establish a diagnosis.


Can this test be performed in my gastroenterologist’s office?

Yes – your provider can order this test and receive results within a few days. Our laboratory in Lynnwood receives the samples typically within one day of collection.

Why would my heath care provider order additional tests?

Additional testing may be done to perform susceptibility testing if required, or because the cause of your symptoms has not yet been identified.

How can I prevent a GI infection?

It is not always possible to prevent a GI infection, but there are things that you can do to lower your risk. The best things to do are to not drink water or eat food that may be contaminated and to follow good sanitary practices, such as thorough and frequent hand washing.  Food that might be contaminated, such as raw meats and eggs, should be cooked thoroughly.  Dairy products should be pasteurized.  Cooked foods and foods that are served raw should not touch any surfaces that may have been contaminated.  If someone in your household has an infection that is causing diarrhea, careful hand washing by all family members is recommended, commonly used surfaces should be disinfected, and the person infected should not prepare food or drink from others until the infection has resolved.

When 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.  The Centers for Disease Control and Prevention has an excellent resource for travelers,