Gastrointestinal Pathogens Panel
A fresh stool sample collected in a clean container; the stool sample should not be contaminated with urine or water; once it has been collected, the stool should either be taken to the laboratory within two hours after collection or transferred into special transport vials containing preservative solutions
A variety of viruses, bacteria, and parasites can cause infections of the digestive system (gastrointestinal (GI) infections). The gastrointestinal pathogen panel simultaneously tests for the presence of multiple disease-causing (pathogenic) microbes in a stool sample.
The GI pathogen panel detects the genetic material (RNA or DNA) of some of the more common pathogens. It can identify co-infections (more than one microbe causing infection) and identify microbes that might be 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. (For more, read Food and Waterborne Illness.)
Microbes causing an infection are shed into (present in) the stool of infected people. Because of this, infections can spread to other people through exposure to infected stool. If people with GI infections don't wash their hands well after using the bathroom, they can spread the infection when others come into contact with surfaces that an infected person has touched, such as door knobs or hand rails. Individuals with diarrheal illness should avoid preparing food for others whenever possible.
Some GI infections are caused by the overgrowth of the bacterium Clostridium difficile. This can cause a decrease in the normally protective "good bacteria" (normal flora) in the lower intestines. This may occur, for example, when treatment with broad-spectrum antibiotics leads to the suppression of normal flora and the growth of antibiotic-resistant C. difficile.
While a wide variety of viruses, bacteria, and parasites can cause GI infections, the list of common ones is much smaller. A healthcare practitioner may have an idea about the cause based upon a person's recent food and drink, medical history, and/or recent travel but will not be able to positively identify the microbe without testing.
If a person's illness is uncomplicated and goes away within a few days, the 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 GI pathogen panel may be ordered. Diarrhea can be sometimes be serious if not diagnosed and treated. 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.
Testing may be also be done 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. The CDC estimates that 30% to 70% of those who travel outside of the U.S. will get a GI infection.
Traditional testing has included a stool culture to identify pathogenic bacteria, an ova and parasite test (O&P) exam to identify parasites, and/or multiple other tests – such as antigen tests. These tests are useful, but some bacteria can be hard to grow successfully in culture, some parasites can be missed if present in low numbers, and testing for viruses is not routinely available. Many tests are also labor-intensive, and it may take 2-3 days or more before a healthcare practitioner has a definitive answer.
If a person has a GI infection caused by a less common bacterium, parasite, or virus not included in the GI pathogen panel, then it will not be detected. Additional tests, such as a stool culture or O&P exam, may be required to help establish a diagnosis.
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.
Is any test preparation needed to ensure the quality of the sample?
No test preparation is needed.
How is it used?
Gastrointestinal (GI) pathogen panels are used to simultaneously test for the presence of multiple disease-causing (pathogenic) viruses, bacteria, and/or parasites in a stool sample and help diagnose an infection of the digestive system (GI tract). Since there are many causes of GI infections, a GI pathogen panel may be used in conjunction with other tests, such as a stool culture or an ova and parasite exam (O&P), to help establish a diagnosis.
The GI pathogen panel detects the genetic material (DNA, RNA) of the microbes that are tested. The number and type of microbes tested depend on the composition of the panel used. While some panels may be limited to testing for a few bacteria that are the most common causes of GI infections, for example, other panels may be more comprehensive and test for a variety of bacteria, viruses, and parasites.
Examples of some of the microbes that might be tested include:
- Viruses, such as norovirus or adenovirus
- Bacteria, such as Campylobacter, Salmonella or Clostridium difficile
- Parasites, such as Giardia or Cryptosporidium
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.
The panels may identify the presence of microbes that a healthcare practitioner might not otherwise suspect and identify co-infections (more than one cause for the infection). This allows treatment (when needed) to be better targeted and to begin sooner. Results of testing may be available within a few hours.
Since the GI panels are relatively new, laboratories and healthcare providers are still in the process of determining how to use them to provide the optimum patient results while being cost-effective. Additional tests, such as stool culture and O&P, may be done if a microbe is not identified by the panel and/or if there is a suspicion of a microbe other than those included in the GI panel.
GI panels are not used to monitor the effectiveness of treatment. Once the specific microbe(s) causing the infection has been identified, a test that is specific for the microbe(s) would be used instead of a GI panel to determine whether treatment has cured the infection. This may be done, for example, when there is an outbreak of foodborne illness. Food handlers would have follow-up testing to ensure that they are no longer shedding the pathogen and will not spread it to others.
When is it ordered?
- Diarrhea with frequent, loose stools
- Blood and/or mucus in the stool in some cases
- Stomach (abdominal) pain and cramping
- Nausea and vomiting
Not everyone who has these symptoms will necessarily have testing done or be treated. In people with healthy immune systems, these infections often resolve with supportive care and without treatment. A GI pathogen panel is more likely to be ordered when a person:
- Has severe symptoms, dehydration, electrolyte imbalance, and other complications
- Is very young, elderly, or has a weakened immune system
- 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
- Is ill and a possible outbreak of food or waterborne illness 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.
What does the test result mean?
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 microbe (co-infection). The following are some exceptions:
- Sometimes, a positive result reflects the presence of bacteria that are present in (colonize) a person's digestive system but do not cause illness.
- The panels detect the presence of genetic material of the microbes and do not distinguish between dead and living ones. Sometimes, a positive result reflects the presence of dead microbes that are not the cause of infection.
- Rarely, a result may be positive when the microbe is not present or may show positive as a different organism because of genetic similarities.
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 that was not tested for. The following are some exceptions:
- When a person has a GI infection caused by a less common bacterium, parasite, or virus not included in the panel, then it will not be detected.
- Microbes are shed into the stool intermittently. A negative result may mean that the microbe causing the person’s infection was not present in the stool at the time the sample was collected.
- Rarely, a person may have a GI infection caused by one of the microbes, but the test does not detect it. The bacteria, virus, or parasite genetic material may be present in very small quantities in the stool sample.
If results are negative and symptoms persist and/or if suspicion of an infection remains high, then other tests may be done to help establish a diagnosis:
- A GI pathogens panel only detects a few of the common parasites. An O&P exam may need to be performed as a follow-up test if a parasite that is not on the panel is suspected. Less common parasites are more frequently encountered when someone has traveled outside of the U.S. but are also found within the U.S.
- A stool culture may be done as a follow-up test to detect bacteria that are not included in the panel.
Is there anything else I should know?
Unlike the stool culture, GI panels do not grow bacteria so there will not be live bacteria available to perform susceptibility testing on to help guide antimicrobial selection. If susceptibility testing is needed, then the bacteria will also need to be cultured.
When a healthcare practitioner has a strong suspicion as to the cause of an infection, then a test for a specific microbe may be ordered instead of a panel. Examples include:
- A person has drunk water from a stream while camping and is likely to be infected with Giardia. A Giardia antigen test may be performed.
- Someone recently completed treatment that involved a broad-spectrum antimicrobial and is likely to have a Clostridium difficile infection. A Clostridium difficile toxin or PCR test may be performed.
Can this test be performed in my healthcare practitioner’s office?
Why would my healthcare provider order additional tests?
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 sanitation 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 touched surfaces should be disinfected, and the person infected should not prepare food or drink for others until the infection is resolved.
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. The Centers for Disease Control and Prevention has an excellent resource for travelers: CDC Health Information for International Travel (the Yellow Book).
Why did I get sick eating something when I travelled internationally, but the locals who ate the same thing did not get sick?
On This Site
Conditions: Diarrhea, Food and Waterborne Illness, Travelers' Diseases, Norovirus
Features: Laboratory Methods: Polymerase Chain Reaction (PCR)
Elsewhere On The Web
Centers for Disease Control and Prevention: Diarrhea: Common Illness, Global Killer
Centers for Disease Control and Prevention: Travelers' Diarrhea
MedlinePlus Medical Encyclopedia: Diarrhea
MedlinePlus Medical Encyclopedia: Viral Gastroenteritis
World Health Organization: Diarrhoea
FoodSafety.gov: Report a Problem with Food
KidsHealth.org: Infections (stomach and intestinal)
Centers for Disease Control and Prevention: Parasites