Laboratory Evaluation of Infectious Diarrhea [Hot Topic]

Bobbi Pritt, M.D.
Bobbi Pritt, M.D.

Gastrointestinal infections can be caused by bacteria, viruses, and parasites. Most of these infections are due to viruses and are self-limited. However, some infections can cause severe and even life-threatening infections, therefore laboratory testing is warranted. Mayo Medical Laboratories offers a new gastrointestinal pathogen panel that detects 22 viral, bacterial, and parasitic pathogens in only one hour. Bobbi Pritt, M.D., explains the testing algorithm to ensure appropriate use of this new test.

Presenters and Credentials:
Bobbi Pritt, M.D., Director of the Clinical Parasitology Laboratory at Mayo Clinic in Rochester, Minnesota




Our speaker for this program is Dr. Bobbi Pritt, Director of the Clinical Parasitology Laboratory at Mayo Clinic, Rochester, Minnesota. Dr. Pritt introduces a new Gastrointestinal Pathogen Panel and outlines an algorithm for Laboratory Testing for Infectious Causes of Diarrhea.

Thank you Dr. Pritt for presenting with us today.


Thank you, Cara, for that introduction. Today I will be discussing the laboratory evaluation of infectious diarrhea and introducing a new gastrointestinal pathogens panel.
Before we begin, I would like to note that I have no disclosures.

Utilization Messages

I’d like to first start with some test utilization messages. As you view this presentation, consider the following important points regarding gastrointestinal pathogen testing:

  • First, it is important to note that most patients with infectious causes of diarrhea will get better on their own, and therefore testing and treatment are not necessary.
  • Instead, testing should generally be reserved for patients with prolonged symptoms or those with risk factors or warning signs for severe disease. We will discuss what these factors and signs are later on in the presentation.
  • Finally, the new gastrointestinal pathogen panel is a rapid and cost-effective option in situations in which multiple tests would otherwise be performed.

Gastrointestinal Pathogens - General

Now let’s talk about some of the general features of gastrointestinal pathogens. There are a number of bacteria, viruses, and parasites that can cause gastrointestinal infections. Most infections in the United States are due to viruses and are self- limited. However, some infections can cause severe and even life-threatening infections, especially in immunocompromised hosts.

Gastrointestinal Pathogens - Testing

Traditional laboratory testing for these pathogens consists of exams performed on stool specimens. They commonly include:

  • Bacterial stool culture for several organisms such as Salmonella, Shigella, and Campylobacter species
  • The so-called “ova and parasite exam” for parasitic protozoa and worms
  • Antigen detection methods for Cryptosporidium species, Giardia duodenalis, rotavirus
  • And PCR tests for norovirus and adenoviruses that cause diarrhea

These tests range in price and can take several days until a result is produced.

New Gastrointestinal Pathogens Panel

Mayo Medical Laboratories will now be offering the GIP / Gastrointestinal Pathogen Panel on Feces. This test is manufactured by Biofire Diagnostics and is named the FilmArray Gastrointestinal Panel. It is cleared by the FDA for in vitro diagnostic use and detects 22 viral, bacterial, and parasitic pathogens in only 1 hour.

The left-hand image on this next screen shows what the instrument looks like. Each patient specimen is put in a separate cartridge, shown in these images on the right. The instrument then takes the specimen through a series of reactions including nucleic acid extraction and PCR. The specimen moves through 1 chamber to the next in this small cartridge, shown here, using microfluidic channels.

Bacterial Analytes

This next slide shows the bacteria that are detected by the gastrointestinal pathogen panel. Note that these are the major bacteria that are detected by routine bacterial stool culture. Clostridium difficile toxin and Shiga toxin are also detected. Therefore, this portion of the panel may replace the need for bacterial culture and 2 separate PCR assays in some patients.

Viral Analytes

There are also several viruses that are detected with this panel, including some such as sapovirus and astrovirus that we did not routinely test for in the clinical laboratory. These viruses are responsible for a large number of cases of infectious diarrhea, and therefore being able to detect them for certain patients is an important advantage of this multiplex panel. This portion of the panel may, therefore, replace the need for several virus specific PCR or antigen detection assays.

Parasiticl Analytes

Finally, here are the 4 parasites that are detected by this panel. These are the 4 main parasites that cause diarrhea in the United States.
This portion of the panel may, therefore, replace the need for the ova and parasite exam, special stains for Cyclospora and Cryptosporidium and some parasite antigen detection tests.

New Gastrointestinal Pathogens Panel

This test is relatively expensive, but it is a cost-effective option when multiple tests were otherwise going to be ordered. It is also significantly faster than traditional bacterial culture, taking only 1 hour from start to finish.

Laboratory Testing for Infectious Causes of Diarrhea

Because it’s not the best test for every scenario, we have created a new algorithm to guide microbiology testing for infectious causes of diarrhea. The entire algorithm is shown on this slide. This algorithm is also available for download from our website at Because there is a lot of information here, let’s go through each component of the algorithm, first starting on the left-hand side.

This first pathway addresses the fact that patients with Community-acquired diarrhea, less than7 days duration WITHOUT warning signs or risk factors for severe diseases do not generally require testing. The foot notes here define exactly what we mean by warning signs and risk factors for severe disease. We also briefly mention here how an individual test for shiga toxin may be indicated in children with diarrhea during the summer months.

If diarrhea persists for 7 or more days, then the patient would enter the middle pathway and testing by the gastrointestinal pathogen panel is indicated. We also mention here ova and parasite testing should be considered in travellers with more than 2 weeks of symptoms.

Now let’s move to the middle pathway of our algorithm. For patients with community-acquired diarrhea <7 days duration OR travel-related diarrhea OR diarrhea with warning signs or risk factors for severe disease, we can move directly to the gastrointestinal pathogen panel since it tests for all of the common bacterial, viral, and parasitic cases of diarrhea. If testing is positive, then no additional testing is required unless the clinical picture indicates. However, if the initial testing is negative and diarrhea persists, then additional testing should be considered. This may include a standard stool culture to detect bacteria such as Aeromonas which is not part of the GI pathogen panel and Giardia antigen testing to account for the sporadic release of Giardia in stool. The microsporidia PCR may also be indicated in immunocompromised patients. If the ova and parasite exam or OAP has not already been performed, then performing at this time might also be indicated.

The last pathway in our algorithm addresses the special situation of patients with healthcare-associated diarrhea or a history of recent antibiotic use. In this case, only the Clostridium difficile toxin PCR test is indicated. Clinical judgement can then be used to guide the need for additional testing.

So here again is our full algorithm.

One last comment is that pathogen-specific tests can be used in outbreak scenarios with a known organism, such as tests with Cyclospora, Cryptosporidium, Giardia and bacterial stool culture.

Thank you for joining me today to learn about laboratory testing for infectious causes of diarrhea.


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This post was developed by our Education and Technical Publications Team.