Diagnosing Gastrointestinal Infection with Multiplex Molecular Panels


Each year, according to the World Health Organization, approximately 1.7 billion total cases of gastrointestinal (GI) disease result in about 750,000 deaths among children less than five years old. GI diseases result from infection with bacteria (e.g., Clostridium difficile, E. coli, Shigella), viruses (e.g., norovirus, rotavirus), or parasites (e.g., Cryptosporidium, Giardia), which are often due to contaminated food/water and poor sanitation.

Historically, the laboratory diagnosis of GI infections has relied on a combination of conventional techniques, including microscopy, culture, antigen detection, and individual real-time polymerase chain reaction (rtPCR) assays. While these methods have performed well, they are time-consuming, as bacteria can take three to five days to grow, and they require trained health care technologists to perform the testing and interpret the results.

Recently, several multiplex molecular assays have been developed for the detection of GI pathogens directly from clinical stool samples. These panels allow for the detection and identification of up to 20 pathogens in as little as one hour. A recent review published in the Journal of Clinical Microbiology focuses on the FDA-cleared multiplex molecular panels for the diagnosis of diarrheal disease and highlights issues related to test performance, result interpretation, and cost-effectiveness of these molecular diagnostic tools.

Matt Binnicker, Ph.D.

“Microscopy lacks sensitivity and is often difficult to interpret. More recently, tests designed to detect bacterial, viral, or parasitic antigens in stool samples have been developed, but these tests have been shown to lack sensitivity and specificity,” said Matt Binnicker, Ph.D., Director of the Clinical Virology Laboratory at Mayo Clinic in Rochester and author of this review. “Due to the limitations of these conventional tests, there has been a lot of interest in molecular tests for the diagnosis of infectious diarrhea.”

In general, molecular tests have been shown to be as sensitive or, in many instances, more sensitive than conventional assays like bacterial culture. Molecular tests, such as rtPCR, have been used in past years in the diagnosis of infectious diarrhea, but until recently, these have mainly been offered as individual tests. This means that a provider would have to order multiple tests if the differential diagnosis was quite broad.

In the past two to three years, multiplex molecular tests have become commercially available, allowing for laboratories to test for up to 20 different pathogens (bacteria, viruses, and parasites) all in one test.

“Several of the new tests are called ‘sample-to-answer’ assays, meaning that the laboratory simply needs to add the clinical sample to the test, hit ‘go,’ and then the results are available in as little as one hour. This is a major benefit to the testing laboratory, as it reduces hands-on time and turnaround time for reporting results,” said Dr. Binnicker.

While all patients with diarrhea do not need a rapid test result, some patients, such as immunocompromised individuals (e.g., bone marrow transplant recipients), need a result as quickly as possible. The rapid result allows health care providers to make quick decisions regarding treatment and also on whether or not it’s necessary to isolate the patient to prevent the spread of disease in the hospital.

According to the study results, the multiplex molecular tests detected more pathogens in stool samples compared to routine tests. Also, the multiplex tests were able to identify mixed infections (those that include at least two pathogens in the same sample) in more cases than routine testing.

These results show that routine tests underestimate the number and types of infectious pathogens that cause diarrhea. In some instances, this is due to lower sensitivity of the routine test. However, in other situations, a test that has been used for years (e.g., viral culture) does not work for a particular type of microbial pathogen that is a common cause of infectious diarrhea.

“A specific example of this is norovirus and sapovirus—two viruses for which we previously did not have specific tests. These two viruses do not grow in viral culture, and there were no individual rtPCR assays or antigen tests available to us for diagnostic testing. But during the study, we found that 5 to 10 percent of stool samples were positive for these viruses. These would have been missed by routine testing,” said Dr. Binnicker.

While the new multiplex tests are beneficial to the laboratory diagnosis of GI infections, there are challenges with how health care providers will interpret the test results and how the results will impact patient care.

“Providers ordering these new multiplex tests will be getting more ‘positive’ results than they have in the past, and a big question centers around how these results will be interpreted. Not all causes of infectious diarrhea can, or should, be treated,” said Dr. Binnicker. “Ultimately, we need to study how these results impact the care and outcomes of patients.”

For more information on Mayo Medical Laboratories’ Gastrointestinal Pathogen Panel, PCR, Feces, visit MayoMedicalLaboratories.com.


Kelley Luedke

Kelley Luedke

Kelley Luedke is a Marketing Channel Manager at Mayo Clinic Laboratories. She is the principle editor and writer of Insights and leads social media and direct marketing strategy. Kelley has worked at Mayo Clinic since 2013. Outside of work, you can find Kelley running, traveling, playing with her kitty, and exploring new foods.