Laboratory testing has many flavors. Let’s take the basic example of respiratory testing. You may recall being at a clinic after feeling a sore throat. At a point in the visit, a provider would take a swab of saliva and leave the rom for a few minutes. The test, in this case an antigen test, may come back as “Negative”. But then you may hear a provider say “we’re sending it to the lab and will call you with results. The lab portion of testing will probably be done with Polymerase Chain Reaction (PCR) to confirm the result of the antigen test.
After respiratory testing, one of the main disease areas where samples are taken from symptomatic individuals is gastroenteritis; an infectious disease caused by several viral, bacterial, and parasitic pathogens that exist in the digestive system. For gastroenteritis, stool samples can be tested by a handful of methods. Although there is antigen testing for enteric pathogen detection, most stool samples are sent for testing at a laboratory.
Stool culture has been used for enteric pathogen detection for many years. After pressing a swab from the stool sample into the culture plate, the plate is placed in a controlled environment to enable microbial growth. This process can take up to 72 hours. A lab technician will then try to observe growth to confirm an infection.
Free infographic: Gastrointestinal Tract Infections: Get the facts
Testing technology by case
While antigen and culture testing are low cost and reliable, other technologies, mainly PCR, have been adopted in recent years to transform how laboratories see stool testing for infectious gastroenteritis. PCR testing enables superior sensitivity and specificity because it searches for traces of the pathogen at the molecular level. PCR is so sensitive that it may detect genetic traces of the pathogen after signs of infection have disappeared.
Different flavors. Similar performance.
PCR is not ONE test. It’s a technology. Today, laboratories have the flexibility to test a stool sample for a specific pathogen infection. When outbreaks happen, like the Norovirus outbreak reported at an elementary school in Utah, USA, it makes sense for labs to target a single pathogen in their PCR workflow. * Especially if a larger volume of samples is coming from the location of a Norovirus outbreak. Time-to-results is also key in an outbreak. PCR takes an average of three hours to return results.
Because infectious gastroenteritis can be caused by multiple viral, bacterial, and parasitic pathogens, there are times when it makes sense to test for multiple possible pathogen infections at the same time. To be clear; this does not mean that a lab must run the same sample through different single-target workflows. PCR can come in multiplex or broad pathogen detection formats.
Multiplex testing is the next level after single-pathogen testing. On-market multiplex assays can contain markers for generally up to five targets. This means that at the end of the PCR run, the sample will have been tested for multiple pathogen infections.
Multiplex assays are usually built by pathogen category. An example would be a multiplex panel focusing on foodborne illness. This multiplex panel may include bacterial targets like Salmonella **, Campylobacter ***, and Shigella ****; all very common pathogens causing infectious gastroenteritis, most likely from consuming infected food. Other multiplex panels may focus on grouping viruses and parasites. Multiplex testing allows the detection of co-infections. Meaning the sample contains genetic traces of two or more microbial pathogens.
The upper level of the pyramid of PCR testing for infectious gastroenteritis is broad pathogen testing. This format can do simultaneous testing of over twenty pathogen targets in the same stool sample. This format can be adopted by laboratories with high sample volumes as some on-market solutions can test hundreds of samples per day. Because broad testing can sometimes detect viruses, bacteria, and parasite targets in the same panel, many of the stool samples can come from crowded hospital facilities, nursing homes, or child day care centers. In these types of facilities, detecting the cause of a gastrointestinal infection outbreak can be considered an emergency given that individuals housed in those places can be very young, elderly, or in an immunocompromised situation.
Path forward
PCR testing is a useful technology that can enable faster, accurate, and specific results when testing stool for infectious gastroenteritis caused by enteric pathogens. While the technology is available, it is key for laboratories to not only implement PCR for stool testing, but to also partner with specialists who will help them select, set up, train, and most importantly be a real resource to their business and laboratory operation.
Let’s discuss your enteric pathogen detection plans.
References
* Gubbi, M. (2023). Norovirus outbreak forces Grand County schools to close, expected to spread. FOX 13 News Utah (KSTU). https://www.fox13now.com/news/local-news/norovirus-outbreak-forces-grand-county-schools-to-close-expected-to-spread
** Questions and Answers | Salmonella | CDC. (n.d.). https://www.cdc.gov/salmonella/general/index.html
*** Questions and Answers | Campylobacter | CDC. (n.d.). https://www.cdc.gov/campylobacter/faq.html
**** Questions & Answers | Shigella – Shigellosis | CDC. (n.d.). https://www.cdc.gov/shigella/general-information.html