PCR testing has become increasingly important for gastrointestinal pathogens. These tests are also key in surveillance to detect what kinds of pathogens affect a particular population, and as a frontline tool in detecting foodborne and waterborne outbreaks.
We spoke to Davidson Hamer, MD, FACP, FIDSA, FASTMH, FISTM, professor of global health and medicine at the Boston University of School of Public Health and Chobanian & Avesidian School of Medicine, and adjunct professor of nutrition at the Tufts University Friedman School of Nutrition Science and Policy, about how molecular tests such as PCR are used in this disease area right now, and what their role could be in the future.
What gastrointestinal pathogens are most common cause of outbreaks in the U.S.?
Norovirus, nontyphoidal Salmonella, and Campylobacter jejuni are all common. There are a host of others, too. Listeria occurs less commonly, but it has a much higher risk of death associated with it. We also see an entire range of different E. coli strains, including enterohemorrhagic E. coli, which are toxin-producing.
How are these infections transmitted?
They’re mostly foodborne, but some are also waterborne and even human-to-human. We see it rarely, but there’s also animal-to-human transmission.
Who is at higher risk of gastrointestinal infections?
To start, younger children are at higher risk because they don’t have immunity, or their immune systems have not yet developed. Older adults are also at risk. In general, anybody with any underlying disorder that predisposes them to more severe diarrhea, like someone with uncontrolled HIV, is also at risk, as are those who are immunocompromised, like transplant patients. Anybody with an immune system deficit is going to be at higher risk.
Do tests based on PCR improve clinician’s approach to care?
In the U.S., there are many hospitals and some bigger group practices that use multiplex PCR to diagnose diarrheal infections. It’s really revolutionized how we test these patients.
In the past, testing required either cultures or enzyme immunoassays for certain organisms, and it was a lot harder to make a diagnosis. A lot of times, we still do not make etiological diagnoses, but increasingly we do. The advantages of these assays are that they are very sensitive, and they’re multiplex, so they’ve helped us offer a specific diagnosis to a lot more patients than we could in the past. Some of these multiplex panels have 22 different pathogens all on one panel. Some of them break them down by category. For example, our hospital breaks them down into bacterial, viral, and protozoa. If you think something is really likely to be viral, you might limit your test to those.
That’s in high-income countries. In low-income countries, PCR tests are sometimes used for field surveillance, or trying to understand the etiology of diarrhea in different populations. But this testing is relatively expensive, so it’s done less frequently. On other hand, people are increasingly using multiplex PCR platforms for diagnosis of intestinal parasites, and trying to define at the population level what the relative prevalence of a parasite is.
These tests are more sensitive than classic methods and are so sensitive that you might find people have a very small amount of a parasite. What does that mean? It’s not quantitative most of the time. Stool exams quantify how many eggs per gram of stool to get an idea of the intensity of infection. That’s hard to do with PCR unless you have quantitative PCR, but even that has limitations.
When used for surveillance, PCR tests help increase the likelihood of identifying a specific pathogen, but multiplex PCR tests are used much more on a clinical basis. For certain diarrhea pathogens in the U.S., there’s required reporting, where hospital laboratories connect to the department of public health and share their data. An etiological specific diagnosis will be made if there’s a reporting requirement for state-level surveillance systems that then report to national surveillance systems.
How do molecular tests impact outbreak response?
Molecular tests can facilitate more rapid identification of potential outbreaks. Say you’re looking for Campylobacter. This is a fastidious organism: You need certain media and days to grow it. If you get a stool sample and run a multiplex PCR assay, you will have results within hours, or within a day at most. If there’s an outbreak going on, you might get an inkling of what pathogens are responsible, faster.
But tying it together — actually knowing it’s an outbreak — is a different thing. There need to be a number of cases or some aspect of surveillance that allows you to connect the dots to say “Oh, we’ve seen so many cases of this, this is above the baseline, looks like we have an outbreak.”
That’s easy if, for example, a group of people at one church dinner all got sick. But there’s a disconnect if it’s an imported food from another part of the world that is sent to 10 different states and there are sporadic cases. That takes a little bit more work to identify.
PCR might be how the first few cases are identified, but if it’s bacterial, the next step is going to be culture and then possibly sequencing. Now, laboratories often perform whole genome sequencing in order to identify a common link among specific pathogens in geographical locations.
What is the impact of implementation of PCR-based tests for GI pathogen detection on public health?
For individual clinicians, it’s become an important and helpful tool to identify potential causes more rapidly for diarrhea in individual patients. Because that data is usually fed into our public health systems, it may also be helping to strengthen them in terms of capacity to identify specific pathogens and to identify outbreaks earlier.
How do you think this technology will progress over the next 10 years?
It’s likely that the tests will become less expensive, so we’ll be using them more widely for clinical purposes. Some institutions may also perform active population surveillance by taking samples from all patients presenting to emergency rooms with diarrhea to understand what they have.
Lower costs could make molecular testing available in more low-income countries, where there’s a much greater burden of foodborne and waterborne pathogens in particular.
One of the limitations for PCR is resistance testing. A PCR test can tell you which bacteria or virus is present, but if you really want to understand the bacteria’s resistance patterns, you need to grow it.
Many places now have a process for stool specimens that are PCR-positive for Salmonella or Listeria. The laboratory will try to grow the organism in a specialized culture. If they can grow it, they can perform antibiotic susceptibility studies on it, and they potentially have it for sequencing, too.
You’ve worked with the World Health Organization on maternal, newborn, and child health. What is a pressing issue in that realm right now?
In the U.S., Listeria is an important pathogen to know in pregnancy because it can lead to pregnancy complications, more severe disease, and potentially death. Pregnant women are at greater risk of having a more complicated course of Listeria. Identifying Listeria and making sure there’s early and effective treatment for pregnant women who are affected is extremely important.
Overuse of antibiotics for childhood diarrhea is another major problem. Many types of watery (nonbloody) diarrhea resolve on their own with just oral rehydration, yet in many parts of the world they are treated unnecessarily with antibiotics. This is one of many drivers of antibiotic resistance worldwide.
Jen A. Miller is a freelance journalist who lives in Audubon, New Jersey. +Twitter: @byJenAMiller