Traditional methods for diagnosing foodborne illness infections such as Salmonella, Campylobacter and E. coli involve cultivating patient samples in an artificial nutrient medium. But tests that don’t require isolates from pure culture are becoming increasingly popular. There are different kinds of culture-independent diagnostic tests (CIDTs), but the type of that public health folks think will really overtake culture tests are syndrome-based panels that can test for multiple agents at once. There are five such tests currently licensed for gastrointestinal illnesses, with more expected to follow in coming years. These CIDTs are particularly attractive to clinicians because, in addition to testing for many different pathogens, they can be faster than traditional methods and can detect bugs that would otherwise be difficult to find. They also don’t need as much equipment or highly trained technicians, so they can save labs money. “It represents a major departure from what we used to see and we’re anticipating: that there’s going to be very rapid adoption,” says Dr. John Besser, deputy chief of the enteric Diseases Laboratory Branch within the Centers for Disease Control and Prevention’s Division of Foodborne, Waterborne, and Environmental Diseases. Despite all the positives, there is real concern about what CIDT adoption will mean for public health surveillance. By definition, these types of tests don’t result in any bacterial or viral isolate, despite the fact that PulseNet, the current government pathogen database, is isolate-based. PulseNet is the national network of public health laboratories that use pulsed-field gel electrophoresis (PFGE) to connect illnesses that have the same pattern, or DNA “fingerprint.” Information from PFGE tests are uploaded to CDC’s central server, where they can monitor trends nationwide and track illness clusters that may indicate an outbreak. This is how most most distributed outbreaks of salmonellosis, Shiga toxin-producing E. coli (STEC) disease, and listeriosis are identified in the U.S.; but without isolates, public health can’t detect the clusters. “The irony is that the adoption of new tests that are arguably better for patient management may actually be a negative for our ability to detect and investigate clusters of disease,” Besser says. Using the example of STEC, a CIDT can tell you if the pathogen is present or not and possibly if it has toxin genes Stx1 or Stx2. “PFGE will tell you if it’s one of a thousand different strains in our database, and it’s that level of specificity that we use to connect cases together,” Besser says. “Without that, the cases pretty much all look alike.” “We haven’t seen a drastic reduction in the number of isolates coming in yet, but it’s something we are anticipating,” said CDC’s Jean Whichard at a National Antimicrobial Resistance Monitoring System (NARMS) conference in August. While they may not be able to be logged in PulseNet, positive CIDT results that were confirmed by culture are included in the Foodborne Diseases Active Surveillance Network’s (FoodNet) statistics every year. But in the network’s most recent foodborne illness report card, the agencies identified an additional 1,487 reports of positive CIDTs that were not confirmed by culture, either because the specimen was not cultured or because a culture did not yield the pathogen. FoodNet decided to start tracking these tests in 2013 to better understand their uptake, calling them “a trend that will challenge the ability to identify cases, monitor trends, detect outbreaks, and characterize pathogens.” How to Proceed The currently-licensed tests do not result in the destruction of the original patient sample, so one temporary solution to the need for an isolate is reflex testing — proceeding to culture after a CIDT shows a positive result. Another option is to send the positive sample on to a public health laboratory for them to do the isolation. The problem there is that the state and local public health agencies don’t have the resources to do this. Furthermore, it slows down the process of obtaining detailed information about the pathogen when a lot of the success in detecting and solving outbreaks comes from the ability to do these things quickly. The longer it takes to get information into PulseNet, the longer it takes to identify illness clusters, and the longer it takes for health departments to contact patients about what they ate and where. The more time that passes between a patient consuming a contaminated meal and the epidemiological interview, the less they’re going to remember. “While we’re probably going to have to go the route of reflex culture because we don’t have any alternative, it’s not optimal,” Besser says. Many food safety experts are excited about whole-genome sequencing because of the increased level of detail it can provide. CDC and the U.S. Food and Drug Administration are in the process of implementing the technology. The program began with Listeria and has so far sequenced hundreds of clinical and environmental isolates and begun real-time sequencing of every Listeria isolate across the country. But, as it’s currently used, whole-genome sequencing also requires an isolate, so it’s also threatened by changing testing practices in clinical labs. The long-range solution for testing is to develop methods for PulseNet that are themselves culture-independent. “Those new tests will almost certainly be DNA sequence-based,” Besser says. By developing whole-genome sequencing, he adds, the agencies are putting together the infrastructure that will be needed for culture-independent tests, taking advantage of the current technology to get more accurate detection of illnesses and building a large library of bacterial genomes that can help in the development of these new CIDTs. “Whole genome sequencing is the first phase of our long-term plan,” Besser says. In September, CDC launched a “No-Petri-Dish” Diagnostic Test Challenge , which offered a $200,000 prize to encourage researchers to straintype and characterize Shiga toxin-producing E. coli (STEC) without using culture-based methods. The contest is open until Nov. 30 and the agency will notify the winner by mid-December.