New diagnostic tests for common foodborne pathogens such as Salmonella, Campylobacter, and Escherichia coli may hinder the ability of public health officials to detect multistate outbreaks. The problem is an inability to trace contamination to its source.

In 2009 Alicia Cronquist, an epidemiologist with the Colorado Department of Public Health and Environment noticed that several rural clinics in her state had switched from traditional laboratory tests that relied on growing a culture to rapid nonculture tests. In the past, when patients were suspected of having certain foodborne illnesses, doctors routinely sent a stool sample to a laboratory, which detected a range of potential bacterial culprits. (Some foodborne infections, like Listeria, are diagnosed with blood tests.) An isolate, or sample of the bacterial colony at fault, would then be forwarded to local, state or federal officials, who had the DNA tested to determine the organism's specific strain. The telling DNA sequence, or "fingerprint," was entered into the PulseNet system so that public health officials could see if samples from other newly diagnosed patients matched the information in the database. Analysis of when and where people contracted an infection of that specific strain can help lead to the source of contamination, allowing investigators to remedy the situation.

But, Cronquist says, over the course of a year, a clear shift in the types of tests being run in local labs had resulted in much less information being shared with her department. "We saw our surveillance data changing, and by 2010, almost 15 percent of total case reports were using the nonculture tests," she says.

The new tests do have a lot going for them. They provide quicker results to the physician and patient. They are often less expensive and, in some cases, may not require a stool sample at all. What is more, some of them can spot pathogens that the culture-based tests do not and diagnose more infections.

Tennessee's state epidemiologist Timothy F. Jones notes, for instance, that culture tests for E. coli look for the 0157 strain, which is among the bacteria that produce the Shiga toxin; that strain infamously accounted for the outbreak of food poisoning from spinach this year. "With the new rapid tests," he says, "we can actually detect the whole class of Shiga-toxin producing bacteria. The rapid test is detecting additional bacteria we would have missed before."

But adoption of the new tests has meant that health officials, like Cronquist, are not always getting the isolate required to do the DNA fingerprinting that is needed to help identify a source of contamination, such as E. coli in lettuce or salmonella in raw spinach.

In that way, Jones says, "these rapid tests put us back where we were when we didn't have the ability to do [DNA] fingerprinting."

The trend is particularly worrisome because other ways of protecting the public from foodborne illnesses are also stumbling. According to the Centers for Disease Control and Prevention, one in six Americans (or 48 million) become sick from a foodborne disease each year and 3,000 die. A study released late last month by the U.S. Public Interest Research Group indicated the problem is not improving in part because laws like the Food Modernization Safety Act continue to languish in the White House's Office of Management and Budget. And a federal monitoring program—the U.S. Department of Agriculture's Microbiological Data Program, which tested produce for pathogens—began to be shut down on November 12.

Jay M. Lieberman, medical director of infectious diseases for Quest Diagnostics, which serves approximately half the physicians and hospitals in the U.S., says that the wide adoption of the new tests means that public health officials will need to come up with new ways to monitor and respond to new outbreaks. For example, health officials will need to work with the labs to figure out how to get an isolate or find another way to characterize pathogens.

"By connecting cases, we can find problems in the food supply we might not have found," says John Besser, deputy chief of the CDC's Enteric Diseases Laboratory Branch. "The challenge for us is to develop a test that will provide all the information that we need without going to the isolate step. That's a significant challenge, but we all believe it's doable."

At present, no one is working on developing a test that can help public health officials trace outbreaks, though several companies continue to develop the new nonculture tests, including Abbott Laboratories, BD, Cepheid and Luminex. Besser says he expects laboratories to quickly adopt them when they become available. For the labs, the new tests mean quicker, cheaper results requiring fewer highly trained staff.

Although the problem of tracking pathogens related to foodborne illness is new, similar concerns were raised when nonculture tests were developed for detecting the sexually transmitted disease gonorrhea.

"When it comes to gonorrhea, almost all testing is done by nonculture techniques now," explains Quest's Lieberman. In response to that sea change, the CDC set up a surveillance project that allows it to monitor trends in a new way. At specified labs in 28 cities across the U.S., cultures are run and isolates taken from samples collected from the first 25 men found to have urethral gonorrhea each month. With that limited data set, public health officials can still track outbreaks while also allowing for broader use of the new nonculture tests.

Although that procedure has worked well for gonorrhea, whether it will also work for foodborne illnesses remains an open question.

An irony of all of this, says the CDC's Besser, is that the new tests for foodborne pathogens may be better than the old ones, but if they disrupt the public health systems, they "could result in a lot more people getting sick. That is the unintended consequence."