On the Trail of Salmonella

The current sequencing platforms used by FDA investigators—they have two—allow them to sequence eight genomes a week. A typical outbreak investigation would require the sequencing of 40-50 genomes in all. “That takes a couple of months, which is far too long,” said Dr. Musser. “And it costs $800 to $1,000 per sequence we run, which would be about $40,000 in total. That’s too much for many clinical labs.”

But times are changing. “It looks like that technology will soon become available for about $100 or less per strain, and it will take about half a day to do the analysis,” he said. “At that point, it will become very practical for people to do in clinical labs, food testing labs, and regulatory labs. Within five years, I can envision laboratories routinely using this tool.”

But it may take longer than that to integrate such an approach into real-time outbreak investigation at the federal level, Dr. Musser cautioned. “I may be able to show how this works in my lab, or several others, but integrating it into a national system like PulseNet requires a lot of coordination and validation. These labs have been doing things the same way for a number of years, and it’s going to take a long time to change. But ultimately, I think this is one of the technologies that will form the basis of future surveillance activities.”

And it’s likely that Salmonella outbreaks may be among the first for which next-generation sequencing is used in real time. “If you have something like E. coli 0157:H7 in lettuce or produce, those tend to be rapid. They quickly come and go. We wouldn’t be able to do a meaningful analysis in one of those cases,” Dr. Musser said. “But if you have something like the Salmonella in peanut butter or eggs that went on for months and months, then we could use this technology right now to help define the outbreak.”

Whole genome sequencing may also become the technology of choice for compliance. Recently, Dr. Musser’s team worked with the FDA’s Office of Compliance to trace a sample taken from the environment of a plant production floor to a specific food sample in the plant. “This allows the Office of Compliance to go beyond a PFGE link and establish a more defined relationship between an environmental isolate and a processed food—in this case, a Salmonella strain in animal treats at a plant in the Midwest,” said Eric Brown, PhD, acting director of the ORS division of microbiology.

That’s a very valuable application, said Michael Doyle, PhD, Regents Professor of food microbiology and director of the Center for Food Safety at the University of Georgia in Griffin. “Many processing plants have resident Salmonella and Listeria strains. If you do the sequencing and isolate strains, then, should a plant have an outbreak or just do some routine retail testing and find the strain that matches a particular fingerprint, you can trace it back to the specific source of the contaminant.”

But the technology may not be quite as powerful a fingerprint as the FDA thinks, Dr. Doyle cautioned. “Bacteria mutate. More information has to be gathered relative to how powerful the assay is with the same strain after many transfers, once it’s been in the field a few years,” he said. “It’s too early to know if there are going to be a lot of mutations that would foul the system, or if there are other issues that would lead to misidentification of the source. They’ve had good results so far, but time will tell.”

It won’t be a magic bullet, agreed John Besser, PhD, deputy chief of the enteric diseases laboratory branch at the CDC. “It’s not like DNA fingerprinting in humans, which could be used to establish guilt or innocence of a crime. While the methods are similar—or even identical—the problem is somewhat different. As pathogens multiply in the environment and are passed from person to person, and from person to animal, animal to food, food to person, and back again, they will change in ways we don’t fully understand. In some cases, the DNA sequence match will be very significant, but in others, it won’t.”