A common disclaimer supplied by public health officials while in the midst of a foodborne illness outbreak investigation goes something like this: “We’re doing our best to find the food source of the outbreak, but it’s important to remember that the majority of outbreaks are never traced back to a source.”
In other words, most outbreaks go unsolved because it’s just too difficult to pinpoint a food source given the constraints of technology and resources. While that may still be the case, more public health agencies are beginning to adopt technology that will help close the gap between the number of solved and unsolved outbreaks.
That technology is whole-genome sequencing (WGS), a method of identifying organisms such as bacteria and other pathogens by analyzing their entire DNA sequence. By comparison, pulsed-field gel electrophoresis (PFGE), the decades-old industry-standard epidemiological technology, looks at less than 1 percent of a pathogen’s genome.
The superior accuracy of WGS allows for much greater certainty when trying to solve relatively small outbreaks, or, even better, outbreaks that have already come and gone.
In recent months, three high-profile foodborne illness outbreaks — which included at least three deaths — have been solved retroactively, thanks to WGS.
In August 2014, the technology was credited with determining the food source of an outbreak that killed two people and hospitalized another three.
Routine testing by the U.S. Food and Drug Administration found the bacteria Listeria monocytogenes on a sample of bean sprouts from Wholesome Soy Products Inc.. Through WGS, that sample was connected back to five samples from sickened individuals in Illinois and Michigan, two of whom had died from their illness.
Until WGS technology came on the scene, such outbreaks would have likely gone undetected, said Martin Wiedmann, Ph.D., professor of food science at Cornell University.
With WGS, health investigators are able to identify the exact organism causing illnesses down to its complete DNA sequence. PFGE, by comparison, allows for more uncertainty because it can’t identify the organism with nearly as much precision.
Wiedmann uses an analogy of a dog-bite investigation when illustrating the precision of WGS compared to other technologies.
“It’s like if three people were separately bitten by a German Shepherd, and they decided, ‘OK, it’s probably the same dog that bit each person’ — that’s like using PFGE,” he said. “But with whole-genome sequencing, it would be like getting blood samples from the victims and analyzing the DNA to see if they all match the same dog.”
Also in August 2014, Oasis Brands Inc., recalled several cheese and dairy products due to Listeria contamination after routine FDA testing found contamination. In that outbreak, WGS retroactively connected one death and four illnesses to the products in Georgia, New York, Tennessee and Texas.
WGS also connected six Salmonella illnesses to nut butter produced by nSpired Natural Foods Inc. from between January and May 2014.
The truth is that, over time, food processors will know that if a pathogen is found in their facility, the genome will be sequenced and checked against a database to look for connected illnesses, Wiedmann said.
Ultimately, he said, that knowledge will be a good thing for both food producers and consumers.
“It’s more important than ever that producers have stringent sampling plans in place to make sure organisms are there and taking care of them,” Wiedmann said. “Many of them are already doing this. We’re starting to see processors improve their sampling game and preventing more outbreaks.”