Whole Genome Sequencing

Going forward, FDA promises to be proactive. “This [genomic] information can be used to help enforce compliance with FDA’s food safety rules and remove contaminated food from the food supply before it results in any illness. This is made possible by collecting samples and cataloging gene sequences from food production facilities,” the FDA announced in a recent Consumer Update.

While few could object to employing WGS during a foodborne illness outbreak, some worry that using it as a monitoring and enforcement tool will open companies to unnecessary risk. “Regulators want food companies to put in preventive controls, look for problems before they occur, and if they find a problem, to fix it,” says David Acheson, MD, founder and CEO of The Acheson Group and a former FDA associate commissioner for foods. The agency’s recent revision proposal of the preventive controls rule for human foods, for example, requires companies to undertake environmental monitoring and product testing for certain high-risk and ready-to-eat foods.

“FDA expects a peanut butter plant to look for Salmonella and if they find it, deal with it,” Dr. Acheson tells Food Quality & Safety magazine. “So if a food company is not actively looking for trouble, so to speak, they will get dinged for not looking.” The quandary, Dr. Acheson says, could come after the peanut butter plant has found Salmonella somewhere in its facility, say in a crack in the floor, and eliminated it. Could FDA obtain the company’s records, its genome sequencing catalog if it has one, and even a sample of the bacteria isolate if retained in a company freezer?

The answer, it seems, is yes to all the above.

FSMA has expanded FDA’s authority for obtaining records related to a specific food article that it “reasonably believes is adulterated and presents a serious health threat to include records relating to any article of food that FDA reasonably believes is likely to be affected in a similar manner,” says FDA spokesman Douglas Karas. FSMA also allows the agency to obtain records related to “any food having a reasonable probability of causing serious illness or death, and any other article of food it reasonably believes is likely to be affected in a similar manner,” he says.

“Once either of the above mentioned circumstances is met, the FDA may request all existing records related to the suspect food and any other food that the FDA believes is likely to be affected in a similar manner that are needed to help determine whether the circumstances that gave rise to the records request exist,” Karas tells Food Quality & Safety magazine. While declining to respond specifically to Dr. Acheson’s hypothetical peanut butter company scenario, Karas noted that in the case of the nSpired recall, “the important point to remember is that the samples were indeed taken by FDA staff during an inspection.”

So what should food companies do, especially those dealing with products having a higher risk of potential pathogenic contamination? “If indeed the FDA did have access to a company’s whole genome sequencing library—even when there is a for-cause inspection—it would raise some serious questions around the wisdom of having such a library,” Dr. Acheson says, because the agency can compare those data with environmental samples taken anywhere in the world. Should the agency find a match, the company will likely find itself in trouble.

And should the company keep a sample of the Salmonella isolate in its freezer, “there’s an untested question of whether or not the FDA can get that isolate,” Dr. Acheson adds. “The FDA can get your records, and they can probably go after the isolate, run it through WGS, and see if it links to an outbreak that happened elsewhere. Obviously, don’t keep the isolate. If you found the Salmonella and got rid of it, it’s gone.”

Networks of Data

FDA and other public health agencies are assembling national and even worldwide networks to share genomic information derived from PFGE and WGS analyses of food samples taken during outbreaks, from contaminated food products, environmental sources, and clinical isolates from infected patients. These sequences are archived and available in a global public database called GenomeTrakr, which currently contains more than 7,000 Salmonella, Listeria, and E. coli isolates. The network of local, state, and federal labs is adding about 500 more isolates monthly. “This is huge,” Dr. Brown says. “As more laboratories contribute to the database, it’s going to be an extraordinary new day in the field of public health and microbiology.”