Opinion: Whole-Genome Sequencing Is a Double-Edged Sword for the Food Industry

If FDA finds Listeria in a food facility or in its review of a company’s environmental monitoring records, then FDA often times responds aggressively. Sometimes, some would argue, too aggressively. It is likely that all food companies would likely test more frequently for Listeria in food facilities, and work harder to find Listeria, if FDA did not take such a critical view of zero-tolerance positive testing results.

This is a major reason why the approach of other countries might be better in the long run. Canada, Australia, and the European Union (via its laboratory Guidance Document), all use an allowable limit of <100 CFU/gm for Listeria monocytogenes.

While the focus of this article is FDA, it is important to note that for dual-jurisdiction plants, USDA quietly watches, and sometimes follows the lead of, FDA. USDA conducts its own environmental sampling for enforcement purposes, but for the most part the agency seems to keep an eye out for what action FDA is pursuing. USDA often asks companies for their FDA data with regard to Listeria, even if the company is not legally obliged to share the data with them.

Why Having Listeria Data Is Good—and Bad

It is also important to note that this article is not advocating a cavalier attitude toward Listeria. A company cannot get a “hit” or “two” and then think they can take some action to avoid the “third strike.” This is indeed a road to perdition, not only for the company but for public health. Rather, the company needs to have a scientifically justified corrective action plan in place, and a very active environmental monitoring program for the organism.

That said, FDA risk becomes even worse if a company has WGS data, and doubly worse should the company know that the sequence of their Listeria sample matches a sequence in FDA’s GenomeTrakr database. This would mean that the company knows of a linkage, and one which may or may not implicate the company. Should FDA be told, or should the company solve the problem and move on?

Let’s say that the company generated its data (and linked an environmental sample to a retail food or, worse, a clinical sample from a patient hospitalized in their immediate vicinity) under a protected status, e.g., attorney-client privilege. The company would seem justified in not sharing the data with FDA. But what if there is a public health problem down the road, and FDA uncovered that same data after the fact?

Almost no company wants to be in either pressure-cooker, i.e., having data that could escape into the public domain, or having data which could be discovered later. What is the result? The result is that few companies want to use WGS under these circumstances, no matter how helpful the data might be to public health protection.

Of course, this is the same reason food companies have their microbiology labs test only for Listeria spp. and not directly for Listeria monocytogenes (Lm). Again, as soon as the Lm notation appears, “zero tolerance” comes to mind. And, once that “Lm” designation is in the corporate files, it could be devastating for the company even if the company is taking all appropriate efforts to eradicate the bacteria from the premises.

The Sword: Double-Edged, or Damocles?

This clash of paradigms is clearly a double-edged sword. FDA wants to encourage use of WGS to help minimize food safety risks to the public, but by its policy execution, it may be driving the industry away from a proven scientific tool that could achieve that very end.

My call to action, then, is for FDA to allow a better path for companies to use WGS testing, without having to face the consequences of an initial positive result. Perhaps, human isolates could be stripped from a custom public database that could be accessed by food companies. If this were made available, it seems likely that a significant number of additional companies would begin using WGS to solve contamination challenges in their facilities.