Should your food company embrace Whole Genome Sequencing (WGS) as a tool to help solve potential persistence issues in your food facility? The jury is still out, but not for long.

As FDA continues to fight its War Against Pathogens, the agency routinely deploys investigators into food facilities to conduct expansive swab-a-thons. During these swab-a-thons, the agency collects anywhere from 100 to 200 environmental samples from various locations, including food contact surfaces, and then tests those samples for the presence of Listeria monocytogenes or Salmonella.

When pathogens are found, the company is issued an FDA Form 483. If pathogens are found on food contact surfaces, the company is expected to destroy any affected product on hold and/or recall any product that may have shipped. When the percentage of pathogens is high, the agency will, in many cases, pursue additional enforcement activities, such as the issuance of Warning Letters.

In all cases, FDA conducts WGS on positive samples. Each sample receives a precise genetic signature that is uploaded into the GenomeTrakr database, where it will reside forever, branding the company for life.

When the agency returns to conduct another swab-a-thon (which it will), and finds the same strain, FDA will conclude that the strain is “resident.” In these cases, in addition to receiving another form 483, the company may find itself floating in Warning Letter territory. And, in the months that follow, the companies targeted will often be forced to spend hundreds, if not millions, of dollars attempting to demonstrate to the agency that they were successful in eliminating the persistent WGS strain.

On a parallel track, FDA encourages food companies to use WGS on their own to identify resident strains in their facilities. The implicit message from FDA is that, when it comes to WGS, there is nothing to fear.

Unfortunately, however, what FDA says and what FDA does are two entirely different things. In some cases, when food companies embrace WGS in good faith to help identify and then solve persistence issues, the agency has unfairly used the company’s own WGS data against them.

Imagine, for instance, a scenario where a company is using WGS to identify and eliminate a potentially resident strain. During these efforts, the company identifies the resident strain on multiple occasions, and then uses the locations where the strain was found to identify and eliminate the source. Months of subsequent testing by the company proves that the resident strain has been eliminated.

But, what if FDA visits, sees the company’s WGS data confirming historical persistence, and rather than embracing the company’s more recent data showing that the stain is gone, instead focuses on the company’s WGS data to prove that the company likely still has a problem? And, what if this happens, even though FDA’s own testing data (i.e., another swab-a-thon) similarly fails to detect the previously resident strain?

If we want to talk about problems, I see this as becoming a huge problem for industry, and it’s going to be a huge problem for FDA. The agency will never convince industry to embrace WGS (and I will never recommend that my clients embrace it), if the agency’s unwritten policy is to use a company’s WGS data against it — especially when it’s used by the agency to contradict more favorable and recent testing data.

I would thus, in the strongest possible terms, urge FDA to quickly and publicly encourage its regulators to find ways reward food companies for using WGS to solve persistence issues, and not punish them with it, as if it were a weapon. If the trend of punishment continues much longer, I predict there will be no turning back, and industry’s verdict will be to shun WGS forever.

WGS: Weaponized Genome Sequencing

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