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

Other techniques are far quicker and can be equally effective at the end game. For example, there is still value in using some of the older techniques such as PFGE and MLVA. Even easier and cheaper, although less informative, is using well-proven standard microbiological techniques to assay for Listeria (e.g., FDA BAM Chap 10). These standard micro tests have widespread proven use in environmental monitoring programs to “seek out and destroy” pathogens in a food facility, regardless of whether those organisms are transient or resident. WGS can then be used sparingly as a means of continued surveillance, ensuring that strains are or are not taking up residency.

The “time and cost” value equation of WGS, however, is still a reason why food companies do not routinely use WGS. Do note that over the past two years, turnaround time and costs have been significantly reduced (e.g., a five-business day turn for Listeria WGS is about $500). However, this value equation is either still not good enough, and/or companies are still saying that the tests are “too long and too costly” as a shield for not wanting to enter FDA’s territory.

FDA and Whole-Genome Sequencing

Clearly FDA sees WGS as a savior; euphemistically speaking, if use of the technology prevents even one illness, then its use is warranted. And, since the technology is available, an informed public would most likely want FDA to use it. So, it may be that as time progresses, public and political pressure may push WGS forward independent of food safety professionals wanting to do so or not.

Having WGS in its toolkit also allows FDA to trumpet what it is doing: WGS is a well-defined technology, and the public can understand it (especially when the public watches crime shows that use DNA testing, or consumers use DNA sequencing for ancestry determination purposes). FDA will continue to use these tools to find organisms, such as Listeria monocytogenes, which can cause significant adverse health consequences or death to the small populations that are highly susceptible to the organism’s effects.

This is also why FDA continues to maintain a “zero tolerance” policy for Listeria monocytogenes. This is not the case worldwide (e.g., Canada and Australia), but it is the position FDA has taken. Granted, the rationale for this is to protect the public health, but it also allows FDA to conduct deeper investigations into a food company’s practices and, when resident pathogens are detected and linked to human illness, initiate the enforcement actions the public would expect them to take.

Why FDA Is the Biggest Reason for Industry Not Using Whole-Genome Sequencing

Setting aside consideration of whether or not FDA should be spending so much time enforcing a zero-tolerance principle, one would surmise that if FDA allowed for some tolerance of Listeria, the food companies might begin using the technology much more widely. But, as everyone knows, they are not.

Why?

FDA has issued a Draft Guidance for Industry: Control of Listeria monocytogenes in Ready-To-Eat Foods. Although still in draft form, the document essentially offers a “three strikes and you’re out” approach for detection of Listeria species in a food production plant. In other words, if there is a new identification of Listeria on a non-food contact surface (for example), this is not the end of the world. Intensified sampling and/or cleaning might be mandated, but production does not necessarily need to halt.

Many people have praised this approach, and for good reason: The odds that an environmental sample is positive for Listeria monocytogenes are generally low, as are the odds of a consumer being exposed to a sufficient number of organisms to become compromised (since the vast majority of people eating the food are healthy). Moreover, many products require further preparation and heating by consumers prior to consumption. Thus, even when Listeria may be present, the risk to consumers is often generally low.