From The Editor | July 25, 2017

Is Whole Genome Sequencing The Fast Lane To Safer Food?

Sam Lewis

By Sam Lewis, associate editor
Follow Me On Twitter @SamIAmOnFood

Is Whole Genome Sequencing The Fast Lane To Safer Food?

Earlier this year, Food Online Editorial Advisory Board (EAB) member Omar Oyarzabal, Ph.D., penned a column on Whole Genome Sequencing (WGS) in the food industry, its benefits, and some of the challenges it’s presenting. In his column, Dr. Oyarzabal clearly offered his stance on WGS, backing it with both scientific and anecdotal evidence. Intrigued by Dr. Oyarzabal’s stance, I wondered what other food industry experts thought about WGS. I reached out to two members of Food Online’s EAB to learn more.

Rick Gilmore, Global Food Safety Forum
WGS is a much-needed technological advancement for food safety regulators. As former Director of the Global Food Safety Forum (GFSF), Eric Wu, pointed out in an article in FOCUS (GFSF’s newsletter), regulatory and surveillance detection systems are still highly dependent on pieces of DNA, such as pulsed-field gel electrophoresis (PFGE) to determine origins of pathogen outbreaks.

Rick GilmoreSince the information from matching a fragment of DNA is incomplete, the standard tests sometimes miss linked cases, provide false leads, or often are imprecise. Along comes WGS and introduces a rapid, cost-effective, laboratory process that determines the complete DNA sequence of an organism's genome. The FDA is using this technology to perform basic foodborne pathogen identification during outbreaks of food borne illnesses. The advent of WGS brings new efficiencies to detection and a default insurance for reliable, safe food.

From a security standpoint, WGS is an effective tool to find the origin of contamination that is used on a multi-state basis by Pulse-Net and is a huge step forward in food fraud detection and food safety.

Presently, the main drawback I see with WGS is infrastructure. An international network of laboratories does not yet exist to comprehensively administer and fully utilize the technology. Another red flag comes down in the arena of trade, primarily due to the diversity of detection systems international suppliers use in the global supply chain. Foreign supplier systems most often do not reconcile with WGS lab systems.

Finally, WGS can trace pathogens back in time when there may have been a regulatory determination that closed a case based on the technology in use. Then, a subsequent outbreak with the use of WGS can find the same pathogen in the closed case as in the new outbreak. To minimize these risks, it looks to me as if regulators have to synchronize the rules with widespread use of WGS.

Jennifer McEntire, Ph.D., United Fresh Produce Association
As a food microbiologist, I’m enamored with WGS. It allows for high fidelity and precise fingerprinting of an organism like nothing we’ve seen before. The power of this technology has regulators and public health officials excited too, and for good reason. But, there is a risk to getting ahead of ourselves and drawing conclusions from a small data set using a technology that’s still in its early stages.

Right now, the concern is this: someone gets listeriosis and the WGS pattern is a match to an environmental swab the FDA grabbed from a facility last month. Is this a smoking gun? For sure, the regulators may be interested in visiting that facility! But, what if that sequence was just traveling through the facility, and really “lived” elsewhere (e.g., on the farm, or in an ingredient that was used in the facility)? The limited dataset available using WGS wouldn’t reveal this. And even if it did, because, for example, the database had another matching isolate from a farm, do you tie this illness to the farm? How widespread is this pattern? Are Listeria 10 feet away from the sample site going to have a different sequence? Is there a different sequence 10 meters away? 10 acres away? Or 10 miles away?

Scientists are still in the process of collecting information to help answer these questions. Until they do, we hope that investigators will view WGS as one piece of the investigative puzzle, but not draw conclusions prematurely. This field will evolve and our understanding of how to use and interpret WGS will advance quickly, so stay tuned!

WGS is quickly becoming an important weapon in the fight against foodborne illness. But, like all up-and-coming and developing technologies, its full scope must be realized. Will both industry and regulatory bodies adopt the technology? How will gaps in bodies using the technology vs. bodies not using the technology be gapped? Will there be long-term negative impacts in the regulatory realm, such as double jeopardy? And, as Melanie Neumann, J.D, M.S., pointed out in her column, Whole Genome Sequencing: Affirmative Or Adverse Outcomes For Food Safety Management?, who will own the data generated by the technology and how it will be used? Right now, it seems there are more questions than answers.