Whole Genome Sequencing

Whole genome sequencing (WGS) or next-generation sequencing is an emerging technology that allows scientists to map the genetic sequence of pathogens and other organisms with such precision that they can distinguish between different strains of a bacterium and even slight variations by geography within the same strain. As the cost of gene sequencing equipment continues to decline, FDA and state public health laboratories will increasingly use WGS to investigate outbreaks of foodborne illnesses. They will store the sequenced genomic information in large databases, which will be publicly accessible nationally and internationally.

But FDA will employ WGS not only during outbreaks; the agency announced it will also use WGS to analyze samples from food companies taken during routine inspections in order to monitor compliance with the Food Safety Modernization Act (FSMA) and other regulations. Thus, WGS may become a two-edged sword—one that can quickly pinpoint the source of an outbreak, preventing illness and potentially saving lives, but also a dagger pointed at the hearts of food companies when no outbreak has occurred.

For years, pathogen testing and bacterial subtyping has been performed using pulsed-field gel electrophoresis (PFGE), an older and less sensitive technology. Among other limitations, PFGE cannot differentiate certain strains of Salmonella or distinguish between samples of isolates associated with previous contaminations. WGS, on the other hand, is far more reliable and sensitive. By pairing a pathogen’s genomic information with geographic information systems, a mapping technology, and applying the principles of evolutionary biology, investigators can identify the root source of contamination—a powerful tool given the rise of food products containing ingredients imported from different countries.

“What genome sequencing allows us to do with food traceback is unprecedented,” says Eric Brown, PhD, director of FDA’s Division of Microbiology. “It’s like upgrading from an old backyard telescope to the Hubble.” PFGE has begun to show its age, adds Brian Sauders, PhD, a senior food bacteriologist at the New York State Department of Agriculture & Markets. “PFGE is like looking at a globe of the Earth with only seven labeled continents, while WGS provides better than Google Earth map resolution of the entire world surface complete with names of many key and detailed features and a searchable database with zoom-to-point of reference capabilities,” Dr. Sauders wrote in an Association of Public Health Laboratories blog post.

Solving Outbreaks

The U.S. FDA and the CDC used WGS to help solve two widely publicized multistate outbreaks in 2014. The first involved an outbreak of Listeria monocytogenes. Reports of listeriosis had been reported as early as August 2013. Investigators first used PFGE to identify cases that may have been part of the outbreak using data archived in PulseNet, a network run by the CDC that connects public health and food regulatory agency laboratories performing molecular surveillance of foodborne infections. After the Listeria strain had been isolated from patients, investigators used WGS to definitively link it to Hispanic-style cheese produced by Roos Foods of Kenton, Del. In early 2014, Roos issued a recall and FDA suspended its facility registration.

“This was the first time we used whole genome sequencing to match the environmental and food samples with the CDC’s human biological samples and it helped support the agency in taking regulatory action,” says Dr. Brown. “We were able to suspend food production at a facility to minimize an outbreak.”

FDA also used WGS to identify a multi-state outbreak strain of Salmonella Braenderup and link it to almond and peanut butter manufactured by nSpired Natural Foods Inc. in Ashland, Wash. Recalled brands included Arrowhead Mills, MaraNatha, Trader Joe’s, Whole Foods, Safeway, and Kroger. In both cases, FDA inspectors had collected pathogen samples during routine inspections of production facilities; in the case of Roos Foods, they also had collected samples from finished food products.

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.”

As good as WGS may be, FDA and other agencies are seeking even more powerful pathogen detection tools. In October 2014, FDA and CDC announced food safety “challenges” in which they are offering cash prizes to private sector scientists, academics, entrepreneurs, or innovators who submit the best ideas for “applying novel methodologies to foster revolutionary improvements in foodborne pathogen detection.” FDA’s Food Safety Challenge targets “cutting-edge techniques” to significantly speed the detection of Salmonella “with identification to the subtype/serovar level in minimally processed fresh produce.” Of special interest are concepts to accelerate or eliminate sample preparation and/or enrichment in the testing process. The contest “is a means to consider approaches (and possible solutions) through others’ eyes, with technology that we may not have considered applicable,” explains Palmer Orlandi, PhD, senior science adviser at FDA’s Office of Foods and Veterinary Medicine.

“Some of the greatest innovations are born from ‘outside-the-box’ thinking and this is what we hope to achieve. The prize purse [$500,000] doesn’t hurt as an added incentive, either,” Dr. Orlandi wrote in an FDA blog posting. The submission deadline was Nov. 9, 2014. Up to five finalists will receive $20,000 each and will be eligible to snag the remainder of the $500,000 jackpot when the winner is announced March 5, 2015.

Agres is a freelance writer based in Laurel, Md. Reach him at [email protected].