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.
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Explore this issueDecember/January 2015
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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.
About Ted Agres
Ted Agres is an award-winning writer who covers food safety regulatory and legislative issues from the nation’s capital in the Washington Report column. He has 40 years of experience in reporting on issues such as health policy, medical technology, and pharmaceutical development. He holds an MBA from Johns Hopkins University and a bachelor’s degree from the University of Chicago. He enjoys playing the piano, amateur radio, and paintball. He lives in Laurel, MD. Reach him at email@example.com.