The Genomic Era Is Here

FDA has created and applied in real time public health use, a U.S.-based open-source whole genome sequencing (WGS) integrated network of state, federal, and commercial partners. The network, known as “GenomeTrakr,” represents the first distributed genomic food shield for identifying and tracing foodborne outbreak pathogens back to their source. In only its third year, GenomeTrakr is already enhancing investigations of outbreaks of foodborne illnesses and compliance actions, enabling more accurate and rapid recalls of contaminated foods, and monitoring of preventive controls effectively in the food manufacturing environment. The resulting public genomic database of foodborne pathogens can support dramatically investigators ability to link specific food products, processing sites, and farms, providing valuable insight into the origin of the contaminated food. GenomeTrakr essentially creates a searchable, digital high-resolution fingerprint of the complete genetic make-up of individual pathogens, permitting otherwise indistinguishable bacteria to be easily separated and identified.

“This [database] is clearly the most powerful approach yet developed for tracking and tracing pathogens, and we expect it to have a very significant positive impact on food safety,” says Steven Musser, PhD, deputy director for scientific operations at FDA’s Center for Food Safety and Applied Nutrition (CFSAN). Considering the limited number of FDA food inspectors and the global nature of the food supply, the development and continual building (adding sequences and metadata) of GenomeTrakr is essential.

The food safety impacts of this network are impressive. Its current membership includes 30 public health, food safety, and academic laboratories from federal, state, and international stakeholders. The network has already shown great promise in enhancing the traceability of food and feed supply contamination events at the national level including Salmonella and Listeria monocytogenes. Moreover, WGS of microbial pathogens is now supplanting traditional microbiological analytics with rapid single data output summaries for antimicrobial resistance profiling, detection of high risk virulence profiles, and general identification strategies that supersede serological, phenotypic, and classical culture testing making the technology critical for an effective public health response to bacterial outbreaks.

An Important Role for WGS

Recent devastating outbreaks associated with consumption of fresh-cut produce have reinforced the notion that foodborne disease remains a substantial global challenge to public health. Mitigating foodborne illness, at times, seems an intractable challenge. One longstanding problem is the ability to rapidly identify the food associated with the outbreak being investigated. Despite the best efforts of food safety experts, the tools available for tracking foodborne outbreaks were sometimes too slow or uninformative to effectively pinpoint the source of the outbreaks. With the limitations of traditional subtyping methods, federal public health and food safety laboratories are exploiting WGS to delimit outbreak scope, traceback to point source, and make early predictions about important traits that a pathogen may harbor such as antimicrobial resistance. Highly parallel robotic genomic sequencers can sequence the DNA of a bacterial pathogen in a matter of hours. When coupled with validated, analytical bioinformatic pipelines such as the one established by FDA’s CFSAN, accurate and stable genetic changes can be identified that can distinguish foodborne outbreak strains down to the source level including specific farms, food types, and geographic regions.

Eric Brown, PhD, director of the division of microbiology at CFSAN, compared the application of WGS for delimiting foodborne outbreaks to the impact that the Hubble Space Telescope had on our understanding of galaxies. “Can you imagine how astronomers felt the day the Hubble sent back its first pictures of the universe? This is exactly how we felt in 2009 when we applied WGS for the first time to a Salmonella-induced foodborne outbreak.”

Numerous recent published examples illustrate the ability of WGS to discern high-resolution genetic relatedness of otherwise indistinguishable isolates. Proof of principle studies have been undertaken using the technology at numerous public health institutes both nationally and internationally. So much so, the success of WGS for rapid source tracking of pathogens is now well documented. In 2012, 425 individuals in the U.S. became sick from ingesting food that contained either Salmonella Bareilly or Salmonella Nchanga. Through traditional epidemiology methods, the illnesses were ultimately linked to a frozen raw yellowfin tuna product known as Nakaochi Scrape, which had been imported from India. (Nakaochi Scrape is tuna backmeat that is scraped from the bones of tuna and may be used in sushi, sashimi, ceviche, and other similar dishes.)