Food Genomics Is Going Global

In PulseNet, the CDC-run network that connects public health and food regulatory agency laboratories nationwide, WGS this year has replaced PFGE as the primary method for detecting and investigating Listeria outbreaks. In the coming months, WGS will also be used for Salmonella, E. coli, and Campylobacter, says Heather A. Carleton, PhD, leader of the bioinformatics team at CDC’s Enteric Diseases Laboratory Branch.

Partially driving this change are the local and state clinical labs that increasingly supply data to PulseNet from culture-independent diagnostic tests (CIDTs), such as immunoassays and nucleic-acid amplified tests. While CIDTs are cheaper, faster, and easier to use than WGS to detect bacteria in sick patients, they are unable to determine the DNA subtype (“fingerprint”) or other characteristics necessary for PulseNet to detect outbreaks, track antibiotic resistance, or monitor disease trends.

Because of this, “PulseNet is preparing for a future without isolate culture,” Dr. Carleton told an IFSH symposium on food safety and high-throughput sequencing in May. First, researchers will employ a technique called core genome multilocus sequence typing, which can determine a bacterial isolate from the internal fragments of a small number of “housekeeping” genes. Second, they will use shotgun sequencing to identify and subtype both known and unrecognized pathogens. “The latter approach will leapfrog pathogen discovery and likely the identification of known and novel pathogens causing outbreaks of unknown etiology,” Dr. Carleton explained.

The U.S. government has also been upgrading public health laboratories that contribute data to PulseNet by equipping facilities with WGS equipment and training personnel. So far, more than 100 scientists in 46 states have been PulseNet trained and certified, Dr. Carleton said. “By the end of 2018, we anticipate that WGS will be the main PulseNet surveillance tool for detecting dispersed outbreaks caused by Listeria monocytogenes, Shiga toxin-producing E. coli, and Salmonella,” Dr. Tauxe said.

Further, the analytic methods have been harmonized with those used in FDA’s GenomeTrakr food testing network, Dr. Tauxe added. GenomeTrakr currently contains more than 200,000 pathogen genome entries in its open-source portal, housed at NIH’s NCBI, with more than 5,000 isolates being sequenced and added monthly. FDA is currently working to expand GenomeTrakr’s distributed network of laboratories internationally and make its reference database more widely available in other countries.

Other current food genomics efforts include characterizing pathogens from CIDTs using metagenomics (cataloging all the species in an environmental sample) and using rapid WGS platforms to mine pathogen adaptations that directly contribute to preventive controls requirements for industry. “Taken together, it is apparent that the role for WGS in microbiological food safety continues to grow as it integrates more and more into pathogen analytic workflow,” says Eric Brown, PhD, director of FDA’s Division of Food Microbiology.

WGS Limits and Challenges

The extent to which WGS and similar technologies will truly mitigate foodborne illnesses remains to be seen. As the ability to identify outbreaks has improved due to new technologies, “paradoxically, the number of outbreaks may increase since we are now able to identify problems that had previously been invisible to us,” Dr. Gottlieb said in a recent statement.

Indeed, improvements in pathogen and risk detection technologies are partially responsible for the more than doubling in the number of food recalls during 2004-08 compared to 2009-13, according to an April 2018 report from USDA’s Economic Research Service. As CDC’s Dr. Tauxe puts it, as WGS matures, “more dispersed outbreaks will be detected and investigated, and that on average, each will involve fewer cases.”

But improvements in WGS and genetic testing are not substitutes for traceability, as illustrated by this year’s E. coli outbreak linked to romaine lettuce. Researchers used WGS to link the strain of E. coli O157:H7 that sickened at least 210 people and killed five in 36 states to lettuce from the Yuma Valley region of Arizona. The bacterium, however, was never actually found on lettuce in fields or in commerce. Indeed, only after the outbreak was declared over in late June did Dr. Gottlieb announce that canal water used for irrigation appears to have been the source of contamination. How E. coli got in the water remains a mystery.