Michael Doyle, University of Georgia, food safety
Michael Doyle, Ph.D., says today's whole genome sequencing technology is facilitating the development of a cloud-based database to facilitate global traceability of foodborne illness outbreaks.
 

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The U.S. Department of Agriculture (U.S.D.A.), Food and Drug Administration (F.D.A.) and the C.D.C. all collect samples from food manufacturers and, in the case of the C.D.C., from patients suffering from foodborne illnesses. The data from the samples are stored using cloud technology that is maintained by the National Institute of Health (N.I.H.).

“The advantage of that is you can go back to it; it can be queried globally, it’s publicly available information,” Mr. Doyle said. “The beauty of that is that it gives us a global network so that if there is a match between certain strains that come up during an outbreak, sequences that are related to an outbreak in this country can be cross-referenced with the global database to see if there are other isolates of the same type of bacteria that had been submitted to the N.I.H. database to establish a connection, if that were the case.”

In mid-2014, the U.S.D.A.’s Food Safety and Inspection Service (F.S.I.S.) began sampling and using W.G.S. for Salmonella and Listeria monocytogenes and later that year added Shiga toxin-producing E. coli (STEC). In 2015 Campylobacter was added. That same year it began to upload W.G.S. data directly to the National Center for Biotechnology Information (N.C.B.I.) Genomic Database. The number of isolates sequenced each year by F.S.I.S. have gone from about 200 in 2015 to just under 2,000 in 2017. The W.G.S. system used by the F.S.I.S. is made up of 12 sequencers and three F.S.I.S. labs.

In 2013, the C.D.C. started a pilot project that used W.G.S. to track Listeria. In 2018, the program will be expanded to identify Salmonella, Campylobacter and E. coli.

In 2012, the F.D.A. launched the GenomeTrakr, which consists of a network of laboratories sequencing foodborne pathogens and uploading them to a public database.

As more labs are added to the public health network and the W.G.S.-derived fingerprints of pathogens continue growing, the time required to identify outbreaks will continue to decrease and fewer cases will be required to confirm an outbreak. Building a database that is universally accessible and sharing data globally is vital in today’s food industry.

“We are certain that the public health benefit of W.G.S. will only become more evident with every foodborne pathogen’s genomic sequence that is shared,” said a recent blog post on the F.D.A.’s website. Steven Musser, Ph.D., deputy director for scientific operations in the Center for Food Safety and Applied Nutrition wrote, “Already, GenomeTrakr has collected more than 142,000 sequenced strains, has made them freely available to anyone in the world, and continues to demonstrate how a database of this kind is being used effectively for food safety within the United States, and throughout the world. As the food supply becomes increasingly global, the use of W.G.S. in a way that crosses national borders will ultimately help keep us all safe from foodborne illness.”

According to Mr. Doyle, “How do you analyze the data to make it useful for PulseNet system,” was the puzzle researchers and public health officials grappled with in the past. PulseNet is used to investigate bacterial isolates from victims of foodborne illnesses and to collect environmental samples from processing plants. PulseNet is the food safety and traceability system utilized by the C.D.C., F.D.A. and U.S.D.A.

Establishing links between foodborne illnesses and the plant where the food was manufactured before W.G.S., was achieved using pulsed-field gel electrophoresis (P.F.G.E.), which has become somewhat obsolete. According to the C.D.C., P.F.G.E. as well as W.G.S., are laboratory techniques used by scientists to produce a D.N.A. fingerprint for a bacterial isolate, a group of the same type of bacteria.

Both techniques are used, Mr. Doyle said, “to identify clusters of cases of foodborne illness that can be used to identify sources of outbreaks.” By 2018, C.D.C. officials plan to do away with pulsed-field gel electrophoresis (the molecular subtyping technology used prior to the advent of W.G.S.) for Listeria, E. coli, Salmonella and Campylobacter.

W.G.S. technology can be conducted in different manners to achieve the same result: analyzing the sequence of the nucleotides in the genome of bacteria. In the early days of the technology this was made more challenging because accurately testing the entire genome wasn’t possible.

“But we’re there now,” Mr. Doyle said, and improvements continue.

As an example, the C.D.C. is utilizing a modified whole genome technique known as multilocus sequence typing (M.L.S.T.). This technology allows C.D.C. researchers to assign a number to a specific group of isolates and group them into clusters.

Another method of W.G.S. is known as single nucleotide polymorphism (S.N.P., or “SNIP”).

“A nucleotide is the backbone of a genome,” Mr. Doyle said, and W.G.S. technology can detect when there is a different sequence between samples. “When they have less than a certain number of SNIP differences, they are identified as being similar or identical strains.”

When that occurs, and there are a certain number of SNIPS that are associated with different isolates, researchers would identify these as being the same whole genome sequence, “and that’s kind of like a fingerprint,” Mr. Doyle said.