Michael Doyle, Ph.D., former director of the Center for Food Safety at the Univ. of Georgia
Michael Doyle, Ph.D., says today's whole genome sequencing technology is facilitating the development of cloud-based database to enhance global traceability of foodborne illness outbreaks.

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The US Dept. of Agriculture (USDA), Food and Drug Administration (FDA) and the Centers for Disease Control (CDC) all collect samples from food manufacturers and, in the case of the CDC, 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 (NIH).

“The advantage of that is you can go back to it; it can be queried globally, it’s publicly available information,” Doyle says. “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 NIH database to establish a connection, if that were the case.”

In mid-2014, the USDA’s Food Safety and Inspection Service (FSIS) began sampling and using WGS forSalmonellaandListeria monocytogenesand later that year added Shiga toxin-producingE. coli (STEC). In 2015Campylobacterwas added. That same year it began to upload WGS data directly to the National Center for Biotechnology Information (NCBI) Genomic Database. The number of isolates sequenced each year by FSIS have gone from about 200 in 2015 to just under 2,000 in 2017. The WGS system used by the FSIS is made up of 12 sequencers and three FSIS labs.

In 2013, the CDC started a pilot project that used WGS to trackListeria. In 2018, the program will be expanded to identifySalmonella,CampylobacterandE. coli.

In 2012, the FDA 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 WGS-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 WGS will only become more evident with every foodborne pathogen’s genomic sequence that is shared,” said a recent blog post on the FDA’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.”

Musser says, “As the food supply becomes increasingly global, the use of WGS in a way that crosses national borders will ultimately help keep us all safe from foodborne illness.”

According to 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 CDC, FDA and USDA.

Establishing links between foodborne illnesses and the plant where the food was manufactured before WGS, was achieved using pulsed-field gel electrophoresis (PFGE), which has become somewhat obsolete. According to the CDC, PFGE as well as WGS, are laboratory techniques used by scientists to produce a DNA fingerprint for a bacterial isolate, a group of the same type of bacteria.

Both techniques are used, Doyle says, “to identify clusters of cases of foodborne illness that can be used to identify sources of outbreaks.” By 2018, CDC officials plan to do away with pulsed-field gel electrophoresis (the molecular subtyping technology used prior to the advent of WGS) forListeria,E. coli,SalmonellaandCampylobacter.

WGS 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,” Doyle says, and improvements continue.

As an example, CDC is utilizing a modified whole genome technique known as multilocus sequence typing (MLST). This technology allows CDC researchers to assign a number to a specific group of isolates and group them into clusters.

Another method of WGS is known as single nucleotide polymorphism (SNP, or “SNIP”). “A nucleotide is the backbone of a genome,” Doyle says, and WGS 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,” Doyle says.