NEW YORK (GenomeWeb) — Researchers from Cornell University and the New York State Department of Health working with the US Food and Drug Administration have demonstrated the accuracy and practicality of whole-genome sequencing in resolving outbreak clusters of Salmonella enterica in the public health and food safety setting.
The team's study, published this month in Emerging Infectious Diseases also serves as an example of the fitness of whole-genome sequencing for food safety and outbreak tracking of food-borne pathogens more broadly as the FDA gears up to embrace NGS as a standard tool in its regulatory activities.
The FDA has been engaged in a program to research the use of whole-genome sequencing of food-borne pathogens for several years. More recently it has been coordinating a pilot project, under which state and federal public health agencies are sequencing pathogens collected from outbreaks, contaminated food products, and environmental sources. The pathogens are then archived in an open-access genomic reference database called Genome Trakr.
The Cornell and NY State team involved in the newly published study of WGS for S. enterica surveillance is one of the several participants in this pilot.
"There are some pathogens, food borne in particular, that show very little genomic diversity," Henk den Bakker, the study's first author told Clinical Sequencing News this week.
"In this case in Salmonella enteritidis, about 25 percent of isolates fall into the same type or cluster, according to [pulse-field gel electrophoresis]," he explained. "So we wanted to use this as a test case.
Marc Allard, the FDA's research area coordinator for genomics and another author of the study, told CSN that the study was a good project because it coordinated and integrated with the FDA's interest in sequencing highly clonal pathogens like S. enterica, which are irresolvable through current subtyping approaches like PFGE.
"The study is significant because it’s the beginning of the states starting to use this technology and saying it's helpful and improves their ability to regulate foods that have these particular bacterial contaminants," Allard said.
"Now there are three state labs — New York since recruited Minnesota and Washington — all sequencing S. enterica to expand this study, contributing in real time to Genome Trakr," he added
In the New York team's study, den Bakker and his colleagues combined a retrospective and a prospective analysis to demonstrate the accuracy of whole-genome sequencing compared to standard approaches in resolving outbreak clusters, as well as to establish that the approach could be practical in real time in the setting of a large public health lab.
Studying retrospective samples from a 2010 outbreak, and then looking at additional prospective samples collected over four months in 2012, the researchers first showed that WGS could accurately identify the isolate subtypes previously defined by PFGE, and that sequencing also identified additional outbreak-associated isolates that PFGE had missed.
"It was quite nice because we almost doubled the number of cases associated with that known outbreak. We initially only knew about patients associated with a long-term care facility, but we showed that there were other people involved, even cases outside of the greater NYC region, so that was quite convincing," den Bakker said.
According to the authors, the study showed that WGS "vastly improved detection of clusters of common PFGE types and outbreak resolution" over PFGE, the current standard.
Additionally, the study demonstrated the feasibility of detecting outbreaks in near real time in the context of public health food safety activities. According to den Bakker, the speed at which the Cornell food safety lab can sequence and analyze isolates has only increased since the study began nearly two years ago.
"Back then it was as real time as we could go at that moment," he said. "We had to put a lot of time into library prep and things like that, and we were kind of pioneering the methods to analyze the data in real time. But in the meantime people have shown that … you can go [straight] from a single culture to whole-genome sequencing. It's much more rapid."
The New York team has not been alone in pioneering WGS as a tool for food-borne pathogen surveillance. Other participants in the FDA's Genome Trakr pilot include a number of FDA field sites and state health labs in Massachusetts, Ohio, Atlanta, Arkansas, California, Colorado, Washington, and Maryland.
According to the study authors, other retrospective studies have demonstrated improved resolution using whole-genome sequencing to resolve clusters in outbreaks of a range of pathogens, including C. difficile, M. tuberculosis, and S. aureus. But whether the approach could be adaptable to the larger public health laboratory setting had previously been an open question.
Since the group's S. enterica study was conducted, den Bakker said that the Cornell lab's throughput in WGS analysis has increased significantly, and the lab can now sequence isolates in an appropriate time frame for the food-safety regulatory environment.
In the recently published study, the lab used the Ion Torrent PGM but has since switched to the Illumina MiSeq in joining the FDA's Genome Trakr pilot.
According to Allard, the benefits and potential of next-gen sequencing have become apparent across the FDA's pilot sites. "We are in the second year of this, and it's clear to everyone that this is going to be fully adopted," he said.
WGS has already been useful to the regulatory mechanism for other pathogens, Allard said. In March, for example, the FDA used WGS to close down a cheese company in Delaware, matching the Listeria strain in the product to a strain found in one of the processing facilities.