This was originally published Nov. 25 in the APHLTech Blog.
In a prior APHLTech blog post (NGS in Action: FDA’s Genome TRAKR Network), Victor Waddell of the Arizona State Public Health Laboratory described the newly formed network of laboratories formed by the U.S. Food and Drug Administration (FDA). Known collectively as Genome TRAKR, the member laboratories perform whole genome sequencing (WGS) on bacterial foodborne pathogens isolated primarily from food and environmental sources.
On Sept. 1, 2013, the Centers for Disease Control and Prevention (CDC) began a partnership with the FDA Genome TRAKR network to utilize the network to conduct WGS of all Listeria monocytogenes collected from reported human illness cases in the United States. This effort leverages public health resources to evaluate and potentially move this promising new technology forward for more routine use in public health laboratories nationwide.
While WGS has been used retrospectively, it has rarely been used to guide public health action during an active outbreak investigation and never for routine surveillance. The cost of this technology has been rapidly declining to the point where it is approaching the cost of pulsed-field gel electrophoresis (PFGE), and a recent initiative was announced at CDC to explore advanced molecular methods. It was welcome news to state public health partners that such a proof of concept evaluation of real time use of WGS for public health surveillance was planned.
PFGE is the current method that the PulseNet network for foodborne disease surveillance relies on for tracking foodborne illness in the U.S. While PulseNet has used this technology reliably for almost 20 years, the technology has begun to show its age when compared to more rapid WGS methods that provide orders of magnitude higher quantifiable genetic data. PFGE is like looking at a globe of the Earth with only seven unlabeled continents, while WGS provides better than Google Earth map resolution of the entire world surface complete with names of many key and detailed features and a searchable database with zoom to point of reference capabilities.
One barrier to making use of this information is the shear enormity of the volume of data and the computing capacity necessary to analyze it. Fortunately, FDA has already brought several bioinformatics specialists on board and is also working closely with the National Center for Biotechnology Information (NCBI) to provide a data repository and analysis tools.
On average, approximately 600-800 cases of listeriosis are reported in the U.S. with concomitant PFGE typing by PulseNet labs. While two enzyme (AscI/ApaI) PFGE diversity of L. monocytogenes is quite high, it can be difficult to completely assess the relatedness of indistinguishable PFGE patterns from human illness, food, and environmental isolates without detailed epidemiologic exposure data. While a large number of small listeriosis clusters are routinely identified by PFGE, the majority occur without identification of a confirmed source. With the increased discriminatory power of WGS applied, it is hypothesized that the new technology will be useful in pointing out clusters that are more likely to have epidemiological significance.
According to Cheryl Tarr of the CDC Enteric Diseases Branch, as of Nov. 7, 2013, there were 328 clinical isolates of Listeria monocytogenes that were whole genome sequenced through the Genome TRAKR network. Peter Gerner-Smidt, PulseNet Branch Chief, plans to present some preliminary data on this surveillance at the upcoming APHL-sponsored Integrated Foodborne Outbreak Response and Management (InFORM) meeting in San Antonio, TX, being held Nov. 18-21, 2013. Their key interest at this point is how well WGS identifies both the clusters identified by PFGE and also how well WGS can discern cases that are truly epidemiologically related versus those that are indistinguishable from each that are not epidemiologically related. Stay tuned for coverage of the InFORM meeting and updates on this surveillance project in future blog posts.© Food Safety News