The Genomic Era Is Here

As part of the outbreak investigation FDA performed WGS on Salmonella isolated from product samples and from clinical samples to determine their DNA makeup. This data helped to more accurately determine which illnesses were part of the outbreak and which illnesses were similar but unrelated. However, FDA also did something else—a retrospective analysis. It performed WGS on about a dozen Salmonella Bareilly isolates stored in freezers from previous Salmonella Bareilly food contamination events. What FDA found was that the Salmonella Bareilly DNA for the samples tied to the 2012 outbreak was very similar to the Salmonella Bareilly DNA isolated from shrimp that came from a processing plant in southwest India several years earlier. In fact, the plant that processed the Nakaochi Scrape was only about five miles away from the plant that processed the shrimp. This observation was significant as it indicated that the paring of genomic information with geographic information might have the potential to be a powerful tool for traceback investigations. This event provided the impetus for creating the GenomeTrakr network and the increased use of genomic information in foodborne outbreak investigations.

As noted by Marc Allard, PhD, the genomics-area coordinator for CFSAN’s microbiology program, “Our freezers are virtually full of Salmonella, Listeria, and other enteric pathogens collected as part of FDA’s own inspection and sampling work. These collections represent a virtual treasure trove of genomic diversity and are invaluable as reference strains in an ever-expanding whole genome sequencing database.”

GenomeTrakr: The Basics

In late 2012, FDA launched its GenomeTrakr network, the first distributed WGS network focused on the development of a highly informative, metadata rich, and fully transparent WGS database of environmental and food-associated enteric pathogens. In short, this database was launched to enhance our ability to use WGS to track foodborne pathogens. The network has created a publicly accessible global database containing the genetic makeup of thousands of foodborne disease-causing bacteria. CFSAN and the National Center for Biotechnology Information (NCBI) at the National Institutes of Health (NIH) collaboratively developed the necessary database and associated software tools. Much of this development continues to make genomic analysis more fully accessible to end-users from federal, state, academic, and industry sectors. Many of the state labs also are members of the Food Emergency Response Network putting them directly into many investigations of food contamination events. Our goal is to further enhance the network by growing the database while also adding more partners from public health, clinical, and regulatory agencies around the country as well as internationally.

The GenomeTrakr was originally comprised of labs in FDA/CFSAN, nine FDA Office of Regulatory Affairs field labs, and public health or agricultural labs from four states including New York, Florida, Washington, and Arizona. Data curation and bioinformatics support was provided by NCBI at NIH. In 2013, GenomeTrakr added labs from Minnesota and Virginia, and in 2014, brought onboard labs in New Mexico, Maryland, and Texas, and another New York lab. In addition, the CDC, USDA’s Food Safety and Inspection Service, academic departments of veterinary science and agriculture, public health laboratories, and several other state-related groups have now acquired WGS technology and are actively collaborating with FDA in the sequencing of food and environmental isolates of Salmonella, Listeria monocytogenes, and Shiga toxin-producing E. coli. Most of these laboratories are equipped with Miseq desktop sequencers, and CFSAN provides technical support for wet-lab and bioinformatic methods and a web-based communication tool for real time data sharing. Currently, sequences are streamed from individual state laboratory Miseqs to a CFSAN computer where they are quality checked and formatted for upload to the GenomeTrakr database. CFSAN is working with NCBI and commercial software vendors to develop simpler tools that will allow individual laboratories to add sequences to the public database directly.

A Paradigm Shift on Two Fronts

Everyone who has seen the potential of WGS applied to food safety microbiology realizes that the technology brings huge paradigm shifts for how enteric pathogens will be tested and how they are tracked back to their source. The first paradigm shift includes using the increased resolution from WGS to intervene earlier in investigations. The second paradigm shift involves the new ability to link isolates across multiple years, whereby low-level contamination events can be linked across geographic time and space. However, there is a third paradigm shift and it relates to how information is shared. The GenomeTrakr database is public, meaning that anyone in the world can freely contribute and obtain information from it.