GenomeTrakr Database 2015: WGS Network for Foodborne Pathogen Traceback

Timme, Ruth

Wednesday, August 3, 2016

America's Center - St. Louis

Ruth Timme, U.S. Food and Drug Administration, College Park, MD

Maria Sanchez Leon, U.S. Food and Drug Administration, College Park, MD

Marc Allard, U.S. Food and Drug Administration-CFSAN, College Park, MD

Maria Hoffmann, U.S. Food and Drug Administration-CFSAN, College Park, MD

Charles Wang, U.S. Food and Drug Administration-CFSAN, College Park, MD

George Kastanis, U.S. Food and Drug Administration, College Park, MD

Tim Muruvanda, U.S. Food and Drug Administration, College Park, MD

Errol Strain, U.S. Food and Drug Administration-CFSAN, College Park, MD

Justin Payne, U.S. Food and Drug Administration, College Park, MD

Arthur Pightling, U.S. Food and Drug Administration, College Park, MD

Hugh Rand, U.S. Food and Drug Administration, College Park, MD

James Pettengill, U.S. Food and Drug Administration-CFSAN, College Park, MD

Yan Luo, U.S. Food and Drug Administration, College Park, MD

Narjol Gonzalez-Escalona, U.S. Food and Drug Administration, College Park, MD

David Melka, U.S. Food and Drug Administration, College Park, MD

Eric Brown, U.S. Food and Drug Administration-CFSAN, College Park, MD

Introduction: In 2012 a pilot project, called GenomeTrakr, was set up to collect whole genome sequence data (WGS) to track foodborne outbreaks. This now mature network comprises about 30 labs (public health labs and academia) that collect and publically share WGS data in real time. This high-resolution, rapidly growing database is actively being used in outbreak investigations at the state, national, and international level.

Purpose: The GenomeTrakr network demonstrates how WGS data can be used in concert with traditional epidemiology for source tracking of foodborne pathogens. Along with the paradigm shift in technology this new “open data” model allows greater transparency between public health agencies, our industry partners, academia, and international partners.

Methods: The network grew rapidly in 2015. Five new labs were added, two new surveillance efforts were added for Escherichia coli and Campylobacter, and multiple data analysis pipelines were tested. The hardware and software implemented in GenomeTrakr allowed us to compare and cluster genomes of 10s of thousands of taxa at a time. Our partner, NCBI, is currently producing daily cluster results for four pathogen surveillance efforts: Salmonella enterica, Listeria monocytogenes, E. coli, and Campylobacter, all of which are publically available.

Results: The high-resolution WGS data in concert with solid epidemiological evidence has drastically enhanced our ability to identify the food source of current outbreaks for Listeria monocytogenes, for which the CDC is also contributing clinical isolates in real time. Here we provide details for one of these outbreaks where WGS provided the lead in a 2015 Virginia sprout outbreak.

Significance: These results demonstrate two major contributions of GenomeTrakr: WGS as a high-resolution sub-typing tool and the global benefits of having an open data model. As the database and analysis capabilities grow GenomeTrakr will become a critical tool in helping our academic, public health and industry partners develop preventative controls to make food safer globally.

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P3-61 GenomeTrakr Database 2015: WGS Network for Foodborne Pathogen Traceback