The Global Importance of a Publically Available, Genomic Database for Environmental and Food Isolates

Stevens, Eric

Wednesday, 29 March 2017: 14:30

314-316 (The Square)

Eric Stevens, FDA/CFSAN/ORS/DM, College Park, MD

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

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

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

Sabrina Lindley, U.S. Food and Drug Administration, 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

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, College Park, MD

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

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

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

Errol Strain, FDA-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

Introduction: In 2012 the United States Food and Drug Administration (FDA) launched GenomeTrakr, a pilot project that aimed to use whole-genome sequence (WGS) technology to respond to foodborne disease outbreaks. This freely available repository is currently supported by a network of about 60 federal, state, international, and public health laboratories, which collect and share WGS data in real time.

Purpose: The GenomeTrakr project provides an example for how public health agencies can use genomic data (with its associated metadata) alongside traditional epidemiologic methods to resolve foodborne outbreaks. As the cost of WGS decreases, its emerging rollout among foodborne disease surveillance systems emphasizes its increasing importance as a public health tool.

Methods: The GenomeTrakr network continued to expand in 2016 by adding new labs and over 50,000 foodborne isolates. The data analysis pipeline implemented within GenomeTrakr, and our partners at NCBI, allowed us to compare and cluster pathogens across four public surveillance efforts: Salmonella enterica, Listeria monocytogenes, E. coli, and Campylobacter. The network also provides daily phylogenetic updates that are both freely and publically available to allow greater transparency between public health agencies, our industry partners, academia, and international partners.

Results: WGS has fundamentally altered the way we approach and respond to foodborne diseases by combining multiple microbiological tests into one (e.g. organism identification, antimicrobial resistance, subtyping). Here we provide two examples for how WGS can provide critical insight into resolving both domestic and global foodborne outbreaks.

Significance: GenomeTrakr serves as a resource for generating possible matches to inform outbreak investigations within the United States and this function only becomes more pronounced as the database grows. These genomic sequences – and the associated metadata (e.g. year of collection, geographic location, food source) – need to be made available for its successful use as a global public health resource to make food safer globally.

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T2-03 The Global Importance of a Publically Available, Genomic Database for Environmental and Food Isolates