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P3-227 GenomeTrakr: A Pathogen Database to Build a Global Genomic Network for Pathogen Traceback and Outbreak Detection

Tuesday, July 28, 2015
Hall B (Oregon Convention Center)
Marc Allard , 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
Cary Pirone
Tim Muruvanda , U.S. Food and Drug Administration , College Park , MD
Errol Strain , U.S. Food and Drug Administration-CFSAN , College Park , MD
Ruth Timme , US Food and Drug Administration, CFSAN , College Park , MD
Justin Payne , U.S. Food and Drug Administration , College Park , MD
Yan Luo , U.S. Food and Drug Administration , College Park , MD
Narjol Gonzalez-Escalona , FDA/CFSAN/ORS/DMMB , College Park , MD
Magaly ToroIbaceta
Andrea Ottesen , U.S. Food and Drug Administration , College Park , MD
David Melka , U.S. Food and Drug Administration , College Park , MD
Peter Evans , U.S. FDA , College Park , MD
Steven Musser
Eric Brown , U.S. Food and Drug Administration-CFSAN , College Park , MD
Introduction: The use of Next Generation Sequencing (NGS) in outbreak investigations is being adopted by public health agencies, and a state and federal pathogen detection network is being implemented: GenomeTrakr. In this network, public health agencies will share genomic data publicly to build a transparent reference database.

Purpose: This pilot study demonstrates how desktop Whole Genome Sequencing (WGS) data can be used, in a combined analysis, for source tracking of foodborne pathogens. Additionally, we describe the components of the NGS pathogen network that integrates state public health laboratories (AK, AZ, FL, HI, MD, MN, NM, NY, NY_Ag, TX, VA, and WA) as well as federal laboratories.

Methods: Multiple data analysis pipelines (Examples) were tested to combine draft bacterial genomes for phylogenetic analyses to provide leads in outbreak investigations. Results of over 12,000 draft bacterial genomes plus the phylogenetic trees of these results are available from the GenomeTrakr bioprojects at the NCBI.

Results: The hardware and software implemented allowed us to compare and cluster complete genomes of thousands of taxa at a time, and the software outputs daily phylogenetic trees for source tracking of food, clinical and environmental isolates.  We report enhanced molecular epidemiological insights gained by comparative analysis of Salmonella and Listeria genomes previously deemed indistinguishable by conventional subtyping methodologies. Details will be provided, for two outbreak case studies with roughly 50 isolates for each case one in nut butter and one in Latin style cheeses The nut butter case documents the ability to link a few clinical cases to an environmental swab from a food facility. The Listeria case was the first example of FDA using WGS for regulatory action.

Significance: These results demonstrate the role of WGS tools within a regulatory environment while highlighting the novel additional insights provided to epidemiological investigations through comparison to a reference database.

Back to: Poster Session 3 – Laboratory and Detection Methods, Sanitation; Antimicrobials; Produce; Epidemiology
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