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P2-144 Patterns of Source Distribution for Salmonella enterica Serotype Typhimurium Revealed by Large-scale Whole Genome Sequencing

Tuesday, July 11, 2017
Exhibit Hall (Tampa Convention Center)
Shaokang Zhang , University of Georgia, Center for Food Safety , Griffin , GA
Dave Boxrud , Minnesota Department of Public Health , Saint Paul , MN
Angie Taylor , Minnesota Department of Public Health , Saint Paul , MN
Chandler Roe , Translational Genomics Research Institute , Phoenix , AZ
Elizabeth Driebe , Translational Genomics Research Institute , Phoenix , AZ
David Engelthaler , Translational Genomics Research Institute , Phoenix , AZ
Paul Keim , Translational Genomics Research Institute , Phoenix , AZ
Eija Trees , Enteric Disease Laboratory Branch, Centers for Disease Control and Prevention , Atlanta , GA
Efrain Ribot , Enteric Disease Laboratory Branch, Centers for Disease Control and Prevention , Atlanta , GA
Patricia Fields , Enteric Disease Laboratory Branch, Centers for Disease Control and Prevention , Atlanta , GA
Xiangyu Deng , University of Georgia, Center for Food Safety , Griffin , GA
Introduction: Routine application of whole genome sequencing (WGS) in the monitoring and surveillance of foodborne pathogens has created a wealth of publicly available genomes and associated metadata, particularly for prevalent pathogens such as Salmonella enterica serotype Typhimurium (ST). It is now possible to study population structures of such pathogens from various sources, at unprecedented scales and in a dynamic spatiotemporal context with constant feeds of new data.

Purpose: The goals of this work were to (1) build a comprehensive phylogeny of ST; (2) identify phylogenetic lineages associated with particular sources; and (3) characterize identified groups/lineages with the purpose of exploring WGS as a method for ST source tracking.

Methods: Genomes of 1,268 ST isolates, collected between 1930 and 2014, were studied. The collection included clinical isolates (n=107) representing diversity of ST molecular subtypes (PFGE and MLVA) from CDC and public genomes of various sources and geographic locations (46 US states and 39 countries; n=1,161). A comprehensive phylogeny was constructed using core-genome SNPs. Gene contents and pseudo genes were compared among major population groups. Overall metabolic potentials of selected strains from major lineages were evaluated with Biolog Phenotype Microarrays. Association between specific lineages and particular sources (e.g., poultry, swine, bovine, avian etc.) was statistically evaluated.

Results: Ten major population groups were identified. Clustering of isolates from the same source was observed in multiple cases, including clades overrepresented by isolates from poultry, bovine, swine, and avian samples. Evolutionary analyses suggest that a least two of these clades originated in recent decades and appeared to be associated with meat production. Representative isolates from an avian clade and a swine clade displayed distinct metabolic profiles from others featuring systemic incapability in utilizing multiple substrates.

Significance: This study built a comprehensive population structure of ST, which provides a framework for evaluating and exploring WGS for foodborne pathogen source tracking.

Back to: Poster Session 2 – Food Chemical Hazards and Food Allergens, Food Toxicology, Meat, Poultry and Eggs, Epidemiology, Retail and Food Service Safety, Communication Outreach and Education, Molecular Analytics, Genomics and Microbiome, Laboratory and Detection Methods, and Dairy
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