title: Tracing Origins of the Salmonella Bareilly Strain Causing a Food-borne Outbreak in the United States.
abstract: BACKGROUND
  Using a novel combination of whole-genome sequencing (WGS) analysis and geographic metadata, we traced the origins of Salmonella Bareilly isolates collected in 2012 during a widespread food-borne outbreak in the United States associated with scraped tuna imported from India.
  
  
  METHODS
  Using next-generation sequencing, we sequenced the complete genome of 100 Salmonella Bareilly isolates obtained from patients who consumed contaminated product, from natural sources, and from unrelated historically and geographically disparate foods. Pathogen genomes were linked to geography by projecting the phylogeny on a virtual globe and produced a transmission network.
  
  
  RESULTS
  Phylogenetic analysis of WGS data revealed a common origin for outbreak strains, indicating that patients in Maryland and New York were infected from sources originating at a facility in India.
  
  
  CONCLUSIONS
  These data represent the first report fully integrating WGS analysis with geographic mapping and a novel use of transmission networks. Results showed that WGS vastly improves our ability to delimit the scope and source of bacterial food-borne contamination events. Furthermore, these findings reinforce the extraordinary utility that WGS brings to global outbreak investigation as a greatly enhanced approach to protecting the human food supply chain as well as public health in general.
authors.affiliation: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition Department of Nutrition & Food Science and Joint Institute for Food Safety & Applied Nutrition, University of Maryland, College Park.
authors.forename: Maria
authors.initials: M
authors.lastname: Hoffmann
authors.affiliation: Division of Public Health and Biostatistics, Office of Food Defense, Communication and Emergency Response, Center for Food Safety and Nutrition, US Food and Drug Administration, College Park.
authors.forename: Yan
authors.initials: Y
authors.lastname: Luo
authors.affiliation: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition.
authors.forename: Steven R
authors.initials: SR
authors.lastname: Monday
authors.affiliation: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition.
authors.forename: Narjol
authors.initials: N
authors.lastname: Gonzalez-Escalona
authors.affiliation: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition.
authors.forename: Andrea R
authors.initials: AR
authors.lastname: Ottesen
authors.affiliation: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition.
authors.forename: Tim
authors.initials: T
authors.lastname: Muruvanda
authors.affiliation: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition.
authors.forename: Charles
authors.initials: C
authors.lastname: Wang
authors.affiliation: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition.
authors.forename: George
authors.initials: G
authors.lastname: Kastanis
authors.affiliation: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition.
authors.forename: Christine
authors.initials: C
authors.lastname: Keys
authors.affiliation: Department of Bioinformatics and Genomics, University North Carolina at Charlotte.
authors.forename: Daniel
authors.initials: D
authors.lastname: Janies
authors.affiliation: Department of Biomedical Informatics, Ohio State University, Columbus.
authors.forename: Izzet F
authors.initials: IF
authors.lastname: Senturk
authors.affiliation: Department of Biomedical Informatics, Ohio State University, Columbus.
authors.forename: Umit V
authors.initials: UV
authors.lastname: Catalyurek
authors.affiliation: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition.
authors.forename: Hua
authors.initials: H
authors.lastname: Wang
authors.affiliation: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition.
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Hammack
authors.affiliation: New York State Department of Health, Wadsworth Center, Albany.
authors.forename: William J
authors.initials: WJ
authors.lastname: Wolfgang
authors.affiliation: New York State Department of Health, Wadsworth Center, Albany.
authors.forename: Dianna
authors.initials: D
authors.lastname: Schoonmaker-Bopp
authors.affiliation: Maryland Department of Health and Mental Hygiene, Baltimore.
authors.forename: Alvina
authors.initials: A
authors.lastname: Chu
authors.affiliation: Maryland Department of Health and Mental Hygiene, Baltimore.
authors.forename: Robert
authors.initials: R
authors.lastname: Myers
authors.affiliation: Maryland Department of Health and Mental Hygiene, Baltimore.
authors.forename: Julie
authors.initials: J
authors.lastname: Haendiges
authors.affiliation: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition.
authors.forename: Peter S
authors.initials: PS
authors.lastname: Evans
authors.affiliation: Department of Nutrition & Food Science and Joint Institute for Food Safety & Applied Nutrition, University of Maryland, College Park.
authors.forename: Jianghong
authors.initials: J
authors.lastname: Meng
authors.affiliation: Division of Public Health and Biostatistics, Office of Food Defense, Communication and Emergency Response, Center for Food Safety and Nutrition, US Food and Drug Administration, College Park.
authors.forename: Errol A
authors.initials: EA
authors.lastname: Strain
authors.affiliation: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition.
authors.forename: Marc W
authors.initials: MW
authors.lastname: Allard
authors.affiliation: Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Nutrition.
authors.forename: Eric W
authors.initials: EW
authors.lastname: Brown
mesh_terms: D000818:Animals; D004196:Disease Outbreaks; D005517:Foodborne Diseases / Q000453:epidemiology* / Q000382:microbiology; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D007194:India; D017720:Molecular Epidemiology; D058889:Molecular Typing; D058974:Phylogeography; D012480:Salmonella Infections / Q000453:epidemiology* / Q000382:microbiology; D019779:Salmonella enterica / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA; D014413:Tuna / Q000382:microbiology; D014481:United States / Q000453:epidemiology
keywords: geographic information systems; next generation sequencing; salmonellosis; single nucleotide polymorphism; traceback