title: Utility of Combining Whole Genome Sequencing with Traditional Investigational Methods To Solve Foodborne Outbreaks of Salmonella Infections Associated with Chicken: A New Tool for Tackling This Challenging Food Vehicle.
abstract: High consumption rates and a multitude of brands make multistate foodborne outbreaks of Salmonella infections associated with chicken challenging to investigate, but whole genome sequencing is a powerful tool that can be used to assist investigators. Whole genome sequencing of pathogens isolated from clinical, environmental, and food samples is increasingly being used in multistate foodborne outbreak investigations to determine with unprecedented resolution how closely related these isolates are to one another genetically. In 2014, federal and state health officials investigated an outbreak of 146 Salmonella Heidelberg infections in 24 states. A follow-up analysis was conducted after the conclusion of the investigation in which 27 clinical and 24 food isolates from the outbreak underwent whole genome sequencing. These isolates formed seven clades, the largest of which contained clinical isolates from a subcluster of case patients who attended a catered party. One isolate from a chicken processed by a large producer was closely related genetically (zero to three single-nucleotide polymorphism differences) to the clinical isolates from these subcluster case patients. Chicken from this large producer was also present in the kitchen of the caterer on the day before the event, thus providing additional evidence that the chicken from this producer was the outbreak source. This investigation highlights how whole genome sequencing can be used with epidemiologic and traceback evidence to identify chicken sources of foodborne outbreaks.
authors.affiliation: 1 Centers for Disease Control and Prevention, Atlanta, Georgia 30333.
authors.forename: Samuel J
authors.initials: SJ
authors.lastname: Crowe
authors.affiliation: 2 U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, D.C. 20250.
authors.forename: Alice
authors.initials: A
authors.lastname: Green
authors.affiliation: 3 Kern County Public Health Services Department, Bakersfield, California 93301.
authors.forename: Kimberly
authors.initials: K
authors.lastname: Hernandez
authors.affiliation: 4 California Department of Public Health, Richmond, California 94804, USA.
authors.forename: Vi
authors.initials: V
authors.lastname: Peralta
authors.affiliation: 1 Centers for Disease Control and Prevention, Atlanta, Georgia 30333.
authors.forename: Lyndsay
authors.initials: L
authors.lastname: Bottichio
authors.affiliation: 2 U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, D.C. 20250.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Defibaugh-Chavez
authors.affiliation: 2 U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, D.C. 20250.
authors.forename: Aphrodite
authors.initials: A
authors.lastname: Douris
authors.affiliation: 1 Centers for Disease Control and Prevention, Atlanta, Georgia 30333.
authors.forename: Laura
authors.initials: L
authors.lastname: Gieraltowski
authors.affiliation: 1 Centers for Disease Control and Prevention, Atlanta, Georgia 30333.
authors.forename: Kelley
authors.initials: K
authors.lastname: Hise
authors.affiliation: 3 Kern County Public Health Services Department, Bakersfield, California 93301.
authors.forename: Karen
authors.initials: K
authors.lastname: La-Pham
authors.affiliation: 1 Centers for Disease Control and Prevention, Atlanta, Georgia 30333.
authors.forename: Karen P
authors.initials: KP
authors.lastname: Neil
authors.affiliation: 2 U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, D.C. 20250.
authors.forename: Mustafa
authors.initials: M
authors.lastname: Simmons
authors.affiliation: 2 U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, D.C. 20250.
authors.forename: Glenn
authors.initials: G
authors.lastname: Tillman
authors.affiliation: 1 Centers for Disease Control and Prevention, Atlanta, Georgia 30333.
authors.forename: Beth
authors.initials: B
authors.lastname: Tolar
authors.affiliation: 1 Centers for Disease Control and Prevention, Atlanta, Georgia 30333.
authors.forename: Darlene
authors.initials: D
authors.lastname: Wagner
authors.affiliation: 2 U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, D.C. 20250.
authors.forename: Jamie
authors.initials: J
authors.lastname: Wasilenko
authors.affiliation: 2 U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, D.C. 20250.
authors.forename: Kristin
authors.initials: K
authors.lastname: Holt
authors.affiliation: 1 Centers for Disease Control and Prevention, Atlanta, Georgia 30333.
authors.forename: Eija
authors.initials: E
authors.lastname: Trees
authors.affiliation: 1 Centers for Disease Control and Prevention, Atlanta, Georgia 30333.
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Wise
mesh_terms: D000818:Animals; D002645:Chickens; D004196:Disease Outbreaks; D005516:Food Microbiology; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D012480:Salmonella Infections / Q000453:epidemiology*
keywords: Chicken; Foodborne outbreak; Salmonella; Whole genome sequencing