title: Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation.
abstract: Listeria monocytogenes (Lm) causes severe foodborne illness (listeriosis). Previous molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE), were critical in detecting outbreaks that led to food safety improvements and declining incidence, but PFGE provides limited genetic resolution. A multiagency collaboration began performing real-time, whole-genome sequencing (WGS) on all US Lm isolates from patients, food, and the environment in September 2013, posting sequencing data into a public repository. Compared with the year before the project began, WGS, combined with epidemiologic and product trace-back data, detected more listeriosis clusters and solved more outbreaks (2 outbreaks in pre-WGS year, 5 in WGS year 1, and 9 in year 2). Whole-genome multilocus sequence typing and single nucleotide polymorphism analyses provided equivalent phylogenetic relationships relevant to investigations; results were most useful when interpreted in context of epidemiological data. WGS has transformed listeriosis outbreak surveillance and is being implemented for other foodborne pathogens.
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: Brendan R
authors.initials: BR
authors.lastname: Jackson
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: Cheryl
authors.initials: C
authors.lastname: Tarr
authors.affiliation: Food and Drug Administration, College Park, Maryland.
authors.forename: Errol
authors.initials: E
authors.lastname: Strain
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Jackson
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: Amanda
authors.initials: A
authors.lastname: Conrad
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: Heather
authors.initials: H
authors.lastname: Carleton
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: Lee S
authors.initials: LS
authors.lastname: Katz
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: Steven
authors.initials: S
authors.lastname: Stroika
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: L Hannah
authors.initials: LH
authors.lastname: Gould
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: Rajal K
authors.initials: RK
authors.lastname: Mody
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Silk
authors.affiliation: Food and Drug Administration, College Park, Maryland.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Beal
authors.affiliation: Food and Drug Administration, College Park, Maryland.
authors.forename: Yi
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Food and Drug Administration, College Park, Maryland.
authors.forename: Ruth
authors.initials: R
authors.lastname: Timme
authors.affiliation: Food and Drug Administration, College Park, Maryland.
authors.forename: Matthew
authors.initials: M
authors.lastname: Doyle
authors.affiliation: Food and Drug Administration, College Park, Maryland.
authors.forename: Angela
authors.initials: A
authors.lastname: Fields
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: Matthew
authors.initials: M
authors.lastname: Wise
authors.affiliation: US Department of Agriculture, Food Safety and Inspection Service, Athens, Georgia.
authors.forename: Glenn
authors.initials: G
authors.lastname: Tillman
authors.affiliation: US Department of Agriculture, Food Safety and Inspection Service, Washington D.C.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Defibaugh-Chavez
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: Zuzana
authors.initials: Z
authors.lastname: Kucerova
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: Ashley
authors.initials: A
authors.lastname: Sabol
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: Katie
authors.initials: K
authors.lastname: Roache
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: Eija
authors.initials: E
authors.lastname: Trees
authors.affiliation: US Department of Agriculture, Food Safety and Inspection Service, Athens, Georgia.
authors.forename: Mustafa
authors.initials: M
authors.lastname: Simmons
authors.affiliation: US Department of Agriculture, Food Safety and Inspection Service, Athens, Georgia.
authors.forename: Jamie
authors.initials: J
authors.lastname: Wasilenko
authors.affiliation: Association of Public Health Laboratories, Silver Spring, Maryland.
authors.forename: Kristy
authors.initials: K
authors.lastname: Kubota
authors.affiliation: Applied Maths, Sint-Martens-Latem, Belgium.
authors.forename: Hannes
authors.initials: H
authors.lastname: Pouseele
authors.affiliation: National Institute for Biotechnology Information, National Institutes of Health, Bethesda, Maryland.
authors.forename: William
authors.initials: W
authors.lastname: Klimke
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: John
authors.initials: J
authors.lastname: Besser
authors.affiliation: Food and Drug Administration, College Park, Maryland.
authors.forename: Eric
authors.initials: E
authors.lastname: Brown
authors.affiliation: Food and Drug Administration, College Park, Maryland.
authors.forename: Marc
authors.initials: M
authors.lastname: Allard
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia.
authors.forename: Peter
authors.initials: P
authors.lastname: Gerner-Smidt
mesh_terms: D004196:Disease Outbreaks; D059022:Food Safety; D005517:Foodborne Diseases / Q000453:epidemiology* / Q000382:microbiology; D016680:Genome, Bacterial / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008089:Listeria monocytogenes / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D008088:Listeriosis / Q000453:epidemiology* / Q000382:microbiology; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D000073336:Whole Genome Sequencing / Q000379:methods*
keywords: DNA sequencing; Listeria monocytogenes; foodborne diseases; outbreaks