title: Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages.
abstract: Salmonella enterica serotype Enteritidis is one of the most commonly reported causes of human salmonellosis. Its low genetic diversity, measured by fingerprinting methods, has made subtyping a challenge. We used whole-genome sequencing to characterize 125 S. enterica Enteritidis and 3 S. enterica serotype Nitra strains. Single-nucleotide polymorphisms were filtered to identify 4,887 reliable loci that distinguished all isolates from each other. Our whole-genome single-nucleotide polymorphism typing approach was robust for S. enterica Enteritidis subtyping with combined data for different strains from 2 different sequencing platforms. Five major genetic lineages were recognized, which revealed possible patterns of geographic and epidemiologic distribution. Analyses on the population dynamics and evolutionary history estimated that major lineages emerged during the 17th-18th centuries and diversified during the 1920s and 1950s.
authors.forename: Xiangyu
authors.initials: X
authors.lastname: Deng
authors.forename: Prerak T
authors.initials: PT
authors.lastname: Desai
authors.forename: Henk C
authors.initials: HC
authors.lastname: den Bakker
authors.forename: Matthew
authors.initials: M
authors.lastname: Mikoleit
authors.forename: Beth
authors.initials: B
authors.lastname: Tolar
authors.forename: Eija
authors.initials: E
authors.lastname: Trees
authors.forename: Rene S
authors.initials: RS
authors.lastname: Hendriksen
authors.forename: Jonathan G
authors.initials: JG
authors.lastname: Frye
authors.forename: Steffen
authors.initials: S
authors.lastname: Porwollik
authors.forename: Bart C
authors.initials: BC
authors.lastname: Weimer
authors.forename: Martin
authors.initials: M
authors.lastname: Wiedmann
authors.forename: George M
authors.initials: GM
authors.lastname: Weinstock
authors.forename: Patricia I
authors.initials: PI
authors.lastname: Fields
authors.forename: Michael
authors.initials: M
authors.lastname: McClelland
mesh_terms: D004196:Disease Outbreaks; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D006801:Humans; D015233:Models, Statistical; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D015995:Prevalence; D012480:Salmonella Infections / Q000453:epidemiology* / Q000382:microbiology*; D012477:Salmonella enteritidis / Q000145:classification* / Q000235:genetics*; D065288:Serogroup