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.
Highlights
IntroductionSalmonella enterica serotype Enteritidis is one of the most commonly reported causes of human salmonellosis
Despite a decrease in serotype Enteritidis infection since 1996 in the United States, outbreaks resulting from contaminated eggs continue to occur [3], and Enteritidis remains among the most common serotypes isolated from humans worldwide [2]
The 3 S. enterica Nitra genomes were highly similar to the reference genome, with numbers of single-nucleotide polymorphism (SNP) comparable to those of other S. enterica Enteritidis strains
Summary
Salmonella enterica serotype Enteritidis is one of the most commonly reported causes of human salmonellosis. P.I. Fields); Technical University of Denmark, Lyngby, Denmark (R.S. Hendriksen); US Department of Agriculture, Athens, Georgia, USA (J.G. Frye); University of California Davis, Davis, California, USA (B.C. Weimer); Washington University School of Medicine, St. Louis, Missouri, USA (G.M. Weinstock); 1970s through the mid-1990s, the incidence of serotype Enteritidis infection increased dramatically; shelled eggs were a major vehicle for transmission. Differentiation of S. enterica Enteritidis challenges traditional subtyping methods, such as pulsed-field gel electrophoresis (PFGE), because isolates of serotype Enteritidis are more genetically homogeneous than are isolates of many other serotypes [4,5]. Of the second-generation methods evaluated for S. enterica Enteritidis subtyping, multilocus variable number–tandem repeat analysis offers slightly better discrimination, but differentiating common patterns remains a substantial problem [6]. We present a broad sampling of WGS to include diversity of other major lineages
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