Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages

Xiangyu Deng, Prerak T. Desai, Henk C. den Bakker, Matthew Mikoleit, Beth Tolar, Eija Trees, Rene S. Hendriksen, Jonathan G. Frye, Steffen Porwollik, Bart C Weimer, Martin Wiedmann, George M. Weinstock, Patricia I. Fields, Michael McClelland

Research output: Contribution to journalArticle

32 Citations (Scopus)

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 wholegenome 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.

Original languageEnglish (US)
Pages (from-to)1481-1489
Number of pages9
JournalEmerging Infectious Diseases
Volume20
Issue number9
DOIs
StatePublished - 2014

Fingerprint

Salmonella enterica
Epidemiology
Salmonella enteritidis
Population
Single Nucleotide Polymorphism
Salmonella Infections
Population Dynamics
History
Genome
Serogroup

ASJC Scopus subject areas

  • Microbiology (medical)
  • Infectious Diseases
  • Epidemiology

Cite this

Deng, X., Desai, P. T., den Bakker, H. C., Mikoleit, M., Tolar, B., Trees, E., ... McClelland, M. (2014). Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages. Emerging Infectious Diseases, 20(9), 1481-1489. https://doi.org/10.3201/eid2009.131095

Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages. / Deng, Xiangyu; Desai, Prerak T.; den Bakker, Henk C.; Mikoleit, Matthew; Tolar, Beth; Trees, Eija; Hendriksen, Rene S.; Frye, Jonathan G.; Porwollik, Steffen; Weimer, Bart C; Wiedmann, Martin; Weinstock, George M.; Fields, Patricia I.; McClelland, Michael.

In: Emerging Infectious Diseases, Vol. 20, No. 9, 2014, p. 1481-1489.

Research output: Contribution to journalArticle

Deng, X, Desai, PT, den Bakker, HC, Mikoleit, M, Tolar, B, Trees, E, Hendriksen, RS, Frye, JG, Porwollik, S, Weimer, BC, Wiedmann, M, Weinstock, GM, Fields, PI & McClelland, M 2014, 'Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages', Emerging Infectious Diseases, vol. 20, no. 9, pp. 1481-1489. https://doi.org/10.3201/eid2009.131095
Deng, Xiangyu ; Desai, Prerak T. ; den Bakker, Henk C. ; Mikoleit, Matthew ; Tolar, Beth ; Trees, Eija ; Hendriksen, Rene S. ; Frye, Jonathan G. ; Porwollik, Steffen ; Weimer, Bart C ; Wiedmann, Martin ; Weinstock, George M. ; Fields, Patricia I. ; McClelland, Michael. / Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages. In: Emerging Infectious Diseases. 2014 ; Vol. 20, No. 9. pp. 1481-1489.
@article{f42e38bb931f48a7bede50708780d370,
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 wholegenome 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.",
author = "Xiangyu Deng and Desai, {Prerak T.} and {den Bakker}, {Henk C.} and Matthew Mikoleit and Beth Tolar and Eija Trees and Hendriksen, {Rene S.} and Frye, {Jonathan G.} and Steffen Porwollik and Weimer, {Bart C} and Martin Wiedmann and Weinstock, {George M.} and Fields, {Patricia I.} and Michael McClelland",
year = "2014",
doi = "10.3201/eid2009.131095",
language = "English (US)",
volume = "20",
pages = "1481--1489",
journal = "Emerging Infectious Diseases",
issn = "1080-6040",
publisher = "Centers for Disease Control and Prevention (CDC)",
number = "9",

}

TY - JOUR

T1 - Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages

AU - Deng, Xiangyu

AU - Desai, Prerak T.

AU - den Bakker, Henk C.

AU - Mikoleit, Matthew

AU - Tolar, Beth

AU - Trees, Eija

AU - Hendriksen, Rene S.

AU - Frye, Jonathan G.

AU - Porwollik, Steffen

AU - Weimer, Bart C

AU - Wiedmann, Martin

AU - Weinstock, George M.

AU - Fields, Patricia I.

AU - McClelland, Michael

PY - 2014

Y1 - 2014

N2 - 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 wholegenome 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.

AB - 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 wholegenome 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.

UR - http://www.scopus.com/inward/record.url?scp=84906260161&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84906260161&partnerID=8YFLogxK

U2 - 10.3201/eid2009.131095

DO - 10.3201/eid2009.131095

M3 - Article

C2 - 25147968

AN - SCOPUS:84906260161

VL - 20

SP - 1481

EP - 1489

JO - Emerging Infectious Diseases

JF - Emerging Infectious Diseases

SN - 1080-6040

IS - 9

ER -