Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica

Henk C. den Bakker, Andrea I. Moreno Switt, Gregory Govoni, Craig A. Cummings, Matthew L. Ranieri, Lovorka Degoricija, Karin Hoelzer, Lorraine D. Rodriguez-Rivera, Stephanie Brown, Elena Bolchacova, Manohar R. Furtado, Martin Wiedmann

Resultado de la investigación: Article

Resumen

Background: Divergence of bacterial populations into distinct subpopulations is often the result of ecological isolation. While some studies have suggested the existence of Salmonella enterica subsp. enterica subclades, evidence for these subdivisions has been ambiguous. Here we used a comparative genomics approach to define the population structure of Salmonella enterica subsp. enterica, and identify clade-specific genes that may be the result of ecological specialization. Results: Multi-locus sequence analysis (MLSA) and single nucleotide polymorphisms (SNPs) data for 16 newly sequenced and 30 publicly available genomes showed an unambiguous subdivision of S. enterica subsp. enterica into at least two subpopulations, which we refer to as clade A and clade B. Clade B strains contain several clade-specific genes or operons, including a β-glucuronidase operon, a S-fimbrial operon, and cell surface related genes, which strongly suggests niche specialization of this subpopulation. An additional set of 123 isolates was assigned to clades A and B by using qPCR assays targeting subpopulation-specific SNPs and genes of interest. Among 98 serovars examined, approximately 20% belonged to clade B. All clade B isolates contained two pathogenicity related genomic islands, SPI-18 and a cytolethal distending toxin islet; a combination of these two islands was previously thought to be exclusive to serovars Typhi and Paratyphi A. Presence of β-glucuronidase in clade B isolates specifically suggests an adaptation of this clade to the vertebrate gastrointestinal environment. Conclusions:S. enterica subsp. enterica consists of at least two subpopulations that differ specifically in genes involved in host and tissue tropism, utilization of host specific carbon and nitrogen sources and are therefore likely to differ in ecology and transmission characteristics.

Idioma originalEnglish
Número de artículo425
PublicaciónBMC Genomics
Volumen12
N.º1
DOI
EstadoPublished - 22 ago 2011

Huella dactilar

Salmonella enterica
Virulence Factors
Genome
Operon
Genes
Glucuronidase
Single Nucleotide Polymorphism
Viral Tropism
Genomic Islands
Genomics
Ecology
Islands
Population
Sequence Analysis
Virulence
Vertebrates
Nitrogen
Carbon

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Citar esto

den Bakker, Henk C. ; Moreno Switt, Andrea I. ; Govoni, Gregory ; Cummings, Craig A. ; Ranieri, Matthew L. ; Degoricija, Lovorka ; Hoelzer, Karin ; Rodriguez-Rivera, Lorraine D. ; Brown, Stephanie ; Bolchacova, Elena ; Furtado, Manohar R. ; Wiedmann, Martin. / Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica. En: BMC Genomics. 2011 ; Vol. 12, N.º 1.
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title = "Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica",
abstract = "Background: Divergence of bacterial populations into distinct subpopulations is often the result of ecological isolation. While some studies have suggested the existence of Salmonella enterica subsp. enterica subclades, evidence for these subdivisions has been ambiguous. Here we used a comparative genomics approach to define the population structure of Salmonella enterica subsp. enterica, and identify clade-specific genes that may be the result of ecological specialization. Results: Multi-locus sequence analysis (MLSA) and single nucleotide polymorphisms (SNPs) data for 16 newly sequenced and 30 publicly available genomes showed an unambiguous subdivision of S. enterica subsp. enterica into at least two subpopulations, which we refer to as clade A and clade B. Clade B strains contain several clade-specific genes or operons, including a β-glucuronidase operon, a S-fimbrial operon, and cell surface related genes, which strongly suggests niche specialization of this subpopulation. An additional set of 123 isolates was assigned to clades A and B by using qPCR assays targeting subpopulation-specific SNPs and genes of interest. Among 98 serovars examined, approximately 20{\%} belonged to clade B. All clade B isolates contained two pathogenicity related genomic islands, SPI-18 and a cytolethal distending toxin islet; a combination of these two islands was previously thought to be exclusive to serovars Typhi and Paratyphi A. Presence of β-glucuronidase in clade B isolates specifically suggests an adaptation of this clade to the vertebrate gastrointestinal environment. Conclusions:S. enterica subsp. enterica consists of at least two subpopulations that differ specifically in genes involved in host and tissue tropism, utilization of host specific carbon and nitrogen sources and are therefore likely to differ in ecology and transmission characteristics.",
author = "{den Bakker}, {Henk C.} and {Moreno Switt}, {Andrea I.} and Gregory Govoni and Cummings, {Craig A.} and Ranieri, {Matthew L.} and Lovorka Degoricija and Karin Hoelzer and Rodriguez-Rivera, {Lorraine D.} and Stephanie Brown and Elena Bolchacova and Furtado, {Manohar R.} and Martin Wiedmann",
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den Bakker, HC, Moreno Switt, AI, Govoni, G, Cummings, CA, Ranieri, ML, Degoricija, L, Hoelzer, K, Rodriguez-Rivera, LD, Brown, S, Bolchacova, E, Furtado, MR & Wiedmann, M 2011, 'Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica', BMC Genomics, vol. 12, n.º 1, 425. https://doi.org/10.1186/1471-2164-12-425

Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica. / den Bakker, Henk C.; Moreno Switt, Andrea I.; Govoni, Gregory; Cummings, Craig A.; Ranieri, Matthew L.; Degoricija, Lovorka; Hoelzer, Karin; Rodriguez-Rivera, Lorraine D.; Brown, Stephanie; Bolchacova, Elena; Furtado, Manohar R.; Wiedmann, Martin.

En: BMC Genomics, Vol. 12, N.º 1, 425, 22.08.2011.

Resultado de la investigación: Article

TY - JOUR

T1 - Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica

AU - den Bakker, Henk C.

AU - Moreno Switt, Andrea I.

AU - Govoni, Gregory

AU - Cummings, Craig A.

AU - Ranieri, Matthew L.

AU - Degoricija, Lovorka

AU - Hoelzer, Karin

AU - Rodriguez-Rivera, Lorraine D.

AU - Brown, Stephanie

AU - Bolchacova, Elena

AU - Furtado, Manohar R.

AU - Wiedmann, Martin

PY - 2011/8/22

Y1 - 2011/8/22

N2 - Background: Divergence of bacterial populations into distinct subpopulations is often the result of ecological isolation. While some studies have suggested the existence of Salmonella enterica subsp. enterica subclades, evidence for these subdivisions has been ambiguous. Here we used a comparative genomics approach to define the population structure of Salmonella enterica subsp. enterica, and identify clade-specific genes that may be the result of ecological specialization. Results: Multi-locus sequence analysis (MLSA) and single nucleotide polymorphisms (SNPs) data for 16 newly sequenced and 30 publicly available genomes showed an unambiguous subdivision of S. enterica subsp. enterica into at least two subpopulations, which we refer to as clade A and clade B. Clade B strains contain several clade-specific genes or operons, including a β-glucuronidase operon, a S-fimbrial operon, and cell surface related genes, which strongly suggests niche specialization of this subpopulation. An additional set of 123 isolates was assigned to clades A and B by using qPCR assays targeting subpopulation-specific SNPs and genes of interest. Among 98 serovars examined, approximately 20% belonged to clade B. All clade B isolates contained two pathogenicity related genomic islands, SPI-18 and a cytolethal distending toxin islet; a combination of these two islands was previously thought to be exclusive to serovars Typhi and Paratyphi A. Presence of β-glucuronidase in clade B isolates specifically suggests an adaptation of this clade to the vertebrate gastrointestinal environment. Conclusions:S. enterica subsp. enterica consists of at least two subpopulations that differ specifically in genes involved in host and tissue tropism, utilization of host specific carbon and nitrogen sources and are therefore likely to differ in ecology and transmission characteristics.

AB - Background: Divergence of bacterial populations into distinct subpopulations is often the result of ecological isolation. While some studies have suggested the existence of Salmonella enterica subsp. enterica subclades, evidence for these subdivisions has been ambiguous. Here we used a comparative genomics approach to define the population structure of Salmonella enterica subsp. enterica, and identify clade-specific genes that may be the result of ecological specialization. Results: Multi-locus sequence analysis (MLSA) and single nucleotide polymorphisms (SNPs) data for 16 newly sequenced and 30 publicly available genomes showed an unambiguous subdivision of S. enterica subsp. enterica into at least two subpopulations, which we refer to as clade A and clade B. Clade B strains contain several clade-specific genes or operons, including a β-glucuronidase operon, a S-fimbrial operon, and cell surface related genes, which strongly suggests niche specialization of this subpopulation. An additional set of 123 isolates was assigned to clades A and B by using qPCR assays targeting subpopulation-specific SNPs and genes of interest. Among 98 serovars examined, approximately 20% belonged to clade B. All clade B isolates contained two pathogenicity related genomic islands, SPI-18 and a cytolethal distending toxin islet; a combination of these two islands was previously thought to be exclusive to serovars Typhi and Paratyphi A. Presence of β-glucuronidase in clade B isolates specifically suggests an adaptation of this clade to the vertebrate gastrointestinal environment. Conclusions:S. enterica subsp. enterica consists of at least two subpopulations that differ specifically in genes involved in host and tissue tropism, utilization of host specific carbon and nitrogen sources and are therefore likely to differ in ecology and transmission characteristics.

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U2 - 10.1186/1471-2164-12-425

DO - 10.1186/1471-2164-12-425

M3 - Article

VL - 12

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

M1 - 425

ER -