A genomic overview of the population structure of Salmonella

For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs) based on the alleles of seve...

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Published in:	PLoS genetics Vol. 14; no. 4; p. e1007261
Main Authors:	Alikhan, Nabil-Fareed, Zhou, Zhemin, Sergeant, Martin J., Achtman, Mark
Format:	Journal Article
Language:	English
Published:	United States Public Library of Science 05.04.2018 Public Library of Science (PLoS)
Subjects:	Archives & records Biology and Life Sciences Computer and Information Sciences Databases, Genetic Epidemics Epidemiology Gene expression Genetic aspects Genome, Bacterial Genomes Genotyping Health aspects Medical schools Medicine and Health Sciences Multilocus Sequence Typing Phylogeny Polymorphism, Single Nucleotide Population Population structure Research and Analysis Methods Review Salmonella Salmonella - classification Salmonella - genetics Salmonella enterica Serotyping Single-nucleotide polymorphism United Kingdom > UK
ISSN:	1553-7404, 1553-7390, 1553-7404
Online Access:	Get full text
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Abstract	For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs) based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST]) corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs). eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus.
AbstractList	For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs) based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST]) corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs). eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus. For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs) based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST]) corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs). eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus.For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs) based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST]) corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs). eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus.
Audience	Academic
Author	Alikhan, Nabil-Fareed Zhou, Zhemin Sergeant, Martin J. Achtman, Mark
AuthorAffiliation	Warwick Medical School, University of Warwick, Coventry, United Kingdom Universidad de Sevilla, SPAIN
AuthorAffiliation_xml	– name: Warwick Medical School, University of Warwick, Coventry, United Kingdom – name: Universidad de Sevilla, SPAIN
Author_xml	– sequence: 1 givenname: Nabil-Fareed orcidid: 0000-0002-1243-0767 surname: Alikhan fullname: Alikhan, Nabil-Fareed – sequence: 2 givenname: Zhemin surname: Zhou fullname: Zhou, Zhemin – sequence: 3 givenname: Martin J. orcidid: 0000-0001-7264-2668 surname: Sergeant fullname: Sergeant, Martin J. – sequence: 4 givenname: Mark orcidid: 0000-0001-6815-0070 surname: Achtman fullname: Achtman, Mark
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/29621240$$D View this record in MEDLINE/PubMed
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Copyright	COPYRIGHT 2018 Public Library of Science 2018 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: . PLoS Genet 14(4): e1007261. https://doi.org/10.1371/journal.pgen.1007261 2018 Alikhan et al 2018 Alikhan et al 2018 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: . PLoS Genet 14(4): e1007261. https://doi.org/10.1371/journal.pgen.1007261
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SubjectTerms	Archives & records Biology and Life Sciences Computer and Information Sciences Databases, Genetic Epidemics Epidemiology Gene expression Genetic aspects Genome, Bacterial Genomes Genotyping Health aspects Medical schools Medicine and Health Sciences Multilocus Sequence Typing Phylogeny Polymorphism, Single Nucleotide Population Population structure Research and Analysis Methods Review Salmonella Salmonella - classification Salmonella - genetics Salmonella enterica Serotyping Single-nucleotide polymorphism
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Title	A genomic overview of the population structure of Salmonella
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