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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Bibliographic Details
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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Summary: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.
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The authors have declared that no competing interests exist.
ISSN:1553-7404
1553-7390
1553-7404
DOI:10.1371/journal.pgen.1007261