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A genomic overview of the population structure of Salmonella
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Alikhan, Nabil-Fareed, Zhou, Zhemin, Sergeant, Martin J. and Achtman, Mark (2018) A genomic overview of the population structure of Salmonella. PLoS Genetics, 14 (4). e1007261. doi:10.1371/journal.pgen.1007261 ISSN 1553-7390.
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Official URL: http://dx.doi.org/10.1371/journal.pgen.1007261
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
| Item Type: | Journal Article | |||||||||
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| Subjects: | Q Science > QH Natural history > QH426 Genetics | |||||||||
| Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) > Warwick HRI (2004-2010) Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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| Library of Congress Subject Headings (LCSH): | Salmonella -- Genetics, Serology, Molecular biology, Gene mapping | |||||||||
| Journal or Publication Title: | PLoS Genetics | |||||||||
| Publisher: | Public Library of Science | |||||||||
| ISSN: | 1553-7390 | |||||||||
| Official Date: | 5 April 2018 | |||||||||
| Dates: |
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| Volume: | 14 | |||||||||
| Number: | 4 | |||||||||
| Article Number: | e1007261 | |||||||||
| DOI: | 10.1371/journal.pgen.1007261 | |||||||||
| Status: | Peer Reviewed | |||||||||
| Publication Status: | Published | |||||||||
| Access rights to Published version: | Open Access (Creative Commons) | |||||||||
| Date of first compliant deposit: | 30 April 2018 | |||||||||
| Date of first compliant Open Access: | 30 April 2018 | |||||||||
| RIOXX Funder/Project Grant: |
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