A proposed core genome scheme for analyses of the Salmonella genus

Madison E. Pearce; Marie A. Chattaway; Kathie Grant; Martin C.J. Maiden

doi:10.1016/j.ygeno.2019.02.016

A proposed core genome scheme for analyses of the Salmonella genus

Madison E. Pearce^*, Marie A. Chattaway, Kathie Grant, Martin C.J. Maiden

^*Corresponding author for this work

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Abstract

The salmonellae are found in a wide range of animal hosts and many food products for human consumption. Most cases of human disease are caused by S. enterica subspecies I; however as opportunistic pathogens the other subspecies (II-VI) and S. bongori are capable of causing disease. Loci that were not consistently present in all of the species and subspecies were removed from a previously proposed core genome scheme (EBcgMLSTv2.0), the removal of these 252 loci resulted in a core genus scheme (SalmcgMLSTv1.0). SalmcgMLSTv1.0 clustered isolates from the same subspecies more rapidly and more accurately grouped isolates from different subspecies when compared with EBcgMLSTv2.0. All loci within the EBcgMLSTv2.0 scheme were present in over 98% of S. enterica subspecies I isolates and should, therefore, continue to be used for subspecies I analyses, while the SalmcgMLSTv1.0 scheme is more appropriate for cross genus investigations.

Original language	English
Pages (from-to)	371-378
Number of pages	8
Journal	Genomics
Volume	112
Issue number	1
Early online date	21 Mar 2019
DOIs	https://doi.org/10.1016/j.ygeno.2019.02.016
Publication status	Published - Jan 2020

Bibliographical note

Funding Information: The research was funded by the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at University of Liverpool in partnership with Public Health England (PHE), in collaboration with University of East Anglia, University of Oxford and the Quadram Institute. Madison Pearce is based at the University of Oxford. The views expressed are those of the author (s) and not necessarily those of the NHS, the NIHR, the Department of Health or Public Health England. With thanks to the Enterobase team for the development and maintenance of the Enterobase database; the MaidenLab team for continued support in research and the development and maintenance of the PubMLST database and the Salmonella Reference Laboratory and sequencing teams at Public Health England.

Open Access: This is an open access article under the CC BY license
(http://creativecommons.org/licenses/BY/4.0/).

Publisher Copyright: © 2019 The Authors

Citation: Madison E. Pearce, Marie A. Chattaway, Kathie Grant, Martin C.J. Maiden,
A proposed core genome scheme for analyses of the Salmonella genus, Genomics, Volume 112, Issue 1, 2020, Pages 371-378, ISSN 0888-7543.

DOI: https://doi.org/10.1016/j.ygeno.2019.02.016.

Keywords

Core genome multilocus sequence typing (cgMLST)
Core genome scheme
Outbreak
Salmonella
Whole genome sequencing

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Pearce2020AProposedCoreGenomeSchemeForAnalysesOfTheSalmonellaGenusGenomicsFinal published version, 400 KBLicence: CC BY

Cite this

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title = "A proposed core genome scheme for analyses of the Salmonella genus",

abstract = "The salmonellae are found in a wide range of animal hosts and many food products for human consumption. Most cases of human disease are caused by S. enterica subspecies I; however as opportunistic pathogens the other subspecies (II-VI) and S. bongori are capable of causing disease. Loci that were not consistently present in all of the species and subspecies were removed from a previously proposed core genome scheme (EBcgMLSTv2.0), the removal of these 252 loci resulted in a core genus scheme (SalmcgMLSTv1.0). SalmcgMLSTv1.0 clustered isolates from the same subspecies more rapidly and more accurately grouped isolates from different subspecies when compared with EBcgMLSTv2.0. All loci within the EBcgMLSTv2.0 scheme were present in over 98\% of S. enterica subspecies I isolates and should, therefore, continue to be used for subspecies I analyses, while the SalmcgMLSTv1.0 scheme is more appropriate for cross genus investigations.",

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note = "Funding Information: The research was funded by the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at University of Liverpool in partnership with Public Health England (PHE), in collaboration with University of East Anglia, University of Oxford and the Quadram Institute. Madison Pearce is based at the University of Oxford. The views expressed are those of the author (s) and not necessarily those of the NHS, the NIHR, the Department of Health or Public Health England. With thanks to the Enterobase team for the development and maintenance of the Enterobase database; the MaidenLab team for continued support in research and the development and maintenance of the PubMLST database and the Salmonella Reference Laboratory and sequencing teams at Public Health England. Open Access: This is an open access article under the CC BY license (http://creativecommons.org/licenses/BY/4.0/). Publisher Copyright: {\textcopyright} 2019 The Authors Citation: Madison E. Pearce, Marie A. Chattaway, Kathie Grant, Martin C.J. Maiden, A proposed core genome scheme for analyses of the Salmonella genus, Genomics, Volume 112, Issue 1, 2020, Pages 371-378, ISSN 0888-7543. DOI: https://doi.org/10.1016/j.ygeno.2019.02.016.",

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KW - Salmonella

KW - Whole genome sequencing

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A proposed core genome scheme for analyses of the Salmonella genus

Abstract

Bibliographical note

Keywords

UN SDGs

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