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

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)
5 Downloads (Pure)


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 languageEnglish
Pages (from-to)371-378
Number of pages8
Issue number1
Early online date21 Mar 2019
Publication statusPublished - 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

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.


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


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