Salmonella nomenclature in the genomic era: a time for change

Marie A. Chattaway*, Gemma C. Langridge, John Wain

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

28 Citations (Scopus)
33 Downloads (Pure)

Abstract

Salmonella enterica nomenclature has evolved over the past one hundred years into a highly sophisticated naming convention based on the recognition of antigens by specific antibodies. This serotyping scheme has led to the definition of over 2500 serovars which are well understood, have standing in nomenclature and, for the majority, biological relevance. Therefore, it is highly desirable for any change in naming convention to maintain backwards compatibility with the information linked to these serovars. The routine use of whole genome sequencing and the well-established link between sequence types and serovars presents an opportunity to update the scheme by incorporating the phylogenetically relevant sequence data whilst preserving the best of serotyping nomenclature. Advantages include: overcoming the variability in antibody preparations; removing the need to use laboratory animals and implementing a truly universal system. However, the issue of trying to reproduce the phenotyping gold standard needs to be relaxed if we are to fully embrace the genomic era. We have used whole genome sequence data from over 46,000 isolates of Salmonella enterica subspecies enterica to define clusters in two stages: Multi Locus Sequence Typing followed by antigen prediction. Sequence type—serotype discrepancies were resolved using core SNP clustering to determine the phylogenetic groups and this was confirmed by overlaying the antigenic prediction onto the core SNP clusters and testing the separation of clusters using cgMLST Hierarchical Clustering. This allowed us to define any major antigenic clusters within an ST—here called the MAC type and written as ST-serovar. Using this method, 99.96% of Salmonella isolates reported in the UK were assigned a MAC type and linked to a serovar name taken from the Kauffmann and White scheme. We propose a change for reporting of Salmonella enterica sub-types using the ST followed by serovar.

Original languageEnglish
Article number7494
JournalScientific Reports
Volume11
Issue number1
DOIs
Publication statusPublished - 5 Apr 2021

Bibliographical note

Funding Information:
We would like to thank Amy Gentle, Martin Day, Andrew Levy, Clare Maguire and Tracey Dealey for undertaking antibody-based typing in the laboratory. This study was funded by Public Health England. The authors gratefully acknowledge the support of the BBSRC; G.C.L. and J.W were funded by the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10352.

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

Publisher Copyright: © 2021, The Author(s).

Chattaway, M.A., Langridge, G.C. & Wain, J. Salmonella nomenclature in the genomic era: a time for change. Sci Rep 11, 7494 (2021).

https://doi.org/10.1038/s41598-021-86243-w

Fingerprint

Dive into the research topics of 'Salmonella nomenclature in the genomic era: a time for change'. Together they form a unique fingerprint.

Cite this