A core genome multi-locus sequence typing scheme for Streptococcus uberis: an evolution in typing a genetically diverse pathogen

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Whiley, D ORCID: https://orcid.org/0000-0002-3972-5100, Jolley, K, Blanchard, A, Coffey, T and Leigh, J, 2024. A core genome multi-locus sequence typing scheme for Streptococcus uberis: an evolution in typing a genetically diverse pathogen. Microbial Genomics, 10 (3): 001225. ISSN 2057-5858

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Official URL: https://doi.org/10.1099/mgen.0.001225

Abstract

Streptococcus uberis is a globally endemic and poorly controlled cause of bovine mastitis impacting the sustainability of the modern dairy industry. A core genome was derived from 579 newly sequenced S. uberis isolates, along with 305 publicly available genome sequences of S. uberis isolated from 11 countries around the world and used to develop a core genome multi-locus sequence typing (cgMLST) scheme. The S. uberis core genome comprised 1475 genes, and these were used to identify 1447 curated loci that were indexed into the cgMLST scheme. This was able to type 1012 of 1037 (>97 %) isolates used and differentiated the associated sequences into 932 discrete core genome sequence types (cgSTs). Analysis of the phylogenetic relationships of cgSTs revealed no clear clustering of isolates based on metadata such as disease status or year of isolation. Geographical clustering of cgSTs was limited to identification of a UK-centric clade, but cgSTs from UK isolates were also dispersed with those originating from other geographical regions across the entire phylogenetic topology. The cgMLST scheme offers a new tool for the detailed analysis of this globally important pathogen of dairy cattle. Initial analysis has re-emphasized and exemplified the genetically diverse nature of the global population of this opportunistic pathogen.

Item Type:	Journal article
Publication Title:	Microbial Genomics
Creators:	Whiley, D., Jolley, K., Blanchard, A., Coffey, T. and Leigh, J.
Publisher:	Microbiology Society
Date:	21 March 2024
Volume:	10
Number:	3
ISSN:	2057-5858
Identifiers:	Number Type 10.1099/mgen.0.001225 DOI 2309340 Other
Rights:	This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author's institution.
Divisions:	Schools > School of Science and Technology
Record created by:	Jonathan Gallacher
Date Added:	10 Dec 2024 14:45
Last Modified:	11 Dec 2024 10:19
URI:	https://irep.ntu.ac.uk/id/eprint/52709