Use of whole-genus genome sequence data to develop a multilocus sequence typing tool that accurately identifies Yersinia isolates to the species and subspecies levels

Hall, M., Chattaway, M.A., Reuter, S., Savin, C., Strauch, E., Carniel, E., Connor, T., Van Damme, I., Rajakaruna, L., Rajendram, D., Jenkins, C., Thomson, N.R. and McNally, A. ORCID: 0000-0002-3099-630X, 2015. Use of whole-genus genome sequence data to develop a multilocus sequence typing tool that accurately identifies Yersinia isolates to the species and subspecies levels. Journal of Clinical Microbiology, 53 (1), pp. 35-42. ISSN 1098-660X

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Abstract

The genus Yersinia is a large and diverse bacterial genus consisting of human-pathogenic species, a fish-pathogenic species, and a large number of environmental species. Recently, the phylogenetic and population structure of the entire genus was elucidated through the genome sequence data of 241 strains encompassing every known species in the genus. Here we report the mining of this enormous data set to create a multilocus sequence typing-based scheme that can identify Yersinia strains to the species level to a level of resolution equal to that for whole-genome sequencing. Our assay is designed to be able to accurately subtype the important human-pathogenic species Yersinia enterocolitica to whole-genome resolution levels. We also report the validation of the scheme on 386 strains from reference laboratory collections across Europe. We propose that the scheme is an important molecular typing system to allow accurate and reproducible identification of Yersinia isolates to the species level, a process often inconsistent in nonspecialist laboratories. Additionally, our assay is the most phylogenetically informative typing scheme available for Y. enterocolitica.

Item Type: Journal article
Publication Title: Journal of Clinical Microbiology
Creators: Hall, M., Chattaway, M.A., Reuter, S., Savin, C., Strauch, E., Carniel, E., Connor, T., Van Damme, I., Rajakaruna, L., Rajendram, D., Jenkins, C., Thomson, N.R. and McNally, A.
Publisher: American Society for Microbiology
Place of Publication: Washington DC
Date: 2015
Volume: 53
Number: 1
ISSN: 1098-660X
Identifiers:
NumberType
10.1128/JCM.02395-14DOI
Divisions: Schools > School of Science and Technology
Depositing User: EPrints Services
Date Added: 09 Oct 2015 10:57
Last Modified: 09 Jun 2017 13:45
URI: http://irep.ntu.ac.uk/id/eprint/20708

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