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

Research output: Contribution to journalArticle

Authors

  • Miquette Hall
  • Marie A Chattaway
  • Sandra Reuter
  • Cyril Savin
  • Eckhard Strauch
  • Elisabeth Carniel
  • Thomas Connor
  • Inge Van Damme
  • Lakshani Rajakaruna
  • Dunstan Rajendram
  • Claire Jenkins
  • Nicholas R Thomson

Colleges, School and Institutes

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.

Details

Original languageEnglish
Pages (from-to)35-42
Number of pages8
JournalJournal of Clinical Microbiology
Volume53
Issue number1
Publication statusPublished - Jan 2015

Keywords

  • Animals, Computational Biology, Genes, Bacterial, Genetic Loci, Genetic Variation, Genome, Bacterial, Humans, Multilocus Sequence Typing, Phylogeny, Reproducibility of Results, Yersinia, Yersinia Infections