title: 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.
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.
authors.affiliation: Pathogen Research Group, Nottingham Trent University, Nottingham, United Kingdom.
authors.forename: Miquette
authors.initials: M
authors.lastname: Hall
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, United Kingdom.
authors.forename: Marie A
authors.initials: MA
authors.lastname: Chattaway
authors.affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
authors.forename: Sandra
authors.initials: S
authors.lastname: Reuter
authors.affiliation: French Yersinia Reference Laboratory and WHO Collaborating Centre, Institut Pasteur, Paris, France.
authors.forename: Cyril
authors.initials: C
authors.lastname: Savin
authors.affiliation: Bundesinstitut für Risikobewertung, Berlin, Germany.
authors.forename: Eckhard
authors.initials: E
authors.lastname: Strauch
authors.affiliation: French Yersinia Reference Laboratory and WHO Collaborating Centre, Institut Pasteur, Paris, France.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Carniel
authors.affiliation: Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom.
authors.forename: Thomas
authors.initials: T
authors.lastname: Connor
authors.affiliation: Department of Veterinary Public Health and Food Safety, University Ghent, Ghent, Belgium.
authors.forename: Inge
authors.initials: I
authors.lastname: Van Damme
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, United Kingdom.
authors.forename: Lakshani
authors.initials: L
authors.lastname: Rajakaruna
authors.affiliation: Genomic Service Unit, Public Health England, London, United Kingdom.
authors.forename: Dunstan
authors.initials: D
authors.lastname: Rajendram
authors.affiliation: Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, United Kingdom.
authors.forename: Claire
authors.initials: C
authors.lastname: Jenkins
authors.affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Thomson
authors.affiliation: Pathogen Research Group, Nottingham Trent University, Nottingham, United Kingdom alan.mcnally@ntu.ac.uk.
authors.forename: Alan
authors.initials: A
authors.lastname: McNally
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D005798:Genes, Bacterial; D056426:Genetic Loci; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D058885:Multilocus Sequence Typing / Q000379:methods; D010802:Phylogeny; D015203:Reproducibility of Results; D015007:Yersinia / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D015009:Yersinia Infections / Q000382:microbiology*