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

Standard

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, Miquette; Chattaway, Marie A; Reuter, Sandra; Savin, Cyril; Strauch, Eckhard; Carniel, Elisabeth; Connor, Thomas; Van Damme, Inge; Rajakaruna, Lakshani; Rajendram, Dunstan; Jenkins, Claire; Thomson, Nicholas R; McNally, Alan.

In: Journal of Clinical Microbiology, Vol. 53, No. 1, 01.2015, p. 35-42.

Research output: Contribution to journalArticle

Harvard

Hall, M, Chattaway, MA, Reuter, S, Savin, C, Strauch, E, Carniel, E, Connor, T, Van Damme, I, Rajakaruna, L, Rajendram, D, Jenkins, C, Thomson, NR & McNally, A 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, vol. 53, no. 1, pp. 35-42. https://doi.org/10.1128/JCM.02395-14

APA

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., & McNally, A. (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), 35-42. https://doi.org/10.1128/JCM.02395-14

Vancouver

Author

Hall, Miquette ; Chattaway, Marie A ; Reuter, Sandra ; Savin, Cyril ; Strauch, Eckhard ; Carniel, Elisabeth ; Connor, Thomas ; Van Damme, Inge ; Rajakaruna, Lakshani ; Rajendram, Dunstan ; Jenkins, Claire ; Thomson, Nicholas R ; McNally, Alan. / 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. In: Journal of Clinical Microbiology. 2015 ; Vol. 53, No. 1. pp. 35-42.

Bibtex

@article{3695cb41d0fc45e18c01c605cfa004ae,
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.",
keywords = "Animals, Computational Biology, Genes, Bacterial, Genetic Loci, Genetic Variation, Genome, Bacterial, Humans, Multilocus Sequence Typing, Phylogeny, Reproducibility of Results, Yersinia, Yersinia Infections",
author = "Miquette Hall and Chattaway, {Marie A} and Sandra Reuter and Cyril Savin and Eckhard Strauch and Elisabeth Carniel and Thomas Connor and {Van Damme}, Inge and Lakshani Rajakaruna and Dunstan Rajendram and Claire Jenkins and Thomson, {Nicholas R} and Alan McNally",
note = "Copyright {\textcopyright} 2015, American Society for Microbiology. All Rights Reserved.",
year = "2015",
month = jan,
doi = "10.1128/JCM.02395-14",
language = "English",
volume = "53",
pages = "35--42",
journal = "Journal of Clinical Microbiology",
issn = "0095-1137",
publisher = "American Society for Microbiology",
number = "1",

}

RIS

TY - JOUR

T1 - 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

AU - Hall, Miquette

AU - Chattaway, Marie A

AU - Reuter, Sandra

AU - Savin, Cyril

AU - Strauch, Eckhard

AU - Carniel, Elisabeth

AU - Connor, Thomas

AU - Van Damme, Inge

AU - Rajakaruna, Lakshani

AU - Rajendram, Dunstan

AU - Jenkins, Claire

AU - Thomson, Nicholas R

AU - McNally, Alan

N1 - Copyright © 2015, American Society for Microbiology. All Rights Reserved.

PY - 2015/1

Y1 - 2015/1

N2 - 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.

AB - 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.

KW - Animals

KW - Computational Biology

KW - Genes, Bacterial

KW - Genetic Loci

KW - Genetic Variation

KW - Genome, Bacterial

KW - Humans

KW - Multilocus Sequence Typing

KW - Phylogeny

KW - Reproducibility of Results

KW - Yersinia

KW - Yersinia Infections

U2 - 10.1128/JCM.02395-14

DO - 10.1128/JCM.02395-14

M3 - Article

C2 - 25339391

VL - 53

SP - 35

EP - 42

JO - Journal of Clinical Microbiology

JF - Journal of Clinical Microbiology

SN - 0095-1137

IS - 1

ER -