Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization - Institut Pasteur Access content directly
Journal Articles Microbial Genomics Year : 2019

Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization

Abstract

The genus Yersinia comprises species that differ widely in their pathogenic potential and public-health significance. Yersinia pestis is responsible for plague, while Yersinia enterocolitica is a prominent enteropathogen. Strains within some species, including Y. enterocolitica, also vary in their pathogenic properties. Phenotypic identification of Yersinia species is time-consuming, labour-intensive and may lead to incorrect identifications. Here, we developed a method to automatically identify and subtype all Yersinia isolates from their genomic sequence. A phylogenetic analysis of Yersinia isolates based on a core subset of 500 shared genes clearly demarcated all existing Yersinia species and uncovered novel, yet undefined Yersinia taxa. An automated taxo-nomic assignment procedure was developed using species-specific thresholds based on core-genome multilocus sequence typing (cgMLST). The performance of this method was assessed on 1843 isolates prospectively collected by the French National Surveillance System and analysed in parallel using phenotypic reference methods, leading to nearly complete (1814; 98.4 %) agreement at species and infra-specific (biotype and serotype) levels. For 29 isolates, incorrect phenotypic assignments resulted from atypical biochemical characteristics or lack of phenotypic resolution. To provide an identification tool, a database of cgMLST profiles and reference taxonomic information has been made publicly accessible (https:// bigsdb. pasteur. fr/ yers-inia). Genomic sequencing-based identification and subtyping of any Yersinia is a powerful and reliable novel approach to define the pathogenic potential of isolates of this medically important genus.
Fichier principal
Vignette du fichier
mgen000301.pdf (2.71 Mo) Télécharger le fichier
Origin : Publication funded by an institution
Loading...

Dates and versions

pasteur-02545814 , version 1 (17-04-2020)

Licence

Attribution

Identifiers

Cite

Cyril Savin, Alexis Criscuolo, Julien Guglielmini, Anne-Sophie Le Guern, Elisabeth Carniel, et al.. Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization. Microbial Genomics, 2019, 5 (10), ⟨10.1099/mgen.0.000301⟩. ⟨pasteur-02545814⟩
52 View
82 Download

Altmetric

Share

Gmail Facebook X LinkedIn More