{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T02:56:35Z","timestamp":1792032995261,"version":"4.4.0"},"reference-count":61,"publisher":"Microbiology Society","issue":"10","license":[{"start":{"date-parts":[[2019,10,1]],"date-time":"2019-10-01T00:00:00Z","timestamp":1569888000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,10,1]]},"abstract":"The genus \n \n Yersinia<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> comprises species that differ widely in their pathogenic potential and public-health significance. Yersinia pestis<\/jats:italic> is responsible for plague, while Yersinia enterocolitica<\/jats:italic> is a prominent enteropathogen. Strains within some species, including Y. enterocolitica,<\/jats:italic> also vary in their pathogenic properties. Phenotypic identification of \n \n Yersinia<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> species is time-consuming, labour-intensive and may lead to incorrect identifications. Here, we developed a method to automatically identify and subtype all \n \n Yersinia<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> isolates from their genomic sequence. A phylogenetic analysis of \n \n Yersinia<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> isolates based on a core subset of 500 shared genes clearly demarcated all existing \n \n Yersinia<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> species and uncovered novel, yet undefined \n \n Yersinia<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> taxa. An automated taxonomic 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\/yersinia<\/jats:ext-link>). Genomic sequencing-based identification and subtyping of any \n \n Yersinia<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> is a powerful and reliable novel approach to define the pathogenic potential of isolates of this medically important genus.<\/jats:p>","DOI":"10.1099\/mgen.0.000301","type":"journal-article","created":{"date-parts":[[2019,10,3]],"date-time":"2019-10-03T17:12:14Z","timestamp":1570122734000},"source":"Crossref","is-referenced-by-count":57,"title":["Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization"],"prefix":"10.1099","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2659-3433","authenticated-orcid":false,"given":"Cyril","family":"Savin","sequence":"first","affiliation":[{"name":"National Reference Laboratory for Plague and Other Yersinioses, Institut Pasteur, Paris, France"},{"name":"WHO Collaborating Centre for Yersinia, Institut Pasteur, Paris, France"},{"name":"Yersinia Research Unit, Institut Pasteur, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8212-5215","authenticated-orcid":false,"given":"Alexis","family":"Criscuolo","sequence":"additional","affiliation":[{"name":"Hub de Bioinformatique et Biostatistique \u2013 D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8566-1726","authenticated-orcid":false,"given":"Julien","family":"Guglielmini","sequence":"additional","affiliation":[{"name":"Hub de Bioinformatique et Biostatistique \u2013 D\u00e9partement Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1051-6740","authenticated-orcid":false,"given":"Anne-Sophie","family":"Le Guern","sequence":"additional","affiliation":[{"name":"WHO Collaborating Centre for Yersinia, Institut Pasteur, Paris, France"},{"name":"Yersinia Research Unit, Institut Pasteur, Paris, France"},{"name":"National Reference Laboratory for Plague and Other Yersinioses, Institut Pasteur, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisabeth","family":"Carniel","sequence":"additional","affiliation":[{"name":"WHO Collaborating Centre for Yersinia, Institut Pasteur, Paris, France"},{"name":"National Reference Laboratory for Plague and Other Yersinioses, Institut Pasteur, Paris, France"},{"name":"Yersinia Research Unit, Institut Pasteur, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4343-0508","authenticated-orcid":false,"given":"Javier","family":"Pizarro-Cerd\u00e1","sequence":"additional","affiliation":[{"name":"National Reference Laboratory for Plague and Other Yersinioses, Institut Pasteur, Paris, France"},{"name":"WHO Collaborating Centre for Yersinia, Institut Pasteur, Paris, France"},{"name":"Yersinia Research Unit, Institut Pasteur, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2516-2108","authenticated-orcid":false,"given":"Sylvain","family":"Brisse","sequence":"additional","affiliation":[{"name":"Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1007\/0-387-30746-X_13","volume-title":"The Prokaryotes","author":"Carniel","year":"2006"},{"key":"R2","first-page":"5500","article-title":"The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2016","volume":"16","year":"2018","journal-title":"Efsa 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