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

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

Parallel independent evolution of pathogenicity within the genus Yersinia

Peer reviewe

Evaluation of a single procedure allowing the isolation of enteropathogenic Yersinia along with other bacterial enteropathogens from human stools.

Enteropathogenic Yersinia are among the most frequent agents of human diarrhea in temperate and cold countries. However, the incidence of yersiniosis is largely underestimated because of the peculiar growth characteristics of pathogenic Yersinia, which make their isolation from poly-contaminated samples difficult. The use of specific procedures for Yersinia isolation is required, but is expensive and time consuming, and therefore is not systematically performed in clinical pathology laboratories. A means to circumvent this problem would be to use a single procedure for the isolation of all bacterial enteropathogens. Since the Statens Serum Institut enteric medium (SSI) has been reported to allow the growth at 37°C of most gram-negative bacteria, including Yersinia, our study aimed at evaluating its performances for Yersinia isolation, as compared to the commonly used Yersinia-specific semi-selective Cefsulodin-Irgasan-Novobiocin medium (CIN) incubated at 28°C. Our results show that Yersinia pseudotuberculosis growth was strongly inhibited on SSI at 37°C, and therefore that this medium is not suitable for the isolation of this species. All Yersinia enterocolitica strains tested grew on SSI, while some non-pathogenic Yersinia species were inhibited. The morphology of Y. enterocolitica colonies on SSI allowed their differentiation from various other gram-negative bacteria commonly isolated from stool samples. However, in artificially contaminated human stools, the recovery of Y. enterocolitica colonies on SSI at 37°C was difficult and was 3 logs less sensitive than on CIN at 28°C. Therefore, despite its limitations, the use of a specific procedure (CIN incubated at 28°C) is still required for an efficient isolation of enteropathogenic Yersinia from stools

Characterization of Atypical Isolates of Yersinia intermedia and Definition of Two New Biotypes▿ †

The species Yersinia intermedia is a member of the genus Yersinia which belongs to the Enterobacteriaceae family. This species is divided into eight biotypes, according to Brenner's biotyping scheme. This scheme relies on five tests (utilization of Simmons citrate and acid production from d-melibiose, d-raffinose, α-methyl-d-glucoside [αMG], and l-rhamnose). The collection of the French Yersinia Reference Laboratory (Institut Pasteur, Paris, France) contained 44 strains that were originally identified as Y. intermedia but whose characteristics did not fit into the biotyping scheme. These 44 strains were separated into two biochemical groups: variant 1 (positive for acid production from l-rhamnose and αMG and positive for Simmons citrate utlization) and variant 2 (positive for acid production from l-rhamnose and αMG). These atypical strains could correspond to new biotypes of Y. intermedia, to Y. frederiksenii strains having the atypical property of fermenting αMG, or to new Yersinia species. These strains did not exhibit growth or phenotypic properties different from those of Y. intermedia and Y. frederiksenii and did not harbor any of the virulence traits usually found in pathogenic species. DNA-DNA hybridizations performed between one strain each of variants 1 and 2 and the Y. intermedia and Y. frederiksenii type strains demonstrated that these variants do belong to the Y. intermedia species. We thus propose that Brenner's biotyping scheme be updated by adding two new biotypes: 9 (for variant 1) and 10 (for variant 2) to the species Y. intermedia

Yersiniosis in France: overview and potential sources of infection

International audienceObjectives: The aim of this study was to exploit the extensive database on strains of Yersinia collected over more than 50 years in France in order to gain an overview of yersiniosis and potential sources of contamination in this country.Methods: The 19 670 strains of Yersinia of human, animal, environmental, and food origin isolated in France were grouped by species, biotype, and serotype.Results: Most human strains (59%) were pathogenic, with a marked predominance of Yersinia enterocolitica bioserotype 4/O:3 (66.8%), followed by Y. enterocolitica 2/O:9 (23.8%) and Yersinia pseudotuberculosis (6.1%). Pigs and pork meat were the nearly exclusive sources of Y. enterocolitica 4/O:3. Other pathogenic strains were rarely isolated from food or environmental samples (0.2%). The major source of pathogenic Yersinia was the animal reservoir, with a remarkable association between Y. enterocolitica 4/O:3 and pigs, Y. pseudotuberculosis and wildlife, Y. enterocolitica 2/O:9 and grazing farm animals, Y. enterocolitica 5/O:2,3 and hares, and Y. enterocolitica 3/O:1,2,3 and chinchillas.Conclusions: The frequency of human infection caused by certain Yersinia subgroups might be related to the frequency of exposure to specific animal sources. In contrast, non-pathogenic Yersinia were commonly isolated from foodstuffs and the environment, most probably accounting for the abundance of non-pathogenic Yersinia recovered from human stools

Colonies of <i>Y. enterocolitica</i> alone or with enterobacteria after 24 h of growth on SSI at 28°C and 37°C.

<p><i>Y. enterocolitica</i> 4/O:3 (strain IP29492) alone (A), or mixed with <i>K. oxytoca</i> (B), <i>E. coli</i>. (C), <i>C. sakazakii</i> (D). Colonies of <i>Y. enterocolitica</i> are indicated with a star on mixed plates. The black bar represents 2 mm.</p

Growth at different temperatures of enteropathogenic <i>Yersinia</i> strains on CIN and SSI, as compared to TSA.

<p>NA: not applicable.</p

Colony morphology of various <i>Yersinia</i> and non-<i>Yersinia</i> enterobacteria grown for 24 h on SSI.

<p>NAG: non-agglutinable; NA: not applicable.</p

Growth of 92 <i>Yersinia</i> strains on SSI and CIN as compared to TSA (control medium).

a<p>: the results are expressed as the difference of the log of the dilution limits between TSA and either CIN or SSI.</p><p>NA: Not applicable; NAG: non-agglutinable.</p

Complete genome sequence of Yersinia pseudotuberculosis strain SP-1303 from lineage 8, associated with Far East scarlet-like fever

The genome sequence of Y. pseudotuberculosis strain SP-1303 has been submitted to NCBI under the BioProject ID PRJNA998338 and the Biosample accession number SAMN36701287. The assembled genome is available in GenBank under assembly accession number GCA_030644845. Sequencing raw reads are available on Sequencing Read Archive (SRA) accession numbers SRR25411577 (Illumina) and SRR25411576 (ONT). In addition, the genome sequence is also available on Yersiniomics, a multi-omics interactive web-based platform for easy visualization of genome organization, rapid access to structural and functional protein properties, and search for protein homologs within the Yersinia genus (31).International audienceWe report the complete genome sequence of Yersinia pseudotuberculosis strain SP-1303, identified as part of lineage 8 and associated with Far East scarlet-like fever. The genome includes the chromosome, the Yersinia-virulence plasmid (pYV) encoding a type III secretion system essential for virulence, the pVM82 plasmid, and two cryptic plasmids. KEYWORDS Yersinia pseudotuberculosis, Far East scarlet-like fever, genome Y ersinia pseudotuberculosis is one of the 26 species of the genus Yersinia, a member Edito