Yersinia

Yersinia performs genomic identification and characterization of isolates within the genus Yersinia by applying a 500-gene core-genome multilocus sequence typing (cgMLST) scheme for taxonomic assignment and phylogenetic analysis.

Key Features:

• Core-Genome Multilocus Sequence Typing (cgMLST): Utilizes a core subset of 500 shared genes across Yersinia species to enable precise phylogenetic analysis that distinguishes existing species and identifies novel taxa.
• Automated Taxonomic Assignment: Applies species-specific thresholds derived from cgMLST data to automate species-level and infra-specific (biotype and serotype) classification.
• Comprehensive Database Access: Contains cgMLST profiles and reference taxonomic information in BigsDB (https://bigsdb.pasteur.fr/yersinia).
• Validation and Phenotypic Resolution: Validated against phenotypic reference methods with 98.4% agreement for species identification and subtyping and resolves discrepancies caused by atypical biochemical characteristics or limited phenotypic resolution.

Scientific Applications:

• Species Identification: Identifies Yersinia species from genomic sequences, addressing limitations of phenotypic methods.
• Strain Characterization: Enables detailed subtyping at biotype and serotype levels to assess pathogenic potential and support epidemiological investigations.
• Surveillance and Research: Supports public health surveillance and research, demonstrated on 1843 isolates from the French National Surveillance System.

Methodology:

Genome sequencing of Yersinia isolates followed by cgMLST analysis using a 500-gene core scheme, with validation against phenotypic reference methods (98.4% agreement).