Yersinia

The genus Yersinia belongs to the Enterobacterales and contains around twenty described species, of which three cause human disease: Y. pestis, the agent of plague; Y. pseudotuberculosis and Y. enterocolitica, both enteric pathogens. The remainder are environmental organisms or are associated with fish and insects.

The genus is a textbook case of how far pathogenicity can diverge within a single genus over a short evolutionary distance. Y. pestis emerged from a Y. pseudotuberculosis population within roughly the last 5000 to 20000 years, and in that time changed transmission route entirely: from faecal-oral spread of an enteric pathogen to flea-borne transmission of a systemic one. The transformation was driven less by gene gain than by a combination of two plasmid acquisitions (pMT1 and pPCP1) and a large-scale loss of function — the invasin, the adhesin YadA and the flagellar regulator are all pseudogenes in Y. pestis while remaining functional in its ancestor.

Typing

For the genus as a whole the reference typing method is cgMLST, not SNP barcoding. Yersinia is not a monomorphic clone, and isolates are compared through allele calls, through the genus-wide 500-locus scheme maintained at BIGSdb-Pasteur. The SNP branch nomenclature that this atlas displays applies to Y. pestis alone, and only because that species is a recent clone in which a branching SNP tree is meaningful.