Yersinia pestis

Yersinia pestis is the agent of plague and the cause of three recorded pandemics: the Justinianic plague of the sixth century, the second pandemic opening with the Black Death of 1347-1351, and the third pandemic that began in Yunnan and spread worldwide from Hong Kong in 1894. It persists today in enzootic rodent foci across Africa, Asia and the Americas, with Madagascar and the Democratic Republic of the Congo reporting the largest numbers of human cases.

A young clone, and what follows from it

The species is monomorphic: it diverged from Y. pseudotuberculosis recently enough that its genomes differ by very few SNPs, and those SNPs are almost entirely free of homoplasy. This is why a branching nomenclature works here and nowhere else in the genus. The scheme used in this atlas is that of Cui and colleagues (2013), which partitions the species into branches 0 through 4, each suffixed by its biovar: 0.PE (Pestoides), 1.ORI (Orientalis), 2.MED (Medievalis) and the several Antiqua branches.

The same recency has a cost: because the species carries so little diversity, distinguishing Y. pestis from Y. pseudotuberculosis on fragmentary or low-coverage data is harder than the clinical difference between them would suggest, and misassignment in public archives is a real risk rather than a theoretical one.

Three plasmids

Virulence is carried largely off the chromosome, on three plasmids that this atlas profiles per genome rather than per species:

• pCD1 (70 kb) encodes a type III secretion system and the Yop effectors. It is shared with the pYV plasmid of the enteropathogenic Yersinia and is therefore ancestral.
• pMT1 (100 kb) carries the F1 capsular antigen and the murine toxin ymt, which is required for the bacterium to survive in the flea midgut.
• pPCP1 (9.5 kb) carries the plasminogen activator pla, required for dissemination from a subcutaneous flea bite.

pMT1 and pPCP1 are the acquisitions that made flea-borne transmission possible, and they are what separates Y. pestis from its ancestor more decisively than any chromosomal change.

Copy number is a per-strain measurement. pPCP1 in particular is present at variable copy number between isolates, and a value measured in one strain must never be reported as a species constant.