Yersinia pestis branch 0.PE
Pestoides / Microtus group. The most basal branches of the species, largely restricted to rodent foci of the former Soviet Union and China; many isolates are attenuated for humans.
Branch 0.PE, the Pestoides or Microtus group, holds the most basal lineages of the species. Its isolates come largely from rodent foci of the former Soviet Union, Mongolia and China, and many of them are attenuated or avirulent for humans while remaining fully virulent for their rodent hosts.
This branch is the one that most often departs from the canonical three-plasmid picture: several Pestoides isolates carry a reduced pPCP1 or lack it altogether. The plasmid profile of 0.PE is therefore not uniform, and it is a branch where reading plasmid content genome by genome rather than assuming a species constant changes the answer.
Its basal position makes it the most informative part of the tree for questions about the origin of the species and about which features of Y. pestis were acquired first.
Plasmid content
Copy number is a per-genome measurement, never a species constant.
| Replicon | present | partial | absent | not measured |
|---|---|---|---|---|
chromosome |
3 | 0 | 0 | 0 |
pMT1 |
3 | 0 | 0 | 0 |
pCD1 |
2 | 0 | 1 | 0 |
pPCP1 |
1 | 1 | 0 | 1 |
Defining markers
cgMLST is the reference typing method for the genus (BIGSdb-Pasteur). SNP branch nomenclature applies to Y. pestis alone, which is a monomorphic clone.
| Type | Code | Source |
|---|---|---|
| other | Biovar Pestoides / Microtus: glycerol +, nitrate -, most isolates avirulent for humans | Cui et al. 2013 PNAS (branch nomenclature); Zhou et al. 2004 (Microtus biovar) |
| other | Frequently lacks or carries a reduced pPCP1 | Reported for several Pestoides isolates; the plasmid profile of this branch is not uniform and must be read per genome |
Typing equivalences
Three cgMLST schemes coexist for the genus and have never been compared in the literature. They are shown side by side; this atlas does not arbitrate between them.
| System | Code | Match |
|---|---|---|
| biovar | Pestoides / Microtus | exact |
| cui2013 | 0.PE | exact |
Genomes (3)
| Accession | Strain | Country | Collection year | Assembly level |
|---|---|---|---|---|
GCA_000007885.1 |
91001 | — | — | Complete Genome |
GCA_000323485.1 |
620024 | — | — | Contig |
GCA_001188755.1 |
8787 | Georgia | — | Complete Genome |
API : /api/v1/taxa/0.PE