Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

Giovanna Morelli, Yajun Song, Camila J. Mazzoni, Mark Eppinger, Philippe Roumagnac, David M. Wagner, Mirjam Feldkamp, Barica Kusecek, Amy J. Vogler, Yanjun Li, Yujun Cui, Nicholas R. Thomson, Thibaut Jombart, Raphael Leblois, Peter Lichtner, Lila Rahalison, Jeannine M. Petersen, Francois Balloux, Paul Keim, Thierry WirthJacques Ravel, Ruifu Yang, Elisabeth Carniel, Mark Achtman

Research output: Contribution to journalArticlepeer-review

422 Scopus citations


Plague is a pandemic human invasive disease caused by the bacterial agent Yersinia pestis. We here report a comparison of 17 whole genomes of Y. pestis isolates from global sources. We also screened a global collection of 286 Y. pestis isolates for 933 SNPs using Sequenom MassArray SNP typing. We conducted phylogenetic analyses on this sequence variation dataset, assigned isolates to populations based on maximum parsimony and, from these results, made inferences regarding historical transmission routes. Our phylogenetic analysis suggests that Y. pestis evolved in or near China and spread through multiple radiations to Europe, South America, Africa and Southeast Asia, leading to country-specific lineages that can be traced by lineage-specific SNPs. All 626 current isolates from the United States reflect one radiation, and 82 isolates from Madagascar represent a second radiation. Subsequent local microevolution of Y. pestis is marked by sequential, geographically specific SNPs.

Original languageEnglish (US)
Pages (from-to)1140-1143
Number of pages4
JournalNature Genetics
Issue number12
StatePublished - Dec 2010

ASJC Scopus subject areas

  • Genetics


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