Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity.

Giovanna Morelli (1) , Yajun Song (2, 3) , Camila J Mazzoni (1, 3) , Mark Eppinger (4) , Philippe Roumagnac (1, 5) , David M Wagner (6) , Mirjam Feldkamp (1) , Barica Kusecek (1) , Amy J Vogler (6) , Yanjun Li (2) , Yujun Cui (2) , Nicholas R Thomson (7) , Thibaut Jombart (8) , Raphael Leblois (9) , Peter Lichtner (10) , Lila Rahalison (11) , Jeannine M Petersen (12) , Francois Balloux (8) , Paul Keim (6, 13) , Thierry Wirth (1, 9) , Jacques Ravel (4) , Ruifu Yang (2) , Elisabeth Carniel (14) , Mark Achtman (1, 3)

1 Department of Molecular Biology [MPIIB Berlin]
2 State Key Laboratory of Pathogen and Biosecurity
3 Department of Microbiology and Environmental Research Institute (Cork, Ireland)
4 Institute for Genome Sciences
5 UMR BGPI - Biologie et Génétique des Interactions Plante-Parasite
6 Department of Biological Sciences [Flagstaff]
7 The Wellcome Trust Genome Campus
8 MRC - Medical Research Council, Centre for Outbreak Analysis and Modelling
9 Département Systématique et Évolution
10 Institute of Human Genetics
11 Laboratoire Central de la Peste (CNR)
12 Division of Vector-Borne Infectious Diseases
13 Pathogen Genomics Division
14 Yersinia

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.

Domains: Life Sciences [q-bio]

Giovanna Morelli, Yajun Song, Camila J Mazzoni, Mark Eppinger, Philippe Roumagnac, et al.. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity.. Nature Genetics, 2010, 42 (12), pp.1140-3. ⟨10.1038/ng.705⟩. ⟨pasteur-00836130⟩