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 Wirth; Jacques Ravel; Ruifu Yang; Elisabeth Carniel; Mark Achtman

doi:10.1038/ng.705

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

Biological Sciences

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Abstract

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 language	English (US)
Pages (from-to)	1140-1143
Number of pages	4
Journal	Nature Genetics
Volume	42
Issue number	12
DOIs	https://doi.org/10.1038/ng.705
State	Published - Dec 2010

ASJC Scopus subject areas

Genetics

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Morelli, G., Song, Y., Mazzoni, C. J., Eppinger, M., Roumagnac, P., Wagner, D. M., Feldkamp, M., Kusecek, B., Vogler, A. J., Li, Y., Cui, Y., Thomson, N. R., Jombart, T., Leblois, R., Lichtner, P., Rahalison, L., Petersen, J. M., Balloux, F., Keim, P., ... Achtman, M. (2010). Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nature Genetics, 42(12), 1140-1143. https://doi.org/10.1038/ng.705

Morelli, G, Song, Y, Mazzoni, CJ, Eppinger, M, Roumagnac, P, Wagner, DM, Feldkamp, M, Kusecek, B, Vogler, AJ, Li, Y, Cui, Y, Thomson, NR, Jombart, T, Leblois, R, Lichtner, P, Rahalison, L, Petersen, JM, Balloux, F, Keim, P, Wirth, T, Ravel, J, Yang, R, Carniel, E & Achtman, M 2010, 'Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity', Nature Genetics, vol. 42, no. 12, pp. 1140-1143. https://doi.org/10.1038/ng.705

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title = "Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity",

abstract = "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.",

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

note = "Funding Information: We gratefully acknowledge technical assistance by R. Nera and A. Doyle and helpful comments from A. Rambaut and D. Falush. Support was provided by grants from the German Army Medical Corps (MSAB15A013) and the Science Foundation of Ireland (05/FE1/B882) to M.A., the National Key Program for Infectious Diseases of China (2008ZX10004-009) and the State Key Development Program for Basic Research of China (2009CB522600) to R.Y. and the US Department of Homeland Security (NBCH2070001; HSHQDC-08-C00158) and US National Institutes of Health (AI065359) to P.K. and D.M.W. Whole genome sequencing of Y. pestis strains IP275, MG05-1020 and UG05-045 was supported by federal funds from the National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Department of Health and Human Services (N01 AI-30071), and sequencing of IP674 was supported by funding for Sanger Institute Pathogen Genomics by the Wellcome Trust. Genomic DNA of Y. pestis MG05-1020 was kindly provided by S. Bearden and M. Schriefer (Centers for Disease Control and Prevention, Fort Collins, Colorado, USA).",

year = "2010",

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doi = "10.1038/ng.705",

language = "English (US)",

volume = "42",

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T1 - Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

AU - Morelli, Giovanna

AU - Song, Yajun

AU - Mazzoni, Camila J.

AU - Eppinger, Mark

AU - Roumagnac, Philippe

AU - Wagner, David M.

AU - Feldkamp, Mirjam

AU - Kusecek, Barica

AU - Vogler, Amy J.

AU - Li, Yanjun

AU - Cui, Yujun

AU - Thomson, Nicholas R.

AU - Jombart, Thibaut

AU - Leblois, Raphael

AU - Lichtner, Peter

AU - Rahalison, Lila

AU - Petersen, Jeannine M.

AU - Balloux, Francois

AU - Keim, Paul

AU - Wirth, Thierry

AU - Ravel, Jacques

AU - Yang, Ruifu

AU - Carniel, Elisabeth

AU - Achtman, Mark

N1 - Funding Information: We gratefully acknowledge technical assistance by R. Nera and A. Doyle and helpful comments from A. Rambaut and D. Falush. Support was provided by grants from the German Army Medical Corps (MSAB15A013) and the Science Foundation of Ireland (05/FE1/B882) to M.A., the National Key Program for Infectious Diseases of China (2008ZX10004-009) and the State Key Development Program for Basic Research of China (2009CB522600) to R.Y. and the US Department of Homeland Security (NBCH2070001; HSHQDC-08-C00158) and US National Institutes of Health (AI065359) to P.K. and D.M.W. Whole genome sequencing of Y. pestis strains IP275, MG05-1020 and UG05-045 was supported by federal funds from the National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Department of Health and Human Services (N01 AI-30071), and sequencing of IP674 was supported by funding for Sanger Institute Pathogen Genomics by the Wellcome Trust. Genomic DNA of Y. pestis MG05-1020 was kindly provided by S. Bearden and M. Schriefer (Centers for Disease Control and Prevention, Fort Collins, Colorado, USA).

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Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

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