G. Morelli, Y. Song, C. Mazzoni, M. Eppinger, and P. Roumagnac, Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity, Nature Genetics, vol.17, issue.12, pp.1140-1143, 2010.
DOI : 10.1128/JB.01786-08
URL : https://hal.archives-ouvertes.fr/pasteur-00836130

R. Perry and J. Fetherston, Yersinia pestis-etiologic agent of plague, Clin Microbiol Rev, vol.10, pp.35-66, 1997.

L. Rotz, A. Khan, S. Lillibridge, S. Ostroff, and J. Hughes, Public Health Assessment of Potential Biological Terrorism Agents, Emerging Infectious Diseases, vol.8, issue.2, pp.225-230, 2002.
DOI : 10.3201/eid0802.010164

M. Galimand, A. Guiyoule, G. Gerbaud, B. Rasoamanana, and S. Chanteau, Mediated by a Transferable Plasmid, New England Journal of Medicine, vol.337, issue.10, pp.677-680, 1997.
DOI : 10.1056/NEJM199709043371004

T. Welch, W. Fricke, P. Mcdermott, D. White, and M. Rosso, Multiple Antimicrobial Resistance in Plague: An Emerging Public Health Risk, PLoS ONE, vol.189, issue.1, p.309, 2007.
DOI : 10.1371/journal.pone.0000309.s001

E. Brygoo, Epidémiologie de la peste a ` Madagascar, Arch Inst Pasteur Madagascar, vol.35, pp.9-147, 1966.

S. Chanteau, L. Ratsifasoamanana, B. Rasoamanana, L. Rahalison, and J. Randriambelosoa, Plague, a Reemerging Disease in Madagascar, Emerging Infectious Diseases, vol.4, issue.1, pp.101-104, 1998.
DOI : 10.3201/eid0401.980114

J. Duplantier, The black rat's role in spreading human plague in Madagascar. L'Institut de recherche pour le développement, Scientific Bulletin, vol.131, pp.1-3, 2001.

J. Duplantier and D. Rakotondravony, The rodent problem in Madagascar: agricultural pest and threat to human health Ecologically-based management of rodent pests. Canberra: Australian Centre for International Agricultural Research, pp.441-459, 1999.

S. Chanteau, M. Ratsitorahina, L. Rahalison, B. Rasoamanana, and F. Chan, Current epidemiology of human plague in Madagascar, Microbes and Infection, vol.2, issue.1, pp.25-31, 2000.
DOI : 10.1016/S1286-4579(00)00289-6

R. Migliani, S. Chanteau, L. Rahalison, M. Ratsitorahina, and J. Boutin, Epidemiological trends for human plague in Madagascar during the second half of the 20th century: a survey of 20 900 notified cases, Tropical Medicine and International Health, vol.78, issue.8, pp.1228-1237, 2006.
DOI : 10.1016/S0140-6736(99)05163-6

S. Laventure, V. Andrianaja, and B. Rasoamanana, Epidémie de peste a ` Majunga en 1991 Rapport de mission de l'Institut Pasteur de Madagascar 1-26, pp.1-26, 1991.

P. Boisier, L. Rahalison, M. Rasolomaharo, M. Ratsitorahina, and M. Mahafaly, Epidemiologic Features of Four Successive Annual Outbreaks of Bubonic Plague in Mahajanga, Madagascar, Emerging Infectious Diseases, vol.8, issue.3, pp.311-316, 2002.
DOI : 10.3201/eid0803.010250

P. Boisier, M. Rasolomaharo, G. Ranaivoson, B. Rasoamanana, and L. Rakoto, Urban epidemic of bubonic plague in Majunga, Madagascar: epidemiological aspects, Tropical Medicine & International Health, vol.346, issue.5, pp.422-427, 1997.
DOI : 10.1111/j.1365-3156.1997.tb00163.x

M. Rasolomaharo, B. Rasoamanana, Z. Andrianirina, P. Buchy, and N. Rakotoarimanana, Plague in Majunga, Madagascar, The Lancet, vol.346, issue.8984, p.1234, 1995.
DOI : 10.1016/S0140-6736(95)92944-4

J. Duplantier, J. Duchemin, S. Chanteau, and E. Carniel, From the recent lessons of the Malagasy foci towards a global understanding of the factors involved in plague reemergence, Veterinary Research, vol.36, issue.3, pp.437-453, 2005.
DOI : 10.1051/vetres:2005007
URL : https://hal.archives-ouvertes.fr/hal-00902976

M. Achtman, K. Zurth, G. Morelli, G. Torrea, and A. Guiyoule, Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis, Proceedings of the National Academy of Sciences, vol.96, issue.24, pp.14043-14048, 1999.
DOI : 10.1073/pnas.96.24.14043

M. Achtman, G. Morelli, P. Zhu, T. Wirth, and I. Diehl, Microevolution and history of the plague bacillus, Yersinia pestis, Proceedings of the National Academy of Sciences, vol.101, issue.51, pp.17837-17842, 2004.
DOI : 10.1073/pnas.0408026101

M. Eppinger, P. Worsham, M. Nikolich, D. Riley, and Y. Sebastian, Genome Sequence of the Deep-Rooted Yersinia pestis Strain Angola Reveals New Insights into the Evolution and Pangenome of the Plague Bacterium, Journal of Bacteriology, vol.192, issue.6, pp.1685-1699, 2010.
DOI : 10.1128/JB.01518-09

A. Guiyoule, F. Grimont, I. Iteman, P. Grimont, and M. Lefévre, Plague pandemics investigated by ribotyping of Yersinia pestis strains, J Clin Microbiol, vol.32, pp.634-641, 1994.

V. Motin, A. Georgescu, J. Elliott, P. Hu, and P. Worsham, Genetic Variability of Yersinia pestis Isolates as Predicted by PCR-Based IS100 Genotyping and Analysis of Structural Genes Encoding Glycerol-3-Phosphate Dehydrogenase (glpD), Journal of Bacteriology, vol.184, issue.4, pp.1019-1027, 2002.
DOI : 10.1128/jb.184.4.1019-1027.2002

T. Lucier and R. Brubaker, Determination of genome size, macrorestriction pattern polymorphism, and nonpigmentation-specific deletion in Yersinia pestis by pulsed-field gel electrophoresis., Journal of Bacteriology, vol.174, issue.7, pp.2078-2086, 1992.
DOI : 10.1128/jb.174.7.2078-2086.1992

A. Guiyoule, B. Rasoamanana, C. Buchrieser, P. Michel, and S. Chanteau, Recent emergence of new variants of Yersinia pestis in Madagascar, J Clin Microbiol, vol.35, pp.2826-2833, 1997.

X. Huang, M. Chu, D. Engelthaler, and L. Lindler, Genotyping of a Homogeneous Group of Yersinia pestis Strains Isolated in the United States, Journal of Clinical Microbiology, vol.40, issue.4, pp.1164-1173, 2002.
DOI : 10.1128/JCM.40.4.1164-1173.2002

Y. Li, E. Dai, Y. Cui, M. Li, and Y. Zhang, Different Region Analysis for Genotyping Yersinia pestis Isolates from China, PLoS ONE, vol.101, issue.5, p.2166, 2008.
DOI : 10.1371/journal.pone.0002166.s002

Y. Cui, Y. Li, O. Gorgé, M. Platonov, and Y. Yan, Insight into Microevolution of Yersinia pestis by Clustered Regularly Interspaced Short Palindromic Repeats, PLoS ONE, vol.101, issue.7, p.2652, 2008.
DOI : 10.1371/journal.pone.0002652.s009
URL : https://hal.archives-ouvertes.fr/hal-00297130

J. Kingston, U. Tuteja, M. Kapil, H. Murali, and H. Batra, Genotyping of Indian Yersinia pestis strains by MLVA and repetitive DNA sequence based PCRs, Antonie van Leeuwenhoek, vol.186, issue.7, pp.303-312, 2009.
DOI : 10.1007/s10482-009-9347-2

Z. Zhang, R. Hai, Z. Song, L. Xia, and Y. Liang, Spatial Variation of Yersinia pestis from Yunnan Province of China, American Journal of Tropical Medicine and Hygiene, vol.81, issue.4, pp.714-717, 2009.
DOI : 10.4269/ajtmh.2009.09-0174

A. Klevytska, L. Price, J. Schupp, P. Worsham, and J. Wong, Identification and Characterization of Variable-Number Tandem Repeats in the Yersinia pestis Genome, Journal of Clinical Microbiology, vol.39, issue.9, pp.3179-3185, 2001.
DOI : 10.1128/JCM.39.9.3179-3185.2001

C. Pourcel, F. André-mazeaud, H. Neubauer, F. Ramisse, and G. Vergnaud, Tandem repeats analysis for the high resolution phylogenetic analysis of Yersinia pestis, BMC Microbiology, vol.4, issue.1, p.22, 2004.
DOI : 10.1186/1471-2180-4-22
URL : https://hal.archives-ouvertes.fr/hal-01158319

J. Girard, D. Wagner, A. Vogler, C. Keys, and C. Allender, From The Cover: Differential plague-transmission dynamics determine Yersinia pestis population genetic structure on local, regional, and global scales, Proceedings of the National Academy of Sciences, vol.101, issue.22, pp.8408-8413, 2004.
DOI : 10.1073/pnas.0401561101

Y. Li, Y. Cui, Y. Hauck, M. Platonov, and E. Dai, Genotyping and Phylogenetic Analysis of Yersinia pestis by MLVA: Insights into the Worldwide Expansion of Central Asia Plague Foci, PLoS ONE, vol.4, issue.6, p.6000, 2009.
DOI : 10.1371/journal.pone.0006000.s005
URL : https://hal.archives-ouvertes.fr/hal-00399011

J. Lowell, A. Zhansarina, B. Yockey, T. Meka-mechenko, and G. Stybayeva, Phenotypic and molecular characterizations of Yersinia pestis isolates from Kazakhstan and adjacent regions, Microbiology, vol.153, issue.1, pp.169-177, 2007.
DOI : 10.1099/mic.0.29059-0

X. Zhang, R. Hai, J. Wei, Z. Cui, and E. Zhang, MLVA distribution characteristics of Yersinia pestis in China and the correlation analysis, BMC Microbiology, vol.9, issue.1, p.205, 2009.
DOI : 10.1186/1471-2180-9-205

P. Keim, V. Ert, M. Pearson, T. Vogler, A. Huynh et al., Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales, Infection, Genetics and Evolution, vol.4, issue.3, pp.205-213, 2004.
DOI : 10.1016/j.meegid.2004.02.005

M. Van-ert, W. Easterday, L. Huynh, R. Okinaka, H. et al., Global Genetic Population Structure of Bacillus anthracis, PLoS ONE, vol.94, issue.5, p.461, 2007.
DOI : 10.1371/journal.pone.0000461.s006

A. Vogler, D. Birdsell, L. Price, J. Bowers, and S. Beckstrom-sternberg, Phylogeography of Francisella tularensis: Global Expansion of a Highly Fit Clone, Journal of Bacteriology, vol.191, issue.8, pp.2474-2484, 2009.
DOI : 10.1128/JB.01786-08

T. Pearson, J. Busch, J. Ravel, T. Read, and S. Rhoton, Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing, Proceedings of the National Academy of Sciences, vol.101, issue.37, pp.13536-13541, 2004.
DOI : 10.1073/pnas.0403844101
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC518758

J. Parkhill, B. Wren, N. Thomson, R. Titball, and M. Holden, Genome sequence of Yersinia pestis, the causative agent of plague, Nature, vol.404, issue.6855, pp.523-527, 2001.
DOI : 10.1038/35097083

J. Touchman, D. Wagner, J. Hao, S. Mastrian, and M. Shah, A North American Yersinia pestis Draft Genome Sequence: SNPs and Phylogenetic Analysis, PLoS ONE, vol.17, issue.2, p.220, 2007.
DOI : 10.1371/journal.pone.0000220.t003
URL : http://doi.org/10.1371/journal.pone.0000220

R. Auerbach, A. Tuanyok, W. Probert, L. Kenefic, and A. Vogler, Yersinia pestis Evolution on a Small Timescale: Comparison of Whole Genome Sequences from North America, PLoS ONE, vol.18, issue.8, p.770, 2007.
DOI : 10.1371/journal.pone.0000770.t006

P. Chain, P. Hu, S. Malfatti, L. Radnedge, and F. Larimer, Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen, Journal of Bacteriology, vol.188, issue.12, pp.4453-4463, 2006.
DOI : 10.1128/JB.00124-06

W. Deng, V. Burland, G. Plunkett, A. Boutin, and G. Mayhew, Genome Sequence of Yersinia pestis KIM, Journal of Bacteriology, vol.184, issue.16, pp.4601-4611, 2002.
DOI : 10.1128/JB.184.16.4601-4611.2002

M. Eppinger, Z. Guo, Y. Sebastian, Y. Song, and L. Lindler, Draft Genome Sequences of Yersinia pestis Isolates from Natural Foci of Endemic Plague in China, Journal of Bacteriology, vol.191, issue.24, pp.7628-7629, 2009.
DOI : 10.1128/JB.01227-09

E. Garcia, P. Worsham, S. Bearden, S. Malfatti, and D. Lang, Pestoides F, an Atypical Yersinia pestis Strain from the Former Soviet Union, Adv Exp Med Biol, vol.603, pp.17-22, 2007.
DOI : 10.1007/978-0-387-72124-8_2

Y. Song, Z. Tong, J. Wang, L. Wang, and Z. Guo, Complete Genome Sequence of Yersinia pestis Strain 91001, an Isolate Avirulent to Humans, DNA Research, vol.11, issue.3, pp.179-197, 2004.
DOI : 10.1093/dnares/11.3.179

A. Delcher, A. Phillippy, J. Carlton, and S. Salzberg, Fast algorithms for large-scale genome alignment and comparison, Nucleic Acids Research, vol.30, issue.11, pp.2478-2483, 2002.
DOI : 10.1093/nar/30.11.2478

B. Ewing, L. Hillier, M. Wendl, and P. Green, ???I. Accuracy???Assessment, Genome Research, vol.8, issue.3, pp.175-185, 1998.
DOI : 10.1101/gr.8.3.175

S. Kumar, K. Tamura, I. Jakobsen, and M. Nei, MEGA2: molecular evolutionary genetics analysis software, Bioinformatics, vol.17, issue.12, pp.1244-1245, 2001.
DOI : 10.1093/bioinformatics/17.12.1244
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/17/12/1244

K. Clarke, Non-parametric multivariate analyses of changes in community structure, Austral Ecology, vol.28, issue.1, pp.117-143, 1993.
DOI : 10.1007/BF00265008

A. Johansson, J. Farlow, P. Larsson, M. Dukerich, and E. Chambers, Worldwide Genetic Relationships among Francisella tularensis Isolates Determined by Multiple-Locus Variable-Number Tandem Repeat Analysis, Journal of Bacteriology, vol.186, issue.17, pp.5808-5818, 2004.
DOI : 10.1128/JB.186.17.5808-5818.2004

R. Migliani, M. Ratsitorahina, L. Rahalison, I. Rakotoarivony, and J. Duchemin, Resurgence of the plague in the Ikongo district of Madagascar in 1998. 1. Epidemiological aspects in the human population], Bull Soc Pathol Exot, vol.94, pp.115-118, 2001.

A. Gilabert, A. Loiseau, J. Duplantier, S. Rahelinirina, and L. Rahalison, Genetic structure of black rat populations in a rural plague focus in Madagascar, Canadian Journal of Zoology, vol.85, issue.9, pp.965-972, 2007.
DOI : 10.1139/Z07-083
URL : https://hal.archives-ouvertes.fr/ird-00261411

S. Rahelinirina, J. Duplantier, J. Ratovonjato, O. Ramilijaona, and M. Ratsimba, and Evaluation of the Plague Dispersion in Madagascar, Vector-Borne and Zoonotic Diseases, vol.10, issue.1, pp.77-84, 2010.
DOI : 10.1089/vbz.2009.0019
URL : https://hal.archives-ouvertes.fr/pasteur-00836185

C. Tollenaere, L. Rahalison, M. Ranjalahy, J. Duplantier, and S. Rahelinirina, Susceptibility to Yersinia pestis Experimental Infection in Wild Rattus rattus, Reservoir of Plague in Madagascar, EcoHealth, vol.78, issue.2, pp.242-247, 2010.
DOI : 10.1007/s10393-010-0312-3
URL : https://hal.archives-ouvertes.fr/pasteur-00836576

P. Keim and D. Wagner, Humans and evolutionary and ecological forces shaped the phylogeography of recently emerged diseases, Nature Reviews Microbiology, vol.126, issue.11, pp.813-821, 2009.
DOI : 10.1038/nrmicro2219