R. Hartskeerl, M. Collares-pereira, and W. Ellis, Emergence, control and re-emerging leptospirosis: dynamics of infection in the changing world, Clinical Microbiology and Infection, vol.17, issue.4, pp.494-501, 2011.
DOI : 10.1111/j.1469-0691.2011.03474.x

B. Abela-ridder, R. Sikkema, and R. Hartskeerl, Estimating the burden of human leptospirosis, International Journal of Antimicrobial Agents, vol.36, issue.1, pp.5-7, 2010.
DOI : 10.1016/j.ijantimicag.2010.06.012

V. Wuthiekanun, N. Sirisukkarn, P. Daengsupa, P. Sakaraserane, and A. Sangkakam, Clinical Diagnosis and Geographic Distribution of Leptospirosis, Thailand, Emerging Infectious Diseases, vol.13, issue.1, pp.124-126, 2007.
DOI : 10.3201/eid1301.060718

A. Ko, G. R. Mitermayer, R. Dourado, C. M. Johnson, W. D. Riley et al., Urban epidemic of severe leptospirosis in Brazil, The Lancet, vol.354, issue.9181, pp.820-825, 1999.
DOI : 10.1016/S0140-6736(99)80012-9

R. Plank and D. Dean, Overview of the epidemiology, microbiology, and pathogenesis of Leptospira spp. in humans, Microbes and Infection, vol.2, issue.10, pp.1265-1276, 2000.
DOI : 10.1016/S1286-4579(00)01280-6

A. Bharti, J. Nally, J. Ricaldi, M. Matthias, and M. Diaz, Leptospirosis: a zoonotic disease of global importance, The Lancet Infectious Diseases, vol.3, issue.12, pp.757-71, 2003.
DOI : 10.1016/S1473-3099(03)00830-2

J. Crump, A. Morrissey, W. Nicholson, R. Massung, and R. Stoddard, Etiology of Severe Non-malaria Febrile Illness in Northern Tanzania: A Prospective Cohort Study, PLoS Neglected Tropical Diseases, vol.55, issue.7, 2013.
DOI : 10.1371/journal.pntd.0002324.s001

A. Berlioz-arthaud, B. Guillard, C. Goarant, and S. Hem, Hospital based active surveillance of human leptospirosis in Cambodia, Bulletin de la Soci??t?? de pathologie exotique, vol.54, issue.2, pp.111-119, 2010.
DOI : 10.1007/s13149-010-0043-2
URL : https://hal.archives-ouvertes.fr/pasteur-00494643

L. Kawaguchi, B. Sengkeopraseuth, R. Tsuyuoka, N. Koizumi, and H. Akashi, Seroprevalence of leptospirosis and risk factor analysis in floodprone rural areas in Lao PDR, Am J Trop Med Hyg, vol.78, pp.957-961, 2008.

W. Tangkanakul, P. Tharmaphornpil, B. Plikaytis, S. Bragg, and D. Poonsuksombat, Risk factors associated with leptospirosis in northeastern Thailand (1998) Am, J. Trop. Med. Hyg, vol.63, pp.204-208, 2000.

G. Trueba, S. Zapata, K. Madrid, P. Cullen, and D. Haake, Cell aggregation: a mechanism of pathogenic Leptospira to survive in fresh water, International Microbiology, vol.7, pp.35-40, 2004.

C. Ganoza, M. Matthias, D. Collins-richards, K. Brouwer, and C. Cunningham, Determining Risk for Severe Leptospirosis by Molecular Analysis of Environmental Surface Waters for Pathogenic Leptospira, PLoS Medicine, vol.73, issue.8, 2006.
DOI : 10.1371/journal.pmed.0030308.sd002

V. Herbreteau, W. Rerkamnuaychoke, S. Jittapalapong, Y. Chaval, J. Cosson et al., Field and laboratory protocols for rodent studies, Kasetsart University Press 46 p. (freely available on http, 2011.
URL : https://hal.archives-ouvertes.fr/ird-00714514

M. Pagès, Y. Chaval, V. Herbreteau, S. Waengsothorn, and J. Cosson, Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries, BMC Evolutionary Biology, vol.10, issue.1, p.184, 2010.
DOI : 10.1186/1471-2148-10-184

M. Galan, M. Pagès, and J. Cosson, Next-Generation Sequencing for Rodent Barcoding: Species Identification from Fresh, Degraded and Environmental Samples, PLoS ONE, vol.16, issue.11, p.48374, 2012.
DOI : 10.1371/journal.pone.0048374.s013

M. Pagès, E. Bazin, Y. Chaval, M. Galan, and V. Herbreteau, complex), Molecular Ecology, vol.15, issue.170, pp.1019-1034, 2013.
DOI : 10.1111/mec.12149

K. Aplin, H. Suzuki, and A. Chinen, Multiple Geographic Origins of Commensalism and Complex Dispersal History of Black Rats, PLoS ONE, vol.55, issue.11, p.26357, 2011.
DOI : 10.1371/journal.pone.0026357.s007
URL : https://hal.archives-ouvertes.fr/ird-00714383

N. Clairon, D. Lepicard, D. Picard, and Y. Chaval, Rodent SEA: a web service for South East Asian Rodent identification, 2010.

D. Badenhorst, C. Tatard, Y. Suputtamongkol, T. Robinson, and G. Dobigny, Host cell/Orientia tsutsugamushi interactions: Evolution and expression of syndecan-4 in Asian rodents (Rodentia, Muridae), Infection, Genetics and Evolution, vol.12, issue.5, pp.1136-1146, 2012.
DOI : 10.1016/j.meegid.2012.03.020

D. Haake, G. Chao, R. Zuerner, J. Barnett, and D. Barnett, The Leptospiral Major Outer Membrane Protein LipL32 Is a Lipoprotein Expressed during Mammalian Infection, Infection and Immunity, vol.68, issue.4, pp.2276-85, 2000.
DOI : 10.1128/IAI.68.4.2276-2285.2000

R. Stoddard, J. Gee, P. Wilkins, K. Mccaustland, and A. Hoffmaster, Detection of pathogenic Leptospira spp. through TaqMan polymerase chain reaction targeting the LipL32 gene, Diagnostic Microbiology and Infectious Disease, vol.64, issue.3, pp.247-55, 2009.
DOI : 10.1016/j.diagmicrobio.2009.03.014

F. Mérien, P. Amouriaux, P. Perolat, and G. Baranton, Saint Girons I (1992) Polymerase chain reaction for detection of Leptospira spp. in clinical samples, J Clin Microbiol, vol.30, issue.9, pp.2219-2243

N. Ahmed, S. Devi, V. Mde, L. Vijayachari, P. Machang-'u et al., Multilocus sequence typing method for identification and genotypic classification of pathogenic Leptospira species, Ann Clin Microbiol Antimicrob, vol.23, issue.5, p.28, 2006.

L. Salaün, F. Mérien, S. Gurianova, G. Baranton, and M. Picardeau, Application of Multilocus Variable-Number Tandem-Repeat Analysis for Molecular Typing of the Agent of Leptospirosis, Journal of Clinical Microbiology, vol.44, issue.11, pp.3954-62, 2006.
DOI : 10.1128/JCM.00336-06

G. Cerqueira, A. Mcbride, R. Hartskeerl, N. Ahmed, O. Dellagostin et al., Bioinformatics describes novel Loci for high resolution discrimination of leptospira isolates Conservation of the S10-spc-alpha locus within otherwise highly plastic genomes provides phylogenetic insight into the genus Leptospira, PLoS One PLoS One, vol.15, issue.37, pp.15335-15362, 2008.

A. Ahmed, J. Thaipadungpanit, S. Boonsilp, V. Wuthiekanun, and K. Nalam, Comparison of Two Multilocus Sequence Based Genotyping Schemes for Leptospira Species, PLoS Neglected Tropical Diseases, vol.48, issue.3, 2011.
DOI : 10.1371/journal.pntd.0001374.t003

K. Nalam, A. Ahmed, S. Devi, P. Francalacci, and M. Baig, Genetic Affinities within a Large Global Collection of Pathogenic Leptospira: Implications for Strain Identification and Molecular Epidemiology, PLoS ONE, vol.4, issue.16, p.12637, 2010.
DOI : 10.1371/journal.pone.0012637.s002

M. Gouy, S. Guindon, and O. Gascuel, SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol.27, issue.2, pp.221-225, 2010.
DOI : 10.1093/molbev/msp259
URL : https://hal.archives-ouvertes.fr/lirmm-00705187

K. Barton, Model selection and model averaging based on information criteria (AICc and alike), 2012.

D. Bates, M. Maechler, and B. Bolker, Linear mixed-effects models using S4 classes, 2012.

K. Burnham, Model Selection and Inference. A Practical Informationtheoretic Approach, 1998.

J. Johnson and K. Omland, Model selection in ecology and evolution, Trends in Ecology & Evolution, vol.19, issue.2, pp.101-108, 2004.
DOI : 10.1016/j.tree.2003.10.013

J. Thaipadungpanit, V. Wuthiekanun, W. Chierakul, L. Smythe, and W. Petkanchanapong, A Dominant Clone of Leptospira interrogans Associated with an Outbreak of Human Leptospirosis in Thailand, PLoS Neglected Tropical Diseases, vol.5, issue.1, 2007.
DOI : 10.1371/journal.pntd.0000056.s001

M. De-faria, M. Calderwood, D. Athanazio, A. Mcbride, and R. Hartskeerl, Carriage of Leptospira interrogans among domestic rats from an urban setting highly endemic for leptospirosis in Brazil, Acta Tropica, vol.108, issue.1, pp.1-5, 2008.
DOI : 10.1016/j.actatropica.2008.07.005

P. Agudelo-florez, A. Londono, V. Quiroz, J. Angel, and N. Moreno, Prevalence of Leptospira spp. in Urban Rodents from a Groceries Trade Center of Medellin, Colombia, American Journal of Tropical Medicine and Hygiene, vol.81, issue.5, pp.906-910, 2009.
DOI : 10.4269/ajtmh.2009.09-0195

J. Perez, F. Brescia, J. Becam, C. Mauron, and C. Goarant, Rodent Abundance Dynamics and Leptospirosis Carriage in an Area of Hyper-Endemicity in New Caledonia, PLoS Neglected Tropical Diseases, vol.6, issue.10, 2011.
DOI : 10.1371/journal.pntd.0001361.s003
URL : https://hal.archives-ouvertes.fr/pasteur-00655437

S. Ivanova, V. Herbreteau, K. Blasdell, Y. Chaval, and P. Buchy, Leptospira and Rodents in Cambodia: Environmental Determinants of Infection, American Journal of Tropical Medicine and Hygiene, vol.86, issue.6, pp.1032-1038, 2012.
DOI : 10.4269/ajtmh.2012.11-0349
URL : https://hal.archives-ouvertes.fr/pasteur-00808144

C. Combes, Parasitism: the ecology and evolution of intimate interactions, 2001.

F. Bordes and S. Morand, The impact of multiple infections on wild animal hosts: a review, Infection Ecology & Epidemiology, vol.1, issue.1, p.7346, 2011.
DOI : 10.3402/iee.v1i0.7346

M. Keeling and P. Rohani, Modeling Infectious Diseases in Humans and Animals, 2008.

S. Klein, The effects of hormones on sex differences in infection: from genes to behavior, Neuroscience & Biobehavioral Reviews, vol.24, issue.6, pp.627-638, 2000.
DOI : 10.1016/S0149-7634(00)00027-0

F. Bordes, V. Herbreteau, S. Dupuy, Y. Chaval, A. Tran et al., The diversity of microparasites of rodents: a comparative analysis that helps in identifying rodent-borne rich habitats in Southeast Asia, Infection Ecology & Epidemiology, vol.81, issue.2, p.20178, 2013.
DOI : 10.1080/10408410902989837
URL : https://hal.archives-ouvertes.fr/hal-01239634

V. Herbreteau, F. Bordes, S. Jittapalapong, Y. Supputamongkol, and S. Morand, Rodent-borne diseases in Thailand: targeting rodent carriers and risky habitats, Infection Ecology & Epidemiology, vol.9, issue.1, p.18637, 2012.
DOI : 10.3402/iee.v2i0.18637
URL : https://hal.archives-ouvertes.fr/ird-00714369

B. Gauffre, E. Petit, S. Brodier, V. Bretagnolle, and J. Cosson, Sex-biased dispersal patterns depend on the spatial scale in a social rodent, Proceedings of the Royal Society B: Biological Sciences, vol.13, issue.4, pp.3487-3494, 2009.
DOI : 10.1046/j.1365-294X.2004.02076.x
URL : https://hal.archives-ouvertes.fr/hal-00408329

T. Bonnet, L. Crespin, A. Pinot, L. Bruneteau, V. Bretagnolle et al., How the common vole copes with modern farming: Insights from a capture???mark???recapture experiment, Agriculture, Ecosystems & Environment, vol.177, pp.21-27, 2013.
DOI : 10.1016/j.agee.2013.05.005
URL : https://hal.archives-ouvertes.fr/hal-00919006

E. Guivier, M. Galan, Y. Chaval, A. Xuereb, R. Salvador et al., Landscape genetics highlight the pre-eminent role of rodent metapopulation host dynamics in the epidemiology of hantavirus Puumala, Molecular Ecology, vol.20, issue.17, pp.3569-3583, 2011.

G. Singleton, L. Smythe, G. Smith, . Sprattdm, K. Aplin et al., Rodent diseases in southeast Asia and Australia: inventory of recent surveys, Rats, Mice and People: Rodent Biology and Management. Canberra: Australian Centre for International Agricultural Research, pp.26-30, 2003.

K. Laras, C. Van, K. Bounlu, N. Tien, and J. Olson, the importance of leptospirosis in Southeast Asia, Am J Trop Med Hyg, vol.67, pp.278-286, 2002.

D. Benacer, M. Zain, S. Amran, F. Galloway, R. et al., Isolation and Molecular Characterization of Leptospira interrogans and Leptospira borgpetersenii Isolates from the Urban Rat Populations of Kuala Lumpur, Malaysia, American Journal of Tropical Medicine and Hygiene, vol.88, issue.4, pp.704-70910, 2013.
DOI : 10.4269/ajtmh.12-0662

K. Vedhagiri, K. Natarajaseenivasan, S. Prabhakaran, J. Selvin, and R. Narayanan, Characterization of Leptospira borgpetersenii isolates from field rats (Rattus norvegicus) by 16S rRNA and lipL32 gene sequencing, Brazilian Journal of Microbiology, vol.41, issue.1, pp.150-157, 2010.
DOI : 10.1590/S1517-83822010000100022

D. Bulach, R. Zuerner, P. Wilson, T. Seemann, and A. Mcgrath, Genome reduction in Leptospira borgpetersenii reflects limited transmission potential, Proceedings of the National Academy of Sciences, vol.103, issue.39, pp.14560-14565, 2006.
DOI : 10.1073/pnas.0603979103