P. Abbot, A. E. Aviles, L. Eller, and L. A. Durden, Mixed Infections, Cryptic Diversity, and Vector-Borne Pathogens: Evidence from Polygenis Fleas and Bartonella Species, Applied and Environmental Microbiology, vol.73, issue.19, pp.6045-605200228, 2007.
DOI : 10.1128/AEM.00228-07
URL : http://aem.asm.org/content/73/19/6045.full.pdf

Y. Bai, M. Y. Kosoy, C. Ray, R. J. Brinkerhoff, and S. K. Collinge, Temporal and Spatial Patterns of Bartonella Infection in Black-tailed Prairie Dogs (Cynomys ludovicianus), Microbial Ecology, vol.66, issue.2, pp.373-382, 2008.
DOI : 10.2307/3809403

Y. Bai, M. F. Rizzo, D. Alvarez, D. Moran, L. F. Peruski et al., in populations of cats and their fleas in Guatemala, Journal of Vector Ecology, vol.6, issue.2, pp.327-332, 2015.
DOI : 10.1093/gbe/evu169

D. Bates, M. Mächler, B. M. Bolker, and S. C. Walker, Fitting linear mixed-effects models using lme4, J. Stat. Softw, vol.67, pp.1-48, 2015.

T. Battisttini, Verruga peruana: Sa transmission par le phlébotome. Rev. Sud-Americaine Med, Chir, vol.2, pp.719-724, 1931.

S. A. Billeter, M. G. Levy, B. B. Chomel, and E. B. Breitschwerdt, Vector transmission of Bartonella species with emphasis on the potential for tick transmission, Medical and Veterinary Entomology, vol.5, issue.1, pp.1-15, 2008.
DOI : 10.1056/NEJM199307013290102

B. Bolker, Ecological Models and Data in R, 2008.

K. J. Bown, M. Bennett, and M. Begon, Flea-borne Bartonella grahamii and Bartonella taylorii in bank voles, Emerg. Infect. Dis, vol.10, pp.6-9, 2004.

E. B. Breitschwerdt and D. L. Kordick, Bartonella Infection in Animals: Carriership, Reservoir Potential, Pathogenicity, and Zoonotic Potential for Human Infection, Clinical Microbiology Reviews, vol.13, issue.3, pp.428-438, 2000.
DOI : 10.1128/CMR.13.3.428-438.2000
URL : http://cmr.asm.org/content/13/3/428.full.pdf

R. J. Brinkerhoff, H. Kabeya, K. Inoue, Y. Bai, and S. Maruyama, Detection of multiple Bartonella species in digestive and reproductive tissues of fleas collected from sympatric mammals, The ISME Journal, vol.33, issue.7, pp.955-958, 2010.
DOI : 10.1093/molbev/msm092

C. E. Brook, Y. Bai, A. P. Dobson, L. M. Osikowicz, H. C. Ranaivoson et al., Bartonella spp. in Fruit Bats and Blood-Feeding Ectoparasites in Madagascar, PLOS Neglected Tropical Diseases, vol.32, issue.2, p.3532, 2015.
DOI : 10.1371/journal.pntd.0003532.t001
URL : https://hal.archives-ouvertes.fr/pasteur-01669060

P. Brouqui, A. Stein, H. T. Dupont, P. Gallian, S. Badiaga et al., Ectoparasitism and Vector-Borne Diseases in 930 Homeless People From Marseilles, Medicine, vol.84, issue.1, pp.61-68, 2005.
DOI : 10.1097/01.md.0000152373.07500.6e
URL : http://pdfs.journals.lww.com/md-journal/2005/01000/Ectoparasitism_and_Vector_Borne_Diseases_in_930.6.pdf?token=method|ExpireAbsolute;source|Journals;ttl|1505237600363;payload|mY8D3u1TCCsNvP5E421JYK6N6XICDamxByyYpaNzk7FKjTaa1Yz22MivkHZqjGP4kdS2v0J76WGAnHACH69s21Csk0OpQi3YbjEMdSoz2UhVybFqQxA7lKwSUlA502zQZr96TQRwhVlocEp/sJ586aVbcBFlltKNKo+tbuMfL73hiPqJliudqs17cHeLcLbV/CqjlP3IO0jGHlHQtJWcICDdAyGJMnpi6RlbEJaRheGeh5z5uvqz3FLHgPKVXJzddFRrD2hcIwdDP9eSnSkfs60p94ykRba6zJ2auKc+a4k=;hash|Wxj/fxDAQkBLVqM4FToaYQ==

J. Buffet, M. Kosoy, and M. Vayssier-taussat, -infecting rodents in light of new knowledge on genomics, diversity and evolution, Future Microbiology, vol.2, issue.9, pp.1117-1128, 2013.
DOI : 10.1017/S0031182000007058

B. B. Chomel, R. W. Kasten, B. Chi, K. Yamamoto, A. N. Gurfield et al., Experimental transmission of Bartonella henselae by the cat flea, J. Clin. Microbiol, vol.34, pp.1952-1956, 1996.

B. B. Chomel, H. Boulouis, E. B. Breitschwerdt, R. W. Kasten, M. Vayssier-taussat et al., Ecological fitness and strategies of adaptation of Bartonella species to their hosts and vectors, Vet. Res. 40, vol.29, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00903106

D. Darriba, G. L. Taboada, R. Doallo, and D. Posada, jModelTest 2: more models, new heuristics and parallel computing, Nature Methods, vol.9, issue.8, 2012.
DOI : 10.1109/TAC.1974.1100705
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4594756/pdf

C. Dehio, Bartonella interactions with endothelial cells and erythrocytes. Trends Microbiol, pp.279-285, 2001.
DOI : 10.1016/s0966-842x(01)02047-9

S. F. Dowell, Seasonal Variation in Host Susceptibility and Cycles of Certain Infectious Diseases, Emerging Infectious Diseases, vol.7, issue.3, pp.369-374, 2001.
DOI : 10.3201/eid0703.017301

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

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340
URL : https://academic.oup.com/nar/article-pdf/32/5/1792/7055030/gkh340.pdf

B. Gerber, S. M. Karpanty, C. Crawford, M. Kotschwar, and J. Randrianantenaina, An assessment of carnivore relative abundance and density in the eastern rainforests of Madagascar using remotely-triggered camera traps, Oryx, vol.62, issue.02, 2010.
DOI : 10.1017/S0030605305000074

A. D. Griffiths and B. W. Brook, Body size and growth in tropical small mammals: examining variation using non-linear mixed effects models, Journal of Zoology, vol.65, issue.02, pp.211-220, 2005.
DOI : 10.1111/j.1095-8312.2004.00357.x

V. A. Gundi, B. Davoust, A. Khamis, D. Raoult, L. Scola et al., Isolation of Bartonella rattimassiliensis sp. nov. and Bartonella phoceensis sp. nov. from European Rattus norvegicus, Journal of Clinical Microbiology, vol.42, issue.8, pp.3816-3818, 2004.
DOI : 10.1128/JCM.42.8.3816-3818.2004

A. N. Gurfield, H. J. Boulouis, B. B. Chomel, R. W. Kasten, R. Heller et al., Epidemiology of Bartonella infection in domestic cats in France, Veterinary Microbiology, vol.80, issue.2, pp.185-198, 2001.
DOI : 10.1016/S0378-1135(01)00304-2

A. R. Hardy, R. J. Quy, and L. W. Huson, Estimation of Age in the Norway Rat (Rattus norvegicus Berkenhout) from the Weight of the Eyelens, The Journal of Applied Ecology, vol.20, issue.1, pp.97-102, 1983.
DOI : 10.2307/2403378

D. M. Heisey, D. O. Joly, and F. Messier, THE FITTING OF GENERAL FORCE-OF-INFECTION MODELS TO WILDLIFE DISEASE PREVALENCE DATA, Ecology, vol.87, issue.9, pp.2356-2365, 2006.
DOI : 10.1017/S0031182000063708

G. M. Ihler, : dangerous pathogen slowly emerging from deep background, FEMS Microbiology Letters, vol.144, issue.1, pp.1-110378, 1996.
DOI : 10.1111/j.1574-6968.1996.tb08501.x

E. Janecek, A. Mietze, R. Goethe, T. Schneider, and C. Strube, in Ticks, Emerging Infectious Diseases, vol.18, issue.10, pp.1689-1690, 2012.
DOI : 10.3201/eid1810.120390

H. Kabeya, M. Sase, M. Yamashita, and S. Maruyama, in Naturally Infected Cats, Microbiology and Immunology, vol.161, issue.3, pp.171-178, 2006.
DOI : 10.1093/clinids/5.5.821

G. Kandelaki, L. Malania, Y. Bai, N. Chakvetadze, G. Katsitadze et al., Human lymphadenopathy caused by ratborne Bartonella, Emerg. Infect. Dis, vol.22, pp.1-3
DOI : 10.3201/eid2203.151823
URL : https://doi.org/10.3201/eid2203.151823

M. J. Keeling and C. A. Gilligan, Metapopulation dynamics of bubonic plague, Nature, vol.407, issue.6806, pp.903-906, 2000.
DOI : 10.1038/35038073

M. Y. Kosoy, R. L. Regnery, T. Tzianabos, E. L. Marston, D. C. Jones et al., Distribution, Diversity, and Host Specificity of Bartonella in Rodents from the Southeastern United States, The American Journal of Tropical Medicine and Hygiene, vol.57, issue.5, pp.578-588, 1997.
DOI : 10.4269/ajtmh.1997.57.578

M. Kosoy, M. Murray, R. D. Gilmore, Y. Bai, and K. L. Gage, Bartonella Strains from Ground Squirrels Are Identical to Bartonella washoensis Isolated from a Human Patient, Journal of Clinical Microbiology, vol.41, issue.2, pp.645-650, 2003.
DOI : 10.1128/JCM.41.2.645-650.2003
URL : http://jcm.asm.org/content/41/2/645.full.pdf

M. Kosoy, E. Mande, D. Green, E. Marston, D. Jones et al., of Rodents. Part II. Diverse Infections in a Single Rodent Community, Vector-Borne and Zoonotic Diseases, vol.4, issue.4, pp.296-305, 2004.
DOI : 10.1089/vbz.2004.4.296

M. Kosoy, E. Mandel, D. Green, E. Marston, and J. Childs, of Rodents. Part I. Demographic and Temporal Patterns in Population Dynamics, Vector-Borne and Zoonotic Diseases, vol.4, issue.4, pp.285-295, 2004.
DOI : 10.1089/vbz.2004.4.285

M. Kosoy, Y. Bai, K. Sheff, C. Morway, H. Baggett et al., Identification of Bartonella Infections in Febrile Human Patients from Thailand and Their Potential Animal Reservoirs, The American Journal of Tropical Medicine and Hygiene, vol.82, issue.6, pp.1140-1145, 2010.
DOI : 10.4269/ajtmh.2010.09-0778

M. Y. Kosoy, Ecological associations between bacteria of the genus Bartonella and mammals, Biology Bulletin, vol.37, issue.7, pp.716-724, 2010.
DOI : 10.1134/S1062359010070071

L. Scola, B. Liang, Z. Zeaiter, Z. Houpikian, P. Grimont et al., Genotypic Characteristics of Two Serotypes of Bartonella henselae, Journal of Clinical Microbiology, vol.40, issue.6, 2002.
DOI : 10.1128/JCM.40.6.2002-2008.2002

J. O. Lloyd-smith, D. George, K. M. Pepin, V. E. Pitzer, J. R. Pulliam et al., Epidemic Dynamics at the Human-Animal Interface, Science, vol.102, issue.7, pp.1362-1367, 2009.
DOI : 10.1073/pnas.0409608102
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3891603/pdf

G. H. Long, D. Sinha, A. F. Read, S. Pritt, B. Kline et al., Identifying the Age Cohort Responsible for Transmission in a Natural Outbreak of Bordetella bronchiseptica, PLoS Pathogens, vol.368, issue.12, 2010.
DOI : 10.1371/journal.ppat.1001224.s001

P. E. Mascarelli, M. Mcquillan, C. A. Harms, R. V. Harms, and E. B. Breitshwerdt, Bartonella henselae and B. koehlerae DNA in birds, Emerg. Infect. Dis, vol.20, pp.6-9, 2014.

C. Morway, M. Kosoy, R. Eisen, J. Montenieri, K. Sheff et al., A longitudinal study of Bartonella infection in populations of woodrats and their fleas, Journal of Vector Ecology, vol.37, issue.2, pp.353-364, 2008.
DOI : 10.3376/1081-1710-33.2.353

H. Muench, Catalytic Models in Epidemiology, 1959.
DOI : 10.4159/harvard.9780674428928

L. K. Pearce, S. V. Radecki, M. Brewer, and M. R. Lappin, Prevalence of Bartonella henselae antibodies in serum of cats with and without clinical signs of central nervous system disease, Journal of Feline Medicine & Surgery, vol.8, issue.5, pp.315-320, 2006.
DOI : 10.1016/j.jfms.2006.04.001

L. W. Pomeroy, O. N. Bjornstad, H. Kim, S. D. Jumbo, S. Abdoulkadiri et al., Serotype-Specific Transmission and Waning Immunity of Endemic Foot-and-Mouth Disease Virus in Cameroon, PLOS ONE, vol.112, issue.3???4, pp.1-16, 2015.
DOI : 10.1371/journal.pone.0136642.s001

S. Rahelinirina, J. M. Duplantier, J. Ratovonjato, O. Ramilijaona, M. Ratsimba et al., 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

P. K. Rajagopalan, Breeding behaviour and development of Rattus rattus wroughtoni Hinton 1919 (Rodentia: Muridae) in the laboratory, J. Bombay Nat. Hist. Soc, vol.67, pp.552-558, 1970.

W. K. Reeves, D. E. Szumlas, J. R. Moriarity, A. D. Loftis, M. M. Abbassy et al., LOUSE-BORNE BACTERIAL PATHOGENS IN LICE (PHTHIRAPTERA) OF RODENTS AND CATTLE FROM EGYPT, Journal of Parasitology, vol.64, issue.2, pp.313-318, 2006.
DOI : 10.1645/GE-717R.1

W. K. Reisen, Landscape Epidemiology of Vector-Borne Diseases, Annual Review of Entomology, vol.55, issue.1, pp.461-483, 2010.
DOI : 10.1146/annurev-ento-112408-085419

W. E. Ricker, Growth rates and models. Fish Physiol, pp.677-743, 1979.

J. M. Rolain, M. Franc, B. Davoust, D. Raoult, B. Quintana et al., Molecular detection of Bartonella clarridgeiae, Rickettsia felis, and Wolbachia pipientis in cat fleas, France. Emerg. Infect. Dis, vol.9, pp.0-4, 2003.

A. K. Sangaré, A. Boutellis, R. Drali, C. Socolovschi, S. C. Barker et al., Detection of Bartonella quintana in African Body and Head Lice, The American Journal of Tropical Medicine and Hygiene, vol.91, issue.2, pp.294-30113, 2014.
DOI : 10.4269/ajtmh.13-0707

F. Sauvage, M. Langlais, and D. Pontier, Predicting the emergence of human hantavirus disease using a combination of viral dynamics and rodent demographic patterns, Epidemiology and Infection, vol.135, issue.01, pp.46-56, 2007.
DOI : 10.1017/S0950268806006595
URL : https://hal.archives-ouvertes.fr/hal-00195448

A. Stamatakis, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, pp.2688-2690, 2006.
DOI : 10.1093/bioinformatics/btl446

H. Swift, TRENCH FEVER, Archives of Internal Medicine, vol.26, issue.1, pp.76-98, 1920.
DOI : 10.1001/archinte.1920.00100010079006

Y. Tsai, S. Chuang, C. Chang, P. H. Kass, and B. B. Chomel, Bartonella Species in Small Mammals and Their Ectoparasites in Taiwan, The American Journal of Tropical Medicine and Hygiene, vol.83, issue.4, pp.917-923, 2010.
DOI : 10.4269/ajtmh.2010.10-0083
URL : http://www.ajtmh.org/deliver/fulltext/14761645/83/4/917.pdf?itemId=/content/journals/10.4269/ajtmh.2010.10-0083&mimeType=pdf&containerItemId=content/journals/14761645

Y. L. Tsai, C. C. Chang, S. T. Chuang, and B. B. Chomel, Bartonella species and their ectoparasites: Selective host adaptation or strain selection between the vector and the mammalian host?, Comparative Immunology, Microbiology and Infectious Diseases, vol.34, issue.4, pp.299-314, 2011.
DOI : 10.1016/j.cimid.2011.04.005

K. H. Valentine, C. A. Harms, M. B. Cadenas, A. J. Birkenheuer, H. S. Marr et al., Bartonella DNA in loggerhead sea turtles, Emerg. Infect. Dis, vol.13, pp.6-7, 2007.

D. Vallan, Influence of forest fragmentation on amphibian diversity in the nature reserve of Ambohitantely, highland Madagascar, Biological Conservation, vol.96, issue.1, pp.31-43, 2000.
DOI : 10.1016/S0006-3207(00)00041-0

M. Vayssier-taussat, D. Le-rhun, S. Bonnet, and V. Cotté, Insights in Bartonella Host Specificity, Annals of the New York Academy of Sciences, vol.304, issue.1, pp.127-132, 2009.
DOI : 10.1645/0022-3395(2000)086[1232:CMKOBB]2.0.CO;2

M. Vayssier-taussat, S. Moutailler, F. Féménia, P. Raymond, O. Croce et al., Identification of Novel Zoonotic Activity of Bartonella spp., France, Emerging Infectious Diseases, vol.22, issue.3, pp.457-462, 2016.
DOI : 10.3201/eid2203.150269
URL : https://hal.archives-ouvertes.fr/hal-01459542

D. F. Welch, D. A. Pickett, L. N. Slater, A. G. Steigerwalt, and D. J. Brenner, Rochalimaea henselae sp. nov. a cause of septicemia, bacillary angiomatosis, and parenchymal bacillary peliosis, J. Clin. Microbiol, vol.30, pp.275-280, 1992.

D. A. Wilkinson, O. Duron, C. Cordonin, Y. Gomard, B. Ramasindrazana et al., ABSTRACT, Applied and Environmental Microbiology, vol.82, issue.6, pp.3505-3520, 2016.
DOI : 10.1128/AEM.03505-15

B. H. Yoon, C. J. Kim, R. Romero, J. K. Jun, K. H. Park et al., The laboratory rat: relating its age with human's, Am. J. Obstet. Gynecol, vol.4, pp.624-630, 2014.

H. S. Young, R. Dirzo, K. M. Helgen, D. J. Mccauley, S. Billeter et al., Declines in large wildlife increase landscape-level prevalence of rodent-borne disease in Africa, Proc. Natl. Acad. Sci, pp.1-6, 2014.
DOI : 10.1128/AEM.06012-11

E. M. Zullinger, R. E. Ricklefs, K. H. Redford, and G. M. Mace, Fitting Sigmoidal Equations to Mammalian Growth Curves, Journal of Mammalogy, vol.65, issue.4, pp.607-636, 1984.
DOI : 10.2307/1380844