R. Regnery, C. Spruill, and B. Plikaytis, Genotypic identification of rickettsiae and estimation of intraspecies sequence divergence for portions of two rickettsial genes., Journal of Bacteriology, vol.173, issue.5, pp.1576-1589, 1991.
DOI : 10.1128/jb.173.5.1576-1589.1991

J. Higgins, Z. Hubalek, J. Halouzka, K. Elkins, A. Sjostedt et al., Detection of Francisella tularensis in infected mammals and vectors using a probe-based polymerase chain reaction., The American Journal of Tropical Medicine and Hygiene, vol.62, issue.2, pp.310-318, 2000.
DOI : 10.4269/ajtmh.2000.62.310

F. Mérien, P. Amouriaux, P. Pérolat, and G. Baranton, Saint-Girons I. Polymerase chain reaction for detection of Leptospira spp. in clinical sample, J Clin Microbiol, vol.30, issue.9, pp.2219-2224, 1992.

D. Postic, N. Riquelme-sertour, F. Merien, P. Pérolat, and G. Baranton, Interest of partial 16S rDNA gene sequences to resolve heterogeneities between Leptospira collections: application to L. meyeri, Research in Microbiology, vol.151, issue.5, pp.333-341, 2000.
DOI : 10.1016/S0923-2508(00)00156-X

J. Beaucournu and H. Launay, Les puces (Siphonaptera): De France et du Bassin mediterraneen occidental (Faune de France): Fédération française des sociétés de sciences naturelles, 1990.

A. Ribas, J. Bellocq, R. A. Ndiaye, P. , and M. J. , Abstract, Acta Parasitologica, vol.26, issue.3, pp.389-398, 2013.
DOI : 10.1093/molbev/msr121.http://dx.doi.org/10.1093/molbev/msr121

M. Del-rosario-robles, G. Navone, and I. Villafañe, New Morphological Details and First Records of Heterakis spumosa and Syphacia muris from Argentina, Comparative Parasitology, vol.75, issue.1, pp.145-149, 2008.
DOI : 10.1654/4277.1

M. Durette-desset, Le genre Nippostrongylus Lane, Nématode?Héligmosomatidé) [French], 1923.

J. Hugot and J. Quentin, Etude morphologique de six espèces nouvelles ou peu connues appartenant au genre Syphacia (Oxyuridae, Nematoda), parasites de Rongeurs, Cricétidés et Muridés, Bull Mus Hist, vol.4, issue.7, pp.383-400, 1985.
DOI : 10.1007/bf00006975

R. Anderson, A. Chabaud, and S. Willmott, Keys to the Nematode Parasites of Vertebrates: Archival volume . Wallingford (UK): CAB International, 2009.

J. Casanova, F. Santalla, P. Durand, C. Vaucher, C. Feliu et al., Morphological and genetic differentiation of Rodentolepis straminea (Goeze, 1752) and Rodentolepis microstoma (Dujardin, 1845) (Hymenolepididae), Parasitol Res, vol.87, issue.6, pp.439-444, 2001.

A. Makarikov and V. Tkach, Abstract, Acta Parasitologica, vol.21, issue.1, pp.37-49, 2013.
DOI : 10.1111/j.1096-3642.1987.tb01417.x.http://dx.doi.org/10.1111/j.1096-3642.1987.tb01417.x

S. Gardner, (Cestoda), Canadian Journal of Zoology, vol.63, issue.6, pp.1463-1469, 1985.
DOI : 10.1139/z85-219

L. Khalil, R. Bray, and A. Jones, Keys to the cestode parasites of vertebrates International, p.CAB, 1994.

T. Pojmanska, . Superfamily-brachylaimoidea, . Joyeux, and . Foley, CAB International and The Natural History Museum, Keys to the Trematoda. CAB International ed, pp.31-45, 2002.

L. Nelson and F. Clark, Correction for Sprung Traps in Catch/Effort Calculations of Trapping Results, Journal of Mammalogy, vol.54, issue.1, pp.295-298, 1973.
DOI : 10.2307/1378903

J. Theuerkauf, S. Rouys, and J. H. , Efficiency of a New Reverse-Bait Trigger Snap Trap for Invasive Rats and a New Standardised Abundance Index, Annales Zoologici Fennici, vol.48, issue.5, pp.308-318, 2011.
DOI : 10.5735/086.048.0505

R. Development and C. Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2016.

M. Nei, Estimation of average heterozygosity and genetic distance from a small number of individuals, Genetics, vol.89, issue.3, pp.583-590, 1978.

B. Weir and C. Cockerham, Estimating F-statistics for the analysis of population structure, Evolution, vol.38, issue.6, pp.1358-1370, 1984.

M. Raymond and F. Rousset, GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism, Journal of Heredity, vol.86, issue.3, pp.248-249, 1995.
DOI : 10.1093/oxfordjournals.jhered.a111573

URL : https://hal.archives-ouvertes.fr/halsde-00186383

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B (Methodological), vol.57, issue.1, pp.289-300, 1995.

S. Hall, J. Kaufman, and T. Ricketts, Defining Urban and Rural Areas in U.S. Epidemiologic Studies, Journal of Urban Health, vol.94, issue.10, pp.162-175, 2006.
DOI : 10.1093/jurban/79.suppl_1.S1

S. Barnett, The rat: a study in behaviour, 1976.

J. Wang, An estimator for pairwise relatedness using molecular markers, Genetics, vol.160, issue.3, pp.1203-1215, 2002.

O. Hardy and X. Vekemans, spagedi: a versatile computer program to analyse spatial genetic structure at the individual or population levels, Molecular Ecology Notes, vol.38, issue.4, pp.618-620, 2002.
DOI : 10.1046/j.1365-294X.1998.00360.x

S. Piry, A. Alapetite, J. Cornuet, D. Paetkau, L. Baudouin et al., GENECLASS2: A Software for Genetic Assignment and First-Generation Migrant Detection, Journal of Heredity, vol.95, issue.6, pp.536-539, 2004.
DOI : 10.1093/jhered/esh074

URL : https://academic.oup.com/jhered/article-pdf/95/6/536/6454882/esh074.pdf

D. Paetkau, R. Slade, M. Burden, and A. Estoup, Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power, Molecular Ecology, vol.16, issue.1, pp.55-65, 2004.
DOI : 10.1016/B978-012323445-2/50005-5

M. Chapuis and A. Estoup, Microsatellite Null Alleles and Estimation of Population Differentiation, Molecular Biology and Evolution, vol.24, issue.3, pp.621-631, 2007.
DOI : 10.1093/molbev/msl191

URL : https://academic.oup.com/mbe/article-pdf/24/3/621/9593504/msl191.pdf

J. Cornuet and G. Luikart, Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data, Genetics, vol.144, issue.4, pp.2001-2014, 1996.

S. Piry, G. Luikart, and J. Cornuet, Computer note. BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data, Journal of Heredity, vol.90, issue.4, pp.502-503, 1999.
DOI : 10.1093/jhered/90.4.502

S. Wasserman and K. Faust, Social network analysis: methods and applications. Cambridge, 1994.
DOI : 10.1017/CBO9780511815478

E. Vaumourin, G. Vourc-'h, S. Telfer, X. Lambin, D. Salih et al., To be or not to be associated: power study of four statistical modeling approaches to identify parasite associations in cross-sectional studies, Frontiers in Cellular and Infection Microbiology, vol.158, pp.62-24860791, 2014.
DOI : 10.1016/j.vetpar.2008.09.025

URL : https://hal.archives-ouvertes.fr/hal-01138870

G. Csardi and T. Nepusz, The igraph software package for complex network research, InterJournal, p.1695, 2006.

J. Turton, C. Hawkey, M. Hart, G. J. Hicks, and R. , Age-related changes in the haematology of female F344 rats, Laboratory Animals, vol.23, issue.4, pp.295-301, 1989.
DOI : 10.1258/002367789780746006

I. Kampfmann, N. Bauer, S. Johannes, and A. Moritz, Differences in hematologic variables in rats of the same strain but different origin, Veterinary Clinical Pathology, vol.29, issue.2, pp.228-234, 2012.
DOI : 10.1006/faat.1996.0022

M. Slatkin, Linkage disequilibrium ??? understanding the evolutionary past and mapping the medical future, Nature Reviews Genetics, vol.29, issue.6, pp.477-485, 2008.
DOI : 10.1371/journal.pgen.0020105

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5124487

B. Clapperton, A review of the current knowledge of rodent behaviour in relation to control devices Wellington ( New Zealand): Science & Technical Publishing Department of Conservation, 2006.

J. Storz, H. Bhat, and T. Kunz, GENETIC CONSEQUENCES OF POLYGYNY AND SOCIAL STRUCTURE IN AN INDIAN FRUIT BAT, CYNOPTERUS SPHINX. I. INBREEDING, OUTBREEDING, AND POPULATION SUBDIVISION, Evolution, vol.15, issue.6, pp.1215-1223, 2001.
DOI : 10.2307/2406450

J. Calhoun, The ecology and sociology of the Norway rat, of Health, Education, and Welfare Public Health Service, 1963.
DOI : 10.5962/bhl.title.112283

P. Greenwood, Mating systems, philopatry and dispersal in birds and mammals, Animal Behaviour, vol.28, issue.4, pp.1140-1162, 1980.
DOI : 10.1016/S0003-3472(80)80103-5

S. Sommer, The importance of immune gene variability (MHC) in evolutionary ecology and conservation, Frontiers in Zoology, vol.2, issue.1, pp.16-16, 2005.
DOI : 10.1186/1742-9994-2-16

T. Lenz, K. Wells, M. Pfeiffer, and S. Sommer, Diverse MHC IIB allele repertoire increases parasite resistance and body condition in the Long-tailed giant rat (Leopoldamys sabanus), BMC Evolutionary Biology, vol.9, issue.1, pp.1-13, 2009.
DOI : 10.1186/1471-2148-9-269

M. Pagès, E. Bazin, M. Galan, Y. Chaval, C. J. Herbreteau et al., complex), Molecular Ecology, vol.15, issue.170, pp.1019-1034, 2013.
DOI : 10.1111/j.1365-294X.2006.02890.x

M. Mckinney, Urbanization, Biodiversity, and Conservation, BioScience, vol.52, issue.10, pp.883-890, 2002.
DOI : 10.1641/0006-3568(2002)052[0883:UBAC]2.0.CO;2

H. Ellegren and N. Galtier, Determinants of genetic diversity, Nature Reviews Genetics, vol.16, issue.7, pp.422-433, 2016.
DOI : 10.1016/j.ajhg.2012.08.030

V. Vandenbroucke, A. Bousquet-melou, D. Backer, P. Croubels, and S. , Pharmacokinetics of eight anticoagulant rodenticides in mice after single oral administration, Journal of Veterinary Pharmacology and Therapeutics, vol.6, issue.Suppl., pp.437-445, 2008.
DOI : 10.1007/978-3-642-74936-0_32

URL : https://hal.archives-ouvertes.fr/hal-00517535

E. Vaumourin, G. Vourc-'h, P. Gasqui, and M. Vayssier-taussat, The importance of multiparasitism: examining the consequences of co-infections for human and animal health, Parasites & Vectors, vol.71, issue.5, pp.1-13, 2015.
DOI : 10.1046/j.1365-2656.2002.00656.x

C. Tollenaere, H. Susi, and A. Laine, Evolutionary and Epidemiological Implications of Multiple Infection in Plants, Trends in Plant Science, vol.21, issue.1, pp.80-90, 2016.
DOI : 10.1016/j.tplants.2015.10.014

W. Stahl, STUDIES ON THE LIFE CYCLE OF Syphacia muris, THE RAT PINWORM, The Keio Journal of Medicine, vol.12, issue.2, pp.55-60, 1963.
DOI : 10.2302/kjm.12.55

S. Klimpel, M. Förster, and G. Schmahl, Parasites of two abundant sympatric rodent species in relation to host phylogeny and ecology, Parasitology Research, vol.48, issue.4, pp.867-875, 2006.
DOI : 10.1046/j.1439-0450.2001.00445.x

S. , V. Utsuki, D. Kato, T. Sunaga, F. Ooi et al., Molecular identification of Heterakis spumosa obtained from brown rats (Rattus norvegicus) in Japan and its infectivity in experimental mice, Parasitol Res, vol.113, issue.9, pp.3449-3455, 2014.

T. Meade and J. Watson, Characterization of rat pinworm (Syphacia muris) epidemiology as a means to increase detection and elimination, J Am Assoc Lab Anim Sci, vol.53, issue.6, pp.661-667, 2014.

A. Psaroulaki, M. Antoniou, P. Toumazos, A. Mazeris, I. Ioannou et al., Rats as indicators of the presence and dispersal of six zoonotic microbial agents in Cyprus, an island ecosystem: a seroepidemiological study, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.104, issue.11, pp.733-739, 2010.
DOI : 10.1016/j.trstmh.2010.08.005

J. Lehmann, M. Matthias, J. Vinetz, and D. Fouts, Leptospiral Pathogenomics, Pathogens, vol.6, issue.2, pp.280-308, 2014.
DOI : 10.1128/CVI.00203-07

URL : http://doi.org/10.3390/pathogens3020280

A. Desvars, F. Naze, G. Vourc-'h, E. Cardinale, M. Picardeau et al., Similarities in Leptospira Serogroup and Species Distribution in Animals and Humans in the Indian Ocean Island of Mayotte, American Journal of Tropical Medicine and Hygiene, vol.87, issue.1, pp.134-140, 2012.
DOI : 10.4269/ajtmh.2012.12-0102

URL : https://hal.archives-ouvertes.fr/hal-01285445

S. Villanueva, H. Ezoe, R. Baterna, Y. Yanagihara, M. Muto et al., Serologic and Molecular Studies of Leptospira and Leptospirosis among Rats in the Philippines, American Journal of Tropical Medicine and Hygiene, vol.82, issue.5, pp.889-898, 2010.
DOI : 10.4269/ajtmh.2010.09-0711

E. Scialfa, J. Bolpe, J. Bardón, G. Ridao, J. Gentile et al., Isolation of Leptospira interrogans from suburban rats in Tandil, Buenos Aires, Argentina. Rev Argent Microbiol, vol.42, issue.2, pp.126-128, 2010.

V. Guernier, E. Lagadec, C. Cordonin, L. Minter, G. Gomard et al., Humanleptospirosis on Reunion island, Indian Ocean: are rodents the (only) ones to blame?, PLoS Negl Trop Dis, vol.10, issue.6, p.27294677, 2016.
DOI : 10.1371/journal.pntd.0004733

URL : http://doi.org/10.1371/journal.pntd.0004733

S. Barnett and M. Spencer, Experiments on the food preferences of wild rats ( Rattus norvegicus Berkenhout), Journal of Hygiene, vol.42, issue.01, pp.16-34, 1953.
DOI : 10.2307/1375143

H. Smith, C. Dickman, and P. Banks, Nest Predation by Commensal Rodents in Urban Bushland Remnants, PLOS ONE, vol.112, issue.2, p.27295091, 2016.
DOI : 10.1371/journal.pone.0156180.g003

URL : http://doi.org/10.1371/journal.pone.0156180

J. Abdelkrim, M. Pascal, C. Calmet, and S. Samadi, Importance of Assessing Population Genetic Structure before Eradication of Invasive Species: Examples from Insular Norway Rat Populations, Conservation Biology, vol.28, issue.5, pp.1509-1518, 2005.
DOI : 10.1016/S0041-1345(97)00052-3

G. Singleton, L. Hinds, H. Leirs, and Z. Zhang, Ecologically-based management of rodent pests, Monograph No. 59. Canbera: Australian Centre for International Agricultural Research (ACIAR), 1999.

D. Traweger, R. Travnitzky, C. Moser, C. Walzer, and G. Bernatzky, Habitat preferences and distribution of the brown rat (Rattus norvegicus Berk.) in the city of Salzburg (Austria): implications for an urban rat management, Journal of Pest Science, vol.19, issue.1, pp.113-125, 2006.
DOI : 10.7589/0090-3558-35.4.660