N. Alikhan, N. K. Petty, N. L. Ben-zakour, and S. A. Beatson, BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, vol.12, p.402, 2011.

K. E. Arnold, N. J. Williams, and M. Bennett, Disperse abroad in the land": The role of wildlife in the dissemination of antimicrobial resistance, Biol. Lett, vol.12, p.20160137, 2016.

R. K. Aziz, D. Bartels, A. A. Best, M. Dejongh, T. Disz et al., The RAST Server: rapid annotations using subsystems technology, BMC Genomics, vol.9, p.75, 2008.

A. Bankevich, S. Nurk, D. Antipov, A. A. Gurevich, M. Dvorkin et al., SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J. Comput. Biol, vol.19, pp.455-477, 2012.

S. Bastian, P. Nordmann, E. Creton, E. Malpote, G. Thiery et al., First case of NDM-1 producing Klebsiella pneumoniae in Caribbean islands, Int. J. Infect. Dis, vol.34, pp.53-54, 2015.

J. Bonnedahl and J. D. Järhult, Antibiotic resistance in wild birds, UPS. J. Med. Sci, vol.119, pp.113-116, 2014.

S. Breurec, S. Bastian, G. Cuzon, S. Bernabeu, T. Foucan et al., Emergence of OXA-48-producing Escherichia coli in the Caribbean islands, J. Glob. Antimicrob. Resist, vol.3, pp.217-218, 2015.

A. Carattoli, L. Villa, D. Fortini, and A. Garcia-fernandez, Contemporary IncI1 plasmids involved in the transmission and spread of antimicrobial resistance in Enterobacteriaceae, 2018.

A. Carattoli, E. Zankari, A. Garciá-fernández, M. V. Larsen, O. Lund et al., In Silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing, Antimicrob. Agents Chemother, vol.58, pp.3895-3903, 2014.

A. Criscuolo and S. Brisse, AlienTrimmer removes adapter oligonucleotides with high sensitivity in short-insert paired-end reads, Commentary on Turner, vol.5, p.130, 2014.

A. C. Darling, B. Mau, F. R. Blattner, and N. T. Perna, Mauve: multiple alignment of conserved genomic sequence with rearrangements, Genome Res, vol.14, pp.1394-1403, 2004.

L. M. Davalos and S. T. Turvey, West Indian mammals. the old, the new and the recently extinct, Bones, Clones and Biomes. The History and Geography of Recent Neotropical Mammals, pp.157-202, 2012.

M. J. Day, K. L. Hopkins, D. W. Wareham, M. A. Toleman, N. Elviss et al., Extended-spectrum beta-lactamase-producing Escherichia coli in human-derived and foodchain-derived samples from England, Wales, and Scotland: an epidemiological surveillance and typing study, Lancet Infect. Dis, vol.19, pp.1325-1335, 2019.

M. Dolejska and C. C. Papagiannitsis, Plasmid-mediated resistance is going wild, Plasmid, vol.99, pp.99-111, 2018.

E. A. Fischer, C. M. Dierikx, A. Van-essen-zandbergen, H. J. Van-roermund, D. J. Mevius et al., The IncI1 plasmid carrying the bla CTX-M-1 gene persists in in vitro culture of a Escherichia coli strain from broilers, BMC Microbiol, vol.14, p.77, 2014.

L. E. Furness, A. Campbell, L. Zhang, W. H. Gaze, and R. A. Mcdonald, Wild small mammals as sentinels for the environmental transmission of antimicrobial resistance, Environ. Res, vol.154, pp.28-34, 2017.

V. Galata, T. Fehlmann, C. Backes, and A. Keller, PLSDB: a resource of complete bacterial plasmids, Nucleic Acids Res, vol.47, pp.195-202, 2018.

S. Grouard, Modes de vie des Précolombiens des Antilles françaises. Les Nouv. l'archéologie 108/109, pp.91-101, 2007.

S. Guenther, K. Aschenbrenner, I. Stamm, A. Bethe, T. Semmler et al., Comparable high rates of extended-spectrum-beta-lactamaseproducing Escherichia coli in birds of prey from germany and mongolia, PLoS One, vol.7, p.53039, 2012.

S. Guenther, J. Wuttke, A. Bethe, J. Vojtìch, K. Schaufler et al., Is Fecal Carriage of Extended-Spectrum-?-Lactamase-Producing Escherichia coli in Urban Rats a Risk for Public Health?, Antimicrob. Agents Chemother, vol.57, pp.2424-2425, 2013.

A. Gurevich, V. Saveliev, N. Vyahhi, and G. Tesler, QUAST: Quality assessment tool for genome assemblies, Bioinformatics, vol.29, pp.1072-1075, 2013.

S. Guyomard-rabenirina, C. Dartron, M. Falord, S. Sadikalay, C. Ducat et al., Resistance to antimicrobial drugs in different surface waters and wastewaters of Guadeloupe, PLoS One, vol.12, p.173155, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01485327

S. Guyomard-rabenirina, J. Malespine, C. Ducat, S. Sadikalay, M. Falord et al., Temporal trends and risks factors for antimicrobial resistant Enterobacteriaceae urinary isolates from outpatients in Guadeloupe, BMC Microbiol, vol.16, p.121, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01351191

J. M. Hassell, M. J. Ward, D. Muloi, J. M. Bettridge, T. P. Robinson et al., Clinically relevant antimicrobial resistance at the wildlifelivestock-human interface in Nairobi: an epidemiological study, Lancet Planet. Heal, vol.3, issue.19, p.30083, 2019.

R. Laxminarayan, A. Duse, C. Wattal, A. K. Zaidi, H. F. Wertheim et al., Antibiotic resistance-the need for global solutions, Lancet Infect. Dis, vol.13, pp.1057-1098, 2013.

I. Letunic and P. Bork, Interactive Tree Of Life (iTOL) v4: recent updates and new developments, Nucleic Acids Res, vol.47, pp.256-259, 2019.

B. R. Levin and F. M. Stewart, The population biology of bacterial plasmids: a priori conditions for the existence of mobilizable nonconjugative factors, Genetics, vol.94, pp.425-443, 1980.

O. Lorvelec, M. Pascal, X. Delloue, and J. L. Chapuis, Les mammifères terrestres non volants des antilles Françaises et l'introduction récente d'un écureuil, Rev. Ecol, vol.62, pp.295-314, 2007.

A. P. Magiorakos, A. Srinivasan, R. B. Carey, Y. Carmeli, M. E. Falagas et al., Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance, Clin. Microbiol. Infect, vol.18, pp.268-281, 2012.

A. R. Manges, H. M. Geum, A. Guo, T. J. Edens, C. D. Fibke et al., Global extraintestinal pathogenic Escherichia coli (ExPEC) Lineages, Clin. Microbiol. Rev, vol.32, pp.1-25, 2019.

B. Mnif, S. Vimont, A. Boyd, E. Bourit, B. Picard et al., Molecular characterization of addiction systems of plasmids encoding extended-spectrum ?-lactamases in Escherichia coli, J. Antimicrob. Chemother, vol.65, pp.1599-1603, 2010.

R. Mostowy, N. J. Croucher, C. P. Andam, J. Corander, W. P. Hanage et al., Efficient inference of recent and ancestral recombination within bacterial populations, Mol. Biol. Evol, vol.34, pp.1167-1182, 2017.

B. D. Ondov, G. J. Starrett, A. Sappington, A. Kostic, S. Koren et al., Mash Screen: high-throughput sequence containment estimation for genome discovery, Bioinformatics, vol.20, pp.3691-3693, 2015.

G. Peirano and J. D. Pitout, Extended-Spectrum ?-Lactamase-Producing Enterobacteriaceae: update on molecular epidemiology and treatment options, Drugs, vol.79, pp.1529-1541, 2019.

L. Pinto, H. Radhouani, C. Coelho, P. Martins-da-costa, R. Simoes et al., Genetic Detection of Extended-Spectrum -Lactamase-Containing Escherichia coli isolates from birds of prey from serra da estrela natural reserve in portugal, Appl. Environ. Microbiol, vol.76, pp.4118-4120, 2010.

R. Powell and R. W. Henderson, Conservation status of Lesser Antillean reptiles, Iguana, vol.12, pp.62-77, 2005.

T. Radimersky, P. Frolkova, D. Janoszowska, M. Dolejska, P. Svec et al., Antibiotic resistance in faecal bacteria (Escherichia coli, Enterococcus spp.) in feral pigeons, J. Appl. Microbiol, vol.109, pp.1687-1695, 2010.

A. M. Ramey, J. Hernandez, V. Tyrlöv, B. D. Uher-koch, J. A. Schmutz et al., Antibiotic-Resistant Escherichia coli in migratory birds inhabiting remote Alaska, Ecohealth, vol.15, pp.72-81, 2018.

E. Saliu, W. Vahjen, and J. Zentek, Types and prevalence of extendedspectrum beta-lactamase producing Enterobacteriaceae in poultry, Anim. Heal. Res. Rev, vol.18, pp.46-57, 2017.

G. Sato, C. Oka, M. Asagi, and N. Ishiguro, Detection of conjugative R plasmids conferring chloramphenicol resistance in Escherichia coli isolated from domestic and feral pigeons and crows, Zentralbl. Bakteriol. Orig. A, pp.407-417, 1978.

T. Seemann, Prokka: rapid prokaryotic genome annotation, Bioinformatics, vol.30, pp.2068-2069, 2014.

S. and E. , Comité de l'antibiogramme de la Société Française de Microbiologie: Recommandations, 2014.

M. Y. Shobrak and A. E. Abo-amer, Role of wild birds as carriers of multidrug resistant Escherichia coli and Escherichia vulneris, Braz. J. Microbiol, vol.45, pp.1199-1209, 2014.

A. Stamatakis, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, pp.1312-1313, 2014.

A. Valcek, L. Roer, S. Overballe-petersen, F. Hansen, V. Bortolaia et al., IncI1 ST3 and IncI1 ST7 plasmids from CTX-M-1-producing Escherichia coli obtained from patients with bloodstream infections are closely related to plasmids from E. coli of animal origin, J. Antimicrob. Chemother, vol.74, pp.2171-2175, 2019.

K. Veldman, P. Van-tulden, A. Kant, J. Testerink, and D. Mevius, Characteristics of cefotaxime-resistant Escherichia coli from wild birds in The Netherlands, Appl. Environ. Microbiol, vol.79, pp.7556-7561, 2013.

N. A. Vogt, D. L. Pearl, E. N. Taboada, S. K. Mutschall, N. Janecko et al., Epidemiology of Campylobacter, Salmonella and antimicrobial resistant Escherichia coli in free-living Canada geese (Branta canadensis) from three sources in southern Ontario, Zoonoses Public Health, vol.65, pp.873-886, 2018.

J. Wang, Z. B. Ma, Z. L. Zeng, X. W. Yang, Y. Huang et al., The role of wildlife (wild birds) in the global transmission of antimicrobial resistance genes, Zool. Res, vol.38, pp.55-80, 2017.

E. Wheeler, P. Hong, L. C. Bedon, and R. I. Mackie, Carriage of antibiotic-resistant enteric bacteria varies among sites in Galapagos reptiles, J. Wildl. Dis, vol.48, pp.56-67, 2012.

R. R. Wick, L. M. Judd, C. L. Gorrie, and K. E. Holt, Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads, PLoS Comput. Biol, vol.13, p.1005595, 2017.

E. Zankari, H. Hasman, S. Cosentino, M. Vestergaard, S. Rasmussen et al., Identification of acquired antimicrobial resistance genes, J. Antimicrob. Chemother, vol.67, pp.2640-2644, 2012.