H. Ackermann, G. Brochu, E. Konjin, and H. , Classification ofAcinetobacter phages, Archives of Virology, vol.51, issue.3-4, pp.345-354, 1994.
DOI : 10.1007/BF01310019

M. Adams, Comparative Genome Sequence Analysis of Multidrug-Resistant Acinetobacter baumannii, Journal of Bacteriology, vol.190, issue.24, pp.8053-8064, 2008.
DOI : 10.1128/JB.00834-08

S. Altschul, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

S. Alvarez-perez, B. Lievens, H. Jacquemyn, and C. Herrera, Acinetobacter nectaris sp. nov. and Acinetobacter boissieri sp. nov., isolated from floral nectar of wild Mediterranean insect-pollinated plants, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.63, issue.Pt 4, pp.1532-1539, 2013.
DOI : 10.1099/ijs.0.043489-0

L. Antunes, F. Imperi, A. Carattoli, and P. Visca, Deciphering the Multifactorial Nature of Acinetobacter baumannii Pathogenicity, PLoS ONE, vol.108, issue.8, p.22674, 2011.
DOI : 10.1371/journal.pone.0022674.s004

L. Antunes, P. Visca, and K. Towner, : evolution of a global pathogen, Pathogens and Disease, vol.71, issue.3, pp.292-301, 2014.
DOI : 10.1111/2049-632X.12125

T. Baba, Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Molecular Systems Biology, vol.170, p.8, 2006.
DOI : 10.1038/msb4100050

V. Barbe, Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium, Nucleic Acids Research, vol.32, issue.19, pp.5766-5779, 2004.
DOI : 10.1093/nar/gkh910

R. Barrangou and L. Marraffini, CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity, Molecular Cell, vol.54, issue.2, pp.234-244, 2014.
DOI : 10.1016/j.molcel.2014.03.011

F. Battistuzzi and S. Hedges, Eubacteria The timetree of life, pp.106-115, 2009.

E. Bergogne-berezin and K. Towner, Acinetobacter spp. as nosocomial pathogens: microbiological, clinical, and epidemiological features, Clin Microbiol Rev, vol.9, pp.148-165, 1996.

T. Billard-pomares, Characterization of a P1-Like Bacteriophage Carrying an SHV-2 Extended-Spectrum ??-Lactamase from an Escherichia coli Strain, Antimicrobial Agents and Chemotherapy, vol.58, issue.11, pp.6550-6557, 2014.
DOI : 10.1128/AAC.03183-14

L. Bissonnette and P. Roy, Characterization of In0 of Pseudomonas aeruginosa plasmid pVS1, an ancestor of integrons of multiresistance plasmids and transposons of gram-negative bacteria., Journal of Bacteriology, vol.174, issue.4, pp.1248-1257, 1992.
DOI : 10.1128/jb.174.4.1248-1257.1992

C. Bland, CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats, BMC Bioinformatics, vol.8, issue.1, p.209, 2007.
DOI : 10.1186/1471-2105-8-209

L. Bobay, E. Rocha, and M. Touchon, The Adaptation of Temperate Bacteriophages to Their Host Genomes, Molecular Biology and Evolution, vol.30, issue.4, pp.737-751, 2013.
DOI : 10.1093/molbev/mss279

URL : https://hal.archives-ouvertes.fr/pasteur-01374945

P. Bouvet and S. Jeanjean, Delineation of new proteolytic genomic species in the genus Acinetobacter, Research in Microbiology, vol.140, issue.4, pp.291-299, 1989.
DOI : 10.1016/0923-2508(89)90021-1

P. Bouvet, S. Jeanjean, J. Vieu, and L. Dijkshoorn, Species, biotype, and bacteriophage type determinations compared with cell envelope protein profiles for typing Acinetobacter strains, J Clin Microbiol, vol.28, pp.170-176, 1990.

P. Bouvet and P. Grimont, Taxonomy of the Genus Acinetobacter with the Recognition of Acinetobacter baumannii sp. nov., Acinetobacter haemolyticus sp. nov., Acinetobacter johnsonii sp. nov., and Acinetobacter junii sp. nov. and Emended Descriptions of Acinetobacter calcoaceticus and Acinetobacter lwoffii, International Journal of Systematic Bacteriology, vol.36, issue.2, pp.228-240, 1986.
DOI : 10.1099/00207713-36-2-228

D. Bradley, B. I5, K. , and Z. , Characteristics and Function of Thick and Thin Conjugative Pili Determined by Transfer-derepressed Plasmids of Incompatibility Groups I1, I2, I5, B, K and Z, I2, pp.1489-1502, 1984.
DOI : 10.1099/00221287-130-6-1489

T. Bruen, H. Philippe, and D. Bryant, A Simple and Robust Statistical Test for Detecting the Presence of Recombination, Genetics, vol.172, issue.4, pp.2665-2681, 2006.
DOI : 10.1534/genetics.105.048975

G. Cambray, Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons, Mobile DNA, vol.2, issue.1, p.6, 2011.
DOI : 10.1101/gr.849004

URL : https://hal.archives-ouvertes.fr/inserm-00598347

J. Castresana, Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis, Molecular Biology and Evolution, vol.17, issue.4, pp.540-552, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026334

J. Chan, M. Halachev, N. Loman, C. Constantinidou, and M. Pallen, Defining bacterial species in the genomic era: insights from the genus Acinetobacter, BMC Microbiology, vol.12, issue.1, p.302, 2012.
DOI : 10.1093/nar/25.17.3389

A. Criscuolo and S. Gribaldo, BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evolutionary Biology, vol.10, issue.1, p.210, 2010.
DOI : 10.1186/1471-2148-10-210

T. Dandekar, B. Snel, M. Huynen, and P. Bork, Conservation of gene order: a fingerprint of proteins that physically interact, Trends in Biochemical Sciences, vol.23, issue.9, pp.324-328, 1998.
DOI : 10.1016/S0968-0004(98)01274-2

V. De-berardinis, A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1, Molecular Systems Biology, vol.9, p.174, 2008.
DOI : 10.1128/JB.187.8.2846-2857.2005

L. Diancourt, V. Passet, A. Nemec, L. Dijkshoorn, and S. Brisse, The Population Structure of Acinetobacter baumannii: Expanding Multiresistant Clones from an Ancestral Susceptible Genetic Pool, PLoS ONE, vol.175, issue.4, p.10034, 2010.
DOI : 10.1371/journal.pone.0010034.s003

X. Didelot and D. Falush, Inference of Bacterial Microevolution Using Multilocus Sequence Data, Genetics, vol.175, issue.3, pp.1251-1266, 2007.
DOI : 10.1534/genetics.106.063305

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1840087

L. Dijkshoorn, A. Nemec, and H. Seifert, An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii, Nature Reviews Microbiology, vol.49, issue.12, pp.939-951, 2007.
DOI : 10.1038/nrmicro1789

F. Doucet-populaire, P. Trieu-cuot, A. Andremont, and P. Courvalin, Conjugal transfer of plasmid DNA from Enterococcus faecalis to Escherichia coli in digestive tracts of gnotobiotic mice., Antimicrobial Agents and Chemotherapy, vol.36, issue.2, pp.502-504, 1992.
DOI : 10.1128/AAC.36.2.502

S. Eddy, Accelerated Profile HMM Searches, PLoS Computational Biology, vol.21, issue.10, p.1002195, 2011.
DOI : 10.1371/journal.pcbi.1002195.g006

URL : http://doi.org/10.1371/journal.pcbi.1002195

R. 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

D. Encinas, Plasmid Conjugation from Proteobacteria as Evidence for the Origin of Xenologous Genes in Cyanobacteria, Journal of Bacteriology, vol.196, issue.8, pp.1551-1559, 2014.
DOI : 10.1128/JB.01464-13

M. Eveillard, M. Kempf, O. Belmonte, H. Pailhories, and M. Joly-guillou, Reservoirs of Acinetobacter baumannii outside the hospital and potential involvement in emerging human community-acquired infections, International Journal of Infectious Diseases, vol.17, issue.10, 2013.
DOI : 10.1016/j.ijid.2013.03.021

M. Falagas, E. Karveli, I. Kelesidis, and T. Kelesidis, Community-acquired Acinetobacter infections, European Journal of Clinical Microbiology & Infectious Diseases, vol.46, issue.6, pp.857-868, 2007.
DOI : 10.1007/s10096-007-0365-6

D. Farrugia, The Complete Genome and Phenome of a Community-Acquired Acinetobacter baumannii, PLoS ONE, vol.5, issue.3, p.58628, 2013.
DOI : 10.1371/journal.pone.0058628.s003

J. Fay and C. Wu, Hitchhiking under positive Darwinian selection, Genetics, vol.155, pp.1405-1413, 2000.

M. Fondi, Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome, BMC Evolutionary Biology, vol.10, issue.1, p.59, 2010.
DOI : 10.1186/1471-2148-10-59

URL : https://hal.archives-ouvertes.fr/hal-00539447

M. Fondi, The genome sequence of the hydrocarbon-degrading Acinetobacter venetianus VE-C3, Research in Microbiology, vol.164, issue.5, pp.439-449, 2013.
DOI : 10.1016/j.resmic.2013.03.003

P. Fournier, Comparative Genomics of Multidrug Resistance in Acinetobacter baumannii, PLoS Genetics, vol.98, issue.1, p.7, 2006.
DOI : 10.1371/journal.pgen.0020007.sd001

D. Fouts, Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences, Nucleic Acids Research, vol.34, issue.20, pp.5839-5851, 2006.
DOI : 10.1093/nar/gkl732

R. Galhardo, R. Rocha, M. Marques, and C. Menck, An SOS-regulated operon involved in damage-inducible mutagenesis in Caulobacter crescentus, Nucleic Acids Research, vol.33, issue.8, pp.2603-2614, 2005.
DOI : 10.1093/nar/gki551

M. Garcillan-barcia, M. Francia, and F. De-la-cruz, The diversity of conjugative relaxases and its application in plasmid classification, FEMS Microbiology Reviews, vol.33, issue.3, pp.657-687, 2009.
DOI : 10.1111/j.1574-6976.2009.00168.x

O. Gascuel, New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst Biol, vol.59, pp.307-321, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

U. Gerischer and L. Ornston, Dependence of linkage of alleles on their physical distance in natural transformation of Acinetobacter sp. strain ADP1, Archives of Microbiology, vol.176, issue.6, pp.465-469, 2001.
DOI : 10.1007/s00203-001-0353-7

P. Gerner-smidt, Frequency of plasmids in strains of Acinetobacter calcoaceticus, Journal of Hospital Infection, vol.14, issue.1, pp.23-28, 1989.
DOI : 10.1016/0195-6701(89)90130-8

F. Goldstein, Transferable plasmid-mediated antibiotic resistance in Acinetobacter, Plasmid, vol.10, issue.2, pp.138-147, 1983.
DOI : 10.1016/0147-619X(83)90066-5

J. Guglielmini, Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion, Nucleic Acids Research, vol.42, issue.9, pp.5715-5727, 2014.
DOI : 10.1093/nar/gku194

URL : https://hal.archives-ouvertes.fr/pasteur-01374962

J. Guglielmini, L. Quintais, M. Garcillan-barcia, F. De-la-cruz, and E. Rocha, The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation, PLoS Genetics, vol.22, issue.8, p.1002222, 2011.
DOI : 10.1371/journal.pgen.1002222.s002

URL : https://hal.archives-ouvertes.fr/pasteur-00647077

C. Harding, Acinetobacter baumannii Strain M2 Produces Type IV Pili Which Play a Role in Natural Transformation and Twitching Motility but Not Surface-Associated Motility, mBio, vol.4, issue.4, pp.360-00313, 2013.
DOI : 10.1128/mBio.00360-13

S. Harris, Evolution of MRSA During Hospital Transmission and Intercontinental Spread, Science, vol.327, issue.5964, pp.469-474, 2010.
DOI : 10.1126/science.1182395

Y. Hauck, Diversity of Acinetobacter baumannii in Four French Military Hospitals, as Assessed by Multiple Locus Variable Number of Tandem Repeats Analysis, PLoS ONE, vol.7, issue.9, p.44597, 2012.
DOI : 10.1371/journal.pone.0044597.s006

URL : https://hal.archives-ouvertes.fr/hal-00734019

K. Hujer, Analysis of Antibiotic Resistance Genes in Multidrug-Resistant Acinetobacter sp. Isolates from Military and Civilian Patients Treated at the Walter Reed Army Medical Center, Antimicrobial Agents and Chemotherapy, vol.50, issue.12, pp.4114-4123, 2006.
DOI : 10.1128/AAC.00778-06

F. Imperi, The genomics of Acinetobacter baumannii: Insights into genome plasticity, antimicrobial resistance and pathogenicity, IUBMB Life, vol.6, issue.12, pp.1068-1074, 2011.
DOI : 10.1002/iub.531

M. Juhas, D. Crook, and D. Hood, Type IV secretion systems: tools of bacterial horizontal gene transfer and virulence, Cellular Microbiology, vol.63, issue.12, pp.2377-2386, 2008.
DOI : 10.1111/j.1462-5822.2008.01187.x

N. Karah, Species identification and molecular characterization of Acinetobacter spp. blood culture isolates from Norway, Journal of Antimicrobial Chemotherapy, vol.66, issue.4, pp.738-744, 2011.
DOI : 10.1093/jac/dkq521

K. Katoh and H. Toh, Recent developments in the MAFFT multiple sequence alignment program, Briefings in Bioinformatics, vol.9, issue.4, pp.286-298, 2008.
DOI : 10.1093/bib/bbn013

L. Kennemann, Helicobacter pylori genome evolution during human infection, Proceedings of the National Academy of Sciences, vol.108, issue.12, pp.5033-5038, 2011.
DOI : 10.1073/pnas.1018444108

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064335

K. Konstantinidis, A. Ramette, and J. Tiedje, The bacterial species definition in the genomic era, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.95, issue.12, pp.1929-1940, 2006.
DOI : 10.1073/pnas.95.12.6578

B. Krawczyk, K. Lewandowski, and J. Kur, Comparative studies of the Acinetobacter genus and the species identification method based on the recA sequences, Molecular and Cellular Probes, vol.16, issue.1, pp.1-11, 2002.
DOI : 10.1006/mcpr.2001.0388

L. Krizova, M. Maixnerova, O. Sedo, and A. Nemec, Acinetobacter bohemicus sp. nov. widespread in natural soil and water ecosystems in the Czech Republic, Systematic and Applied Microbiology, vol.37, issue.7, pp.467-473, 2014.
DOI : 10.1016/j.syapm.2014.07.001

L. Scola, B. Gundi, V. Khamis, A. Raoult, and D. , Sequencing of the rpoB Gene and Flanking Spacers for Molecular Identification of Acinetobacter Species, Journal of Clinical Microbiology, vol.44, issue.3, pp.827-832, 2006.
DOI : 10.1128/JCM.44.3.827-832.2006

P. Librado and J. Rozas, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, vol.25, issue.11, pp.1451-1452, 2009.
DOI : 10.1093/bioinformatics/btp187

K. Makarova, Evolution and classification of the CRISPR???Cas systems, Nature Reviews Microbiology, vol.35, issue.6, pp.467-477, 2011.
DOI : 10.1038/nrmicro2577

D. Martin, RDP3: a flexible and fast computer program for analyzing recombination, Bioinformatics, vol.26, issue.19, pp.2462-2463, 2010.
DOI : 10.1093/bioinformatics/btq467

A. Mather, Distinguishable Epidemics of Multidrug-Resistant Salmonella Typhimurium DT104 in Different Hosts, Science, vol.341, issue.6153, pp.1514-1517, 2013.
DOI : 10.1126/science.1240578

P. Mcgann, Amplification of Aminoglycoside Resistance Gene aphA1 in Acinetobacter baumannii Results in Tobramycin Therapy Failure, mBio, vol.5, issue.2, p.915, 2014.
DOI : 10.1128/mBio.00915-14

D. Metzgar, Acinetobacter sp. ADP1: an ideal model organism for genetic analysis and genome engineering, Nucleic Acids Research, vol.32, issue.19, pp.5780-5790, 2004.
DOI : 10.1093/nar/gkh881

V. Miele, S. Penel, and L. Duret, Ultra-fast sequence clustering from similarity networks with SiLiX, BMC Bioinformatics, vol.12, issue.1, p.116, 2011.
DOI : 10.1186/1471-2105-8-396

URL : https://hal.archives-ouvertes.fr/hal-00698365

F. Miller, The Hypervariable Region of Meningococcal Major Pilin PilE Controls the Host Cell Response via Antigenic Variation, mBio, vol.5, issue.1, pp.1024-01013, 2014.
DOI : 10.1128/mBio.01024-13

M. Muniesa, M. Colomer-lluch, and J. Jofre, Potential impact of environmental bacteriophages in spreading antibiotic resistance genes, Future Microbiology, vol.8, issue.6, pp.739-751, 2013.
DOI : 10.2217/fmb.13.32

X. Nassif, Antigenic variation of pilin regulates adhesion of Neisseria meningitidis to human epithelial cells, Molecular Microbiology, vol.6, issue.4, pp.719-725, 1993.
DOI : 10.1084/jem.173.6.1395

A. Nemec, Acinetobacter ursingii sp. nov. and Acinetobacter schindleri sp. nov., isolated from human clinical specimens, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.51, issue.5, pp.1891-1899, 2001.
DOI : 10.1099/00207713-51-5-1891

A. Nemec, Acinetobacter parvus sp. nov., a small-colony-forming species isolated from human clinical specimens, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.53, issue.5, pp.1563-1567, 2003.
DOI : 10.1099/ijs.0.02631-0

A. Nemec, Acinetobacter beijerinckii sp. nov. and Acinetobacter gyllenbergii sp. nov., haemolytic organisms isolated from humans, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.59, issue.1, 2009.
DOI : 10.1099/ijs.0.001230-0

A. Nemec, Acinetobacter bereziniae sp. nov. and Acinetobacter guillouiae sp. nov., to accommodate Acinetobacter genomic species 10 and 11, respectively, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.60, issue.4, pp.896-903, 2010.
DOI : 10.1099/ijs.0.013656-0

A. Nemec, Genotypic and phenotypic characterization of the Acinetobacter calcoaceticus???Acinetobacter baumannii complex with the proposal of Acinetobacter pittii sp. nov. (formerly Acinetobacter genomic species 3) and Acinetobacter nosocomialis sp. nov. (formerly Acinetobacter genomic species 13TU), Research in Microbiology, vol.162, issue.4, pp.393-404, 2011.
DOI : 10.1016/j.resmic.2011.02.006

A. Nemec, M. Musilek, M. Vaneechoute, E. Falsen, and L. Dijkshoorn, Lack of Evidence for "Acinetobacter septicus" as a Species Different from Acinetobacter ursingii?, Journal of Clinical Microbiology, vol.46, issue.8, pp.2826-2827, 2008.
DOI : 10.1128/JCM.01003-08

K. Nielsen, A. Bones, and J. Van-elsas, Induced natural transformation of Acinetobacter calcoaceticus in soil microcosms, Appl Environ Microbiol, vol.63, pp.3972-3977, 1997.

Y. Nishimura, T. Ino, and H. Iizuka, Acinetobacter radioresistens sp. nov. Isolated from Cotton and Soil, International Journal of Systematic Bacteriology, vol.38, issue.2, pp.209-211, 1988.
DOI : 10.1099/00207713-38-2-209

M. Norton, A. Spilkia, and V. Godoy, Antibiotic Resistance Acquired through a DNA Damage-Inducible Response in Acinetobacter baumannii, Journal of Bacteriology, vol.195, issue.6, pp.1335-1345, 2013.
DOI : 10.1128/JB.02176-12

H. Ochman and N. Moran, Genes Lost and Genes Found: Evolution of Bacterial Pathogenesis and Symbiosis, Science, vol.292, issue.5519, pp.1096-1099, 2001.
DOI : 10.1126/science.1058543

E. Paradis, C. J. Strimmer, and K. , APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-290, 2004.
DOI : 10.1093/bioinformatics/btg412

A. Peleg, The Success of Acinetobacter Species; Genetic, Metabolic and Virulence Attributes, PLoS ONE, vol.2009, issue.10, p.46984, 2012.
DOI : 10.1371/journal.pone.0046984.s005

A. Peleg, H. Seifert, and D. Paterson, Acinetobacter baumannii: Emergence of a Successful Pathogen, Clinical Microbiology Reviews, vol.21, issue.3, pp.538-582, 2008.
DOI : 10.1128/CMR.00058-07

B. Perichon, Identification of 50 Class D ??-Lactamases and 65 Acinetobacter-Derived Cephalosporinases in Acinetobacter spp., Antimicrobial Agents and Chemotherapy, vol.58, issue.2, pp.936-949, 2014.
DOI : 10.1128/AAC.01261-13

M. Ploy, F. Denis, P. Courvalin, and T. Lambert, Molecular characterization of integrons in Acinetobacter baumannii: description of Genomic Diversification of Acinetobacter GBE, 2000.

L. Poirel, S. Figueiredo, V. Cattoir, A. Carattoli, and P. Nordmann, Acinetobacter radioresistens as a Silent Source of Carbapenem Resistance for Acinetobacter spp., Antimicrobial Agents and Chemotherapy, vol.52, issue.4, pp.1252-1256, 2008.
DOI : 10.1128/AAC.01304-07

D. Porstendorfer, O. Gohl, F. Mayer, and B. Averhoff, ComP, a Pilin-Like Protein Essential for Natural Competence in Acinetobacter sp. Strain BD413: Regulation, Modification, and Cellular Localization, Journal of Bacteriology, vol.182, issue.13, pp.3673-3680, 2000.
DOI : 10.1128/JB.182.13.3673-3680.2000

M. Price, P. Dehal, and A. Arkin, FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix, Molecular Biology and Evolution, vol.26, issue.7, pp.1641-1650, 2009.
DOI : 10.1093/molbev/msp077

K. Pruitt, T. Tatusova, and D. Maglott, NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins, Nucleic Acids Research, vol.35, issue.Database, pp.61-65, 2007.
DOI : 10.1093/nar/gkl842

R. Team, R: a language and environment for statistical computing . Vienna (Austria): R Foundation for Statistical Computing, 2014.

M. Richter and R. Rossello-mora, Shifting the genomic gold standard for the prokaryotic species definition, Proceedings of the National Academy of Sciences, vol.106, issue.45, pp.19126-19131, 2009.
DOI : 10.1073/pnas.0906412106

A. Robinson, Essential Biological Processes of an Emerging Pathogen: DNA Replication, Transcription, and Cell Division in Acinetobacter spp., Microbiology and Molecular Biology Reviews, vol.74, issue.2, pp.273-297, 2010.
DOI : 10.1128/MMBR.00048-09

E. Rocha, Order and disorder in bacterial genomes, Current Opinion in Microbiology, vol.7, issue.5, pp.519-527, 2004.
DOI : 10.1016/j.mib.2004.08.006

E. Rocha, Inference and Analysis of the Relative Stability of Bacterial Chromosomes, Molecular Biology and Evolution, vol.23, issue.3, pp.513-522, 2006.
DOI : 10.1093/molbev/msj052

E. Rocha, Comparisons of dN/dS are time dependent for closely related bacterial genomes, Journal of Theoretical Biology, vol.239, issue.2, pp.226-235, 2006.
DOI : 10.1016/j.jtbi.2005.08.037

J. Rodriguez-bano, Nosocomial Bacteremia Due to an As Yet Unclassified Acinetobacter Genomic Species 17-Like Strain, Journal of Clinical Microbiology, vol.44, issue.4, pp.1587-1589, 2006.
DOI : 10.1128/JCM.44.4.1587-1589.2006

J. Sahl, Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity, BMC Genomics, vol.28, issue.11, p.291, 2011.
DOI : 10.1086/522680

J. Sahl, Evolution of a Pathogen: A Comparative Genomics Analysis Identifies a Genetic Pathway to Pathogenesis in Acinetobacter, PLoS ONE, vol.10, issue.3, p.54287, 2013.
DOI : 10.1371/journal.pone.0054287.s007

G. Shen, Isolation and Characterization of ??km18p, a Novel Lytic Phage with Therapeutic Potential against Extensively Drug Resistant Acinetobacter baumannii, PLoS ONE, vol.7, issue.10, p.46537, 2012.
DOI : 10.1371/journal.pone.0046537.t001

A. Smet, OXA-23-producing Acinetobacter species from horses: a public health hazard?, Journal of Antimicrobial Chemotherapy, vol.67, issue.12, pp.3009-3010, 2012.
DOI : 10.1093/jac/dks311

C. Smillie, M. Garcillan-barcia, M. Francia, E. Rocha, and F. De-la-cruz, Mobility of Plasmids, Microbiology and Molecular Biology Reviews, vol.74, issue.3, pp.434-452, 2010.
DOI : 10.1128/MMBR.00020-10

URL : https://hal.archives-ouvertes.fr/pasteur-01374958

M. Smith, New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis, Genes & Development, vol.21, issue.5, pp.601-614, 2007.
DOI : 10.1101/gad.1510307

B. Snel, P. Bork, and M. Huynen, Genome phylogeny based on gene content, Nature Genetics, vol.21, issue.1, pp.108-110, 1999.
DOI : 10.1038/5052

E. Snitkin, Genome-wide recombination drives diversification of epidemic strains of Acinetobacter baumannii, Proceedings of the National Academy of Sciences, vol.108, issue.33, pp.13758-13763, 2011.
DOI : 10.1073/pnas.1104404108

R. Sorek, C. Lawrence, and B. Wiedenheft, CRISPR-Mediated Adaptive Immune Systems in Bacteria and Archaea, Annual Review of Biochemistry, vol.82, issue.1, pp.237-266, 2013.
DOI : 10.1146/annurev-biochem-072911-172315

F. Tajima, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, vol.123, pp.585-595, 1989.

O. Tenaillon, E. Denamur, and I. Matic, Evolutionary significance of stress-induced mutagenesis in bacteria, Trends in Microbiology, vol.12, issue.6, pp.264-270, 2004.
DOI : 10.1016/j.tim.2004.04.002

K. Thornton, Recombination and the Properties of Tajima's D in the Context of Approximate-Likelihood Calculation, Genetics, vol.171, issue.4, pp.2143-2148, 2005.
DOI : 10.1534/genetics.105.043786

I. Tjernberg and J. Ursing, Clinical strains of Acinetobacter classified by DNA-DNA hybridization, APMIS, vol.37, issue.7-12, pp.595-605, 1989.
DOI : 10.1111/j.1699-0463.1989.tb00449.x

M. Touchon, Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths, PLoS Genetics, vol.68, issue.1, p.1000344, 2009.
DOI : 10.1371/journal.pgen.1000344.s016

URL : https://hal.archives-ouvertes.fr/hal-00390293

M. Touchon and E. Rocha, The Small, Slow and Specialized CRISPR and Anti-CRISPR of Escherichia and Salmonella, PLoS ONE, vol.14, issue.6, p.11126, 2010.
DOI : 10.1371/journal.pone.0011126.s006

URL : https://hal.archives-ouvertes.fr/pasteur-01374940

K. Towner, J. Dworkin, S. Falkow, E. Rosenberg, K. Schleifer et al., The Genus Acinetobacter, The prokaryotes, pp.746-758, 2006.

J. Turton, The role of ISAba1 in expression of OXA carbapenemase genes in Acinetobacter baumannii, FEMS Microbiology Letters, vol.258, issue.1, pp.72-77, 2006.
DOI : 10.1111/j.1574-6968.2006.00195.x

J. Turton, J. Shah, C. Ozongwu, and R. Pike, Incidence of Acinetobacter Species Other than A. baumannii among Clinical Isolates of Acinetobacter: Evidence for Emerging Species, Journal of Clinical Microbiology, vol.48, issue.4, pp.1445-1449, 2010.
DOI : 10.1128/JCM.02467-09

D. Vallenet, Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles, PLoS ONE, vol.20, issue.3, p.1805, 2008.
DOI : 10.1371/journal.pone.0001805.s003

M. Vaneechoutte, Reclassification of Acinetobacter grimontii Carr et al. 2003 as a later synonym of Acinetobacter junii Bouvet and Grimont 1986, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.58, issue.4, pp.937-940, 2008.
DOI : 10.1099/ijs.0.65129-0

I. Vaz-moreira, Acinetobacter rudis sp. nov., isolated from raw milk and raw wastewater, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.61, issue.12, pp.2837-2843, 2011.
DOI : 10.1099/ijs.0.027045-0

G. Wilharm, J. Piesker, M. Laue, and E. Skiebe, DNA Uptake by the Nosocomial Pathogen Acinetobacter baumannii Occurs during Movement along Wet Surfaces, Journal of Bacteriology, vol.195, issue.18, pp.4146-4153, 2013.
DOI : 10.1128/JB.00754-13

K. Williams, Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies, Nucleic Acids Research, vol.30, issue.4, pp.866-875, 2002.
DOI : 10.1093/nar/30.4.866

K. Williams, Phylogeny of Gammaproteobacteria, Journal of Bacteriology, vol.192, issue.9, pp.2305-2314, 2010.
DOI : 10.1128/JB.01480-09

M. Wright, New Insights into Dissemination and Variation of the Health Care-Associated Pathogen Acinetobacter baumannii from Genomic Analysis, mBio, vol.5, issue.1, pp.963-00913, 2014.
DOI : 10.1128/mBio.00963-13

K. Yamahira, Acinetobacter sp. strain Ths, a novel psychrotolerant and alkalitolerant bacterium that utilizes hydrocarbon, Extremophiles, vol.52, issue.5, pp.729-734, 2008.
DOI : 10.1007/s00792-008-0180-8

S. Yamamoto, P. Bouvet, and S. Harayama, Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA-DNA hybridization, International Journal of Systematic Bacteriology, vol.49, issue.1, pp.87-95, 1999.
DOI : 10.1099/00207713-49-1-87

Z. Yang, PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, pp.1586-1591, 2007.
DOI : 10.1093/molbev/msm088

E. Yoon, P. Courvalin, and C. Grillot-courvalin, RND-Type Efflux Pumps in Multidrug-Resistant Clinical Isolates of Acinetobacter baumannii: Major Role for AdeABC Overexpression and AdeRS Mutations, Antimicrobial Agents and Chemotherapy, vol.57, issue.7, pp.2989-2995, 2013.
DOI : 10.1128/AAC.02556-12