Classification ofAcinetobacter phages, Archives of Virology, vol.51, issue.3-4, pp.345-354, 1994. ,
DOI : 10.1007/BF01310019
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
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
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
Deciphering the Multifactorial Nature of Acinetobacter baumannii Pathogenicity, PLoS ONE, vol.108, issue.8, p.22674, 2011. ,
DOI : 10.1371/journal.pone.0022674.s004
: evolution of a global pathogen, Pathogens and Disease, vol.71, issue.3, pp.292-301, 2014. ,
DOI : 10.1111/2049-632X.12125
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
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
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
Eubacteria The timetree of life, pp.106-115, 2009. ,
Acinetobacter spp. as nosocomial pathogens: microbiological, clinical, and epidemiological features, Clin Microbiol Rev, vol.9, pp.148-165, 1996. ,
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
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
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
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
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
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. ,
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
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
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
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
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
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
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
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
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
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
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
An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii, Nature Reviews Microbiology, vol.49, issue.12, pp.939-951, 2007. ,
DOI : 10.1038/nrmicro1789
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
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
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
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
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
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
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
Hitchhiking under positive Darwinian selection, Genetics, vol.155, pp.1405-1413, 2000. ,
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
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
Comparative Genomics of Multidrug Resistance in Acinetobacter baumannii, PLoS Genetics, vol.98, issue.1, p.7, 2006. ,
DOI : 10.1371/journal.pgen.0020007.sd001
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
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
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
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
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
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
Transferable plasmid-mediated antibiotic resistance in Acinetobacter, Plasmid, vol.10, issue.2, pp.138-147, 1983. ,
DOI : 10.1016/0147-619X(83)90066-5
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
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
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
Evolution of MRSA During Hospital Transmission and Intercontinental Spread, Science, vol.327, issue.5964, pp.469-474, 2010. ,
DOI : 10.1126/science.1182395
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
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
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
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
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
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
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
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
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
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
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
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
Evolution and classification of the CRISPR???Cas systems, Nature Reviews Microbiology, vol.35, issue.6, pp.467-477, 2011. ,
DOI : 10.1038/nrmicro2577
RDP3: a flexible and fast computer program for analyzing recombination, Bioinformatics, vol.26, issue.19, pp.2462-2463, 2010. ,
DOI : 10.1093/bioinformatics/btq467
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
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
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
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
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
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
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
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
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
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
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
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
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
Induced natural transformation of Acinetobacter calcoaceticus in soil microcosms, Appl Environ Microbiol, vol.63, pp.3972-3977, 1997. ,
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
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
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
APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-290, 2004. ,
DOI : 10.1093/bioinformatics/btg412
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
Acinetobacter baumannii: Emergence of a Successful Pathogen, Clinical Microbiology Reviews, vol.21, issue.3, pp.538-582, 2008. ,
DOI : 10.1128/CMR.00058-07
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
Molecular characterization of integrons in Acinetobacter baumannii: description of Genomic Diversification of Acinetobacter GBE, 2000. ,
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
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
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
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: a language and environment for statistical computing . Vienna (Austria): R Foundation for Statistical Computing, 2014. ,
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
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
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
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
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
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
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
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
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
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
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
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
Genome phylogeny based on gene content, Nature Genetics, vol.21, issue.1, pp.108-110, 1999. ,
DOI : 10.1038/5052
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
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
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, vol.123, pp.585-595, 1989. ,
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
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
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
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
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
The Genus Acinetobacter, The prokaryotes, pp.746-758, 2006. ,
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
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
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
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
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
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
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
Phylogeny of Gammaproteobacteria, Journal of Bacteriology, vol.192, issue.9, pp.2305-2314, 2010. ,
DOI : 10.1128/JB.01480-09
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
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
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
PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, pp.1586-1591, 2007. ,
DOI : 10.1093/molbev/msm088
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