Y. Abbott, R. O'mahony, N. Leonard, P. J. Quinn, T. Van-der-reijden et al., Characterization of a 2.6 kbp variable region within a class 1 integron found in an Acinetobacter baumannii strain isolated from a horse, J. Antimicrob. Chemother, vol.55, pp.367-370, 2005.

M. Abella, S. Campoy, I. Erill, F. Rojo, and J. Barbé, Cohabitation of two different lexA regulons in Pseudomonas putida, J. Bacteriol, vol.189, pp.8855-8862, 2007.

D. F. Ackerley, Y. Barak, S. V. Lynch, J. Curtin, and A. Matin, Effect of chromate stress on Escherichia coli K-12, J. Bacteriol, vol.188, pp.3371-3381, 2006.

M. D. Adams, K. Goglin, N. Molyneaux, K. M. Hujer, H. Lavender et al., Comparative genome sequence analysis of multidrug-resistant Acinetobacter baumannii, J. Bacteriol, vol.190, pp.8053-8064, 2008.

A. Aertsen and C. W. Michiels, Mrr instigates the SOS response after high pressure stress in Escherichia coli, Mol. Microbiol, vol.58, pp.1381-1391, 2005.

A. Aertsen, R. Van-houdt, K. Vanoirbeek, and C. W. Michiels, An SOS response induced by high pressure in Escherichia coli, J. Bacteriol, vol.186, pp.6133-6141, 2004.

A. M. Ahmed, H. Nakano, and T. Shimamoto, Molecular characterization of integrons in non-typhoid Salmonella serovars isolated in Japan: description of an unusual class 2 integron, J. Antimicrob. Chemother, vol.55, pp.371-374, 2005.

A. Atrouni, A. Joly-guillou, M. Hamze, M. Kempf, and M. , Reservoirs of Non-baumannii Acinetobacter Species. Front. Microbiol, vol.7, p.49, 2016.

A. Bayssari, C. Dabboussi, F. Hamze, M. Rolain, and J. , Emergence of carbapenemaseproducing Pseudomonas aeruginosa and Acinetobacter baumannii in livestock animals in Lebanon, J. Antimicrob. Chemother, vol.70, pp.950-951, 2015.

A. Alonso, E. Campanario, and J. L. Martínez, Emergence of multidrug-resistant mutants is increased under antibiotic selective pressure in Pseudomonas aeruginosa, Microbiol. Read. Engl, vol.145, pp.2857-2862, 1999.

M. S. Alves, A. Pereira, S. M. Araújo, B. B. Castro, A. C. Correia et al., Seawater is a reservoir of multi-resistant Escherichia coli, including strains hosting plasmid-mediated quinolones resistance and extended-spectrum beta-lactamases genes, Front. Microbiol, vol.5, p.426, 2014.

S. G. Andersson, A. Zomorodipour, J. O. Andersson, T. Sicheritz-pontén, U. C. Alsmark et al., The genome sequence of Rickettsia prowazekii and the origin of mitochondria, Nature, vol.396, pp.133-140, 1998.

L. C. Antunes, P. Visca, and K. J. Towner, Acinetobacter baumannii: evolution of a global pathogen, Pathog. Dis, vol.71, pp.292-301, 2014.

P. Antunes, J. Machado, and L. Peixe, Dissemination of sul3-containing elements linked to class 1 integrons with an unusual 3' conserved sequence region among Salmonella isolates, Antimicrob. Agents Chemother, vol.51, pp.1545-1548, 2007.

P. Antunes, J. Machado, J. C. Sousa, and L. Peixe, Dissemination amongst humans and food products of animal origin of a Salmonella typhimurium clone expressing an integronborne OXA-30 beta-lactamase, J. Antimicrob. Chemother, vol.54, pp.429-434, 2004.

A. Apisarnthanarak, T. Khawcharoenporn, and L. M. Mundy, Patterns of nosocomial infections, multidrug-resistant microorganisms, and mold detection after extensive black-water flooding: a survey from central Thailand, Infect. Control Hosp. Epidemiol, vol.34, pp.861-863, 2013.

Y. Arakawa, M. Murakami, K. Suzuki, H. Ito, R. Wacharotayankun et al., A novel integron-like element carrying the metallo-beta-lactamase gene blaIMP, Antimicrob. Agents Chemother, vol.39, pp.1612-1615, 1995.

J. Aranda, C. Bardina, A. Beceiro, S. Rumbo, M. P. Cabral et al., Acinetobacter baumannii RecA protein in repair of DNA damage, antimicrobial resistance, general stress response, and virulence, J. Bacteriol, vol.193, pp.3740-3747, 2011.

J. Aranda, M. López, E. Leiva, A. Magán, B. Adler et al., Role of Acinetobacter baumannii UmuD homologs in antibiotic resistance acquired through DNA damage-induced mutagenesis, Antimicrob. Agents Chemother, vol.58, pp.1771-1773, 2014.

J. Aranda, M. Poza, M. Shingu-vázquez, P. Cortés, J. D. Boyce et al., Identification of a DNA-damage-inducible regulon in Acinetobacter baumannii, J. Bacteriol, vol.195, pp.5577-5582, 2013.

P. Argos, A. Landy, K. Abremski, J. B. Egan, E. Haggard-ljungquist et al., The integrase family of site-specific recombinases: regional similarities and global diversity, EMBO J, vol.5, pp.433-440, 1986.

K. Asadollahi, M. Taherikalani, A. Maleki, E. Alizadeh, H. Valadbaigi et al., Diversity of aminoglycoside modifying enzyme genes among multidrug resistant Acinetobacter baumannii genotypes isolated from nosocomial infections in Tehran hospitals and their association with class 1 integrons, Acta Microbiol. Immunol. Hung, vol.58, pp.359-370, 2011.

Z. Baharoglu, D. Bikard, and D. Mazel, Conjugative DNA transfer induces the bacterial SOS response and promotes antibiotic resistance development through integron activation, PLoS Genet, vol.6, p.1001165, 2010.

Z. Baharoglu, E. Krin, and D. Mazel, Connecting environment and genome plasticity in the characterization of transformation-induced SOS regulation and carbon catabolite control of the Vibrio cholerae integron integrase, J. Bacteriol, vol.194, pp.1659-1667, 2012.

Z. Baharoglu and D. Mazel, SOS, the formidable strategy of bacteria against aggressions, FEMS Microbiol. Rev, vol.38, pp.1126-1145, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01423593

Z. Baharoglu and D. Mazel, Vibrio cholerae triggers SOS and mutagenesis in response to a wide range of antibiotics: a route towards multiresistance, Antimicrob. Agents Chemother, vol.55, pp.2438-2441, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-01423615

J. K. Bailey, J. L. Pinyon, S. Anantham, and R. M. Hall, Commensal Escherichia coli of healthy humans: a reservoir for antibiotic-resistance determinants, J. Med. Microbiol, vol.59, pp.1331-1339, 2010.

S. L. Baines, K. E. Holt, M. B. Schultz, T. Seemann, B. O. Howden et al., Convergent adaptation in the dominant global hospital clone ST239 of methicillin-resistant Staphylococcus aureus, vol.6, p.80, 2015.

A. M. Bardbari, M. R. Arabestani, M. Karami, F. Keramat, M. Y. Alikhani et al., Correlation between ability of biofilm formation with their responsible genes and MDR patterns in clinical and environmental, Acinetobacter baumannii isolates. Microb. Pathog, vol.108, pp.122-128, 2017.

A. L. Barkovskii, C. Green, and D. Hurley, The occurrence, spatial and temporal distribution, and environmental routes of tetracycline resistance and integrase genes in Crassostrea virginica beds, Mar. Pollut. Bull, vol.60, pp.2215-2224, 2010.

R. S. Barlow and K. S. Gobius, Diverse class 2 integrons in bacteria from beef cattle sources, J. Antimicrob. Chemother, vol.58, pp.1133-1138, 2006.

S. G. Bartual, H. Seifert, C. Hippler, M. A. Luzon, H. Wisplinghoff et al., Development of a multilocus sequence typing scheme for characterization of clinical isolates of Acinetobacter baumannii, J. Clin. Microbiol, vol.43, pp.4382-4390, 2005.

O. Barraud, E. Badell, F. Denis, N. Guiso, and M. Ploy, Antimicrobial drug resistance in Corynebacterium diphtheriae mitis, Emerg. Infect. Dis, vol.17, pp.2078-2080, 2011.

O. Barraud, C. Isnard, R. Lienhard, F. Guérin, E. Couvé-deacon et al., Sulphonamide resistance associated with integron derivative Tn6326 in Actinotignum schaalii, J. Antimicrob. Chemother, vol.71, pp.2670-2671, 2016.

O. Barraud and M. Ploy, Diversity of Class 1 Integron Gene Cassette Rearrangements Selected under Antibiotic Pressure, J. Bacteriol, vol.197, pp.2171-2178, 2015.

S. G. Bartual, H. Seifert, C. Hippler, M. A. Luzon, H. Wisplinghoff et al., Development of a multilocus sequence typing scheme for characterization of clinical isolates of Acinetobacter baumannii, J. Clin. Microbiol, vol.43, pp.4382-4390, 2005.

J. W. Beaber, B. Hochhut, and M. K. Waldor, SOS response promotes horizontal dissemination of antibiotic resistance genes, Nature, vol.427, pp.72-74, 2004.

O. Belmonte, H. Pailhoriès, M. Kempf, M. P. Gaultier, C. Lemarié et al., High prevalence of closely-related Acinetobacter baumannii in pets according to a multicentre study in veterinary clinics, Reunion Island, Vet. Microbiol, vol.170, pp.446-450, 2014.

J. Bengtsson-palme, M. Angelin, M. Huss, S. Kjellqvist, E. Kristiansson et al., The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents, Antimicrob. Agents Chemother, vol.59, pp.6551-6560, 2015.

P. M. Bennett, Integrons and gene cassettes: a genetic construction kit for bacteria, J. Antimicrob. Chemother, vol.43, pp.1-4, 1999.

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

J. Berlau, H. M. Aucken, E. Houang, and T. L. Pitt, Isolation of Acinetobacter spp. including A. baumannii from vegetables: implications for hospital-acquired infections, J. Hosp. Infect, vol.42, pp.201-204, 1999.

C. T. Binh, H. Heuer, M. Kaupenjohann, and K. Smalla, Diverse aadA gene cassettes on class 1 integrons introduced into soil via spread manure, Res. Microbiol, vol.160, pp.427-433, 2009.

K. M. Bischoff, D. G. White, M. E. Hume, T. L. Poole, and D. J. Nisbet, The chloramphenicol resistance gene cmlA is disseminated on transferable plasmids that confer multipledrug resistance in swine Escherichia coli, FEMS Microbiol. Lett, vol.243, pp.285-291, 2005.

L. Biskri and D. Mazel, Erythromycin esterase gene ere(A) is located in a functional gene cassette in an unusual class 2 integron, Antimicrob. Agents Chemother, vol.47, pp.3326-3331, 2003.

L. Bissonnette and P. H. Roy, Characterization of In0 of Pseudomonas aeruginosa plasmid pVS1, an ancestor of integrons of multiresistance plasmids and transposons of gramnegative bacteria, J. Bacteriol, vol.174, pp.1248-1257, 1992.

J. Björkman, D. Hughes, and D. I. Andersson, Virulence of antibiotic-resistant Salmonella typhimurium, Proc. Natl. Acad. Sci. U. S. A, vol.95, pp.3949-3953, 1998.

G. A. Blackwell, M. Hamidian, and R. M. Hall, IncM Plasmid R1215 Is the Source of Chromosomally Located Regions Containing Multiple Antibiotic Resistance Genes in the Globally Disseminated Acinetobacter baumannii GC1 and GC2 Clones, 2016.

G. A. Blackwell, K. E. Holt, S. D. Bentley, L. Y. Hsu, and R. M. Hall, Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore, J. Antimicrob. Chemother, vol.72, pp.1031-1039, 2017.

G. A. Blackwell, S. J. Nigro, and R. M. Hall, Evolution of AbGRI2-0, the Progenitor of the AbGRI2 Resistance Island in Global Clone 2 of Acinetobacter baumannii, Antimicrob. Agents Chemother, vol.60, pp.1421-1429, 2015.

S. Bordenave, M. S. Goñi-urriza, P. Caumette, and R. Duran, Effects of heavy fuel oil on the bacterial community structure of a pristine microbial mat, Appl. Environ. Microbiol, vol.73, pp.6089-6097, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01631901

Y. Boucher, O. X. Cordero, A. Takemura, D. E. Hunt, K. Schliep et al., Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations, vol.2, 2011.

P. J. Bouvet and P. A. 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, Int. J. Syst. Evol. Microbiol, vol.36, pp.228-240, 1986.

M. Bouvier, G. Demarre, and D. Mazel, Integron cassette insertion: a recombination process involving a folded single strand substrate, EMBO J, vol.24, pp.4356-4367, 2005.

M. Bouvier, M. Ducos-galand, C. Loot, D. Bikard, D. Mazel et al., Identification of some DNA damageinducible genes of Mycobacterium tuberculosis: apparent lack of correlation with LexA binding, J. Bacteriol, vol.5, pp.4459-4467, 2001.

T. Burr, J. Mitchell, A. Kolb, S. Minchin, and S. Busby, DNA sequence elements located immediately upstream of the-10 hexamer in Escherichia coli promoters: a systematic study, Nucleic Acids Res, vol.28, pp.1864-1870, 2000.

M. Butala, D. Klose, V. Hodnik, A. Rems, Z. Podlesek et al., Interconversion between bound and free conformations of LexA orchestrates the bacterial SOS response, Nucleic Acids Res, vol.39, pp.6546-6557, 2011.

M. Butala, D. Zgur-bertok, and S. J. Busby, The bacterial LexA transcriptional repressor, Cell. Mol. Life Sci. CMLS, vol.66, pp.82-93, 2009.

K. G. Byrne-bailey, W. H. Gaze, L. Zhang, P. Kay, A. Boxall et al., Integron prevalence and diversity in manured soil, Appl. Environ. Microbiol, vol.77, pp.684-687, 2011.

Y. Cai, J. Yang, Q. Kan, X. Nie, R. Wang et al., Mutant prevention concentration of colistin alone and in combination with levofloxacin or tobramycin against multidrug-resistant Acinetobacter baumannii, Int. J. Antimicrob. Agents, vol.40, pp.477-478, 2012.

G. Cambray, A. Guerout, and D. Mazel, Integrons. Annu. Rev. Genet, vol.44, pp.141-166, 2010.

S. Campoy, G. Mazón, A. R. Fernández-de-henestrosa, M. Llagostera, P. B. Monteiro et al., A new regulatory DNA motif of the gamma subclass Proteobacteria: identification of the LexA protein binding site of the plant pathogen Xylella fastidiosa, Microbiol. Read. Engl, vol.148, pp.3583-3597, 2002.

S. Campoy, N. Salvador, P. Cortés, I. Erill, and J. Barbé, Expression of canonical SOS genes is not under LexA repression in Bdellovibrio bacteriovorus, J. Bacteriol, vol.187, pp.5367-5375, 2005.

L. G. Casella, A. Weiss, E. Pérez-rueda, A. Ibarra, J. Shaw et al., Towards the complete proteinaceous regulome of Acinetobacter baumannii, Microb. Genomics, vol.3, p.107, 2017.

S. Caucci, A. Karkman, D. Cacace, M. Rybicki, P. Timpel et al., Seasonality of antibiotic prescriptions for outpatients and resistance genes in sewers and wastewater treatment plant outflow, MMWR Morb. Mortal. Wkly. Rep, vol.92, pp.1063-1066, 2004.

D. Chainier, O. Barraud, G. Masson, E. Couve-deacon, B. François et al., Integron Digestive Carriage in Human and Cattle: A "One Health, CultivationIndependent Approach. Front. Microbiol, vol.8, p.1891, 2017.

H. Chang, C. Tang, Y. Hsu, L. Wan, Y. Chang et al., Nosocomial outbreak of infection with multidrug-resistant Acinetobacter baumannii in a medical center in Taiwan, Infect. Control Hosp. Epidemiol, vol.30, pp.34-38, 2009.

Y. Chang, D. Y. Shih, J. Wang, and S. Yang, Molecular characterization of class 1 integrons and antimicrobial resistance in Aeromonas strains from foodborne outbreaksuspect samples and environmental sources in Taiwan, Diagn. Microbiol. Infect, vol.59, pp.191-197, 2007.

X. Charpentier, E. Kay, D. Schneider, and H. A. Shuman, Antibiotics and UV radiation induce competence for natural transformation in Legionella pneumophila, J. Bacteriol, vol.193, pp.1114-1121, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00800691

X. Charpentier, P. Polard, and J. Claverys, Induction of competence for genetic transformation by antibiotics: convergent evolution of stress responses in distant bacterial species lacking SOS?, Curr. Opin. Microbiol, vol.15, pp.570-576, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00787606

S. Chen, S. Zhao, D. G. White, C. M. Schroeder, R. Lu et al., Characterization of multiple-antimicrobial-resistant Salmonella serovars isolated from retail meats, Appl. Environ. Microbiol, vol.70, pp.1-7, 2004.

X. Chen, G. X. Li, H. Zhang, M. Yuan, X. P. Hou et al., Characterization of class 1 integron gene cassettes among clinical bacteria isolated from one large hospital in northern China, Biomed. Environ. Sci. BES, vol.26, pp.1003-1007, 2013.

D. L. Cheo, K. W. Bayles, and R. E. Yasbin, Cloning and characterization of DNA damageinducible promoter regions from Bacillus subtilis, J. Bacteriol, vol.173, pp.1696-1703, 1991.

T. Chopra, D. Marchaim, R. A. Awali, A. Krishna, P. Johnson et al., Epidemiology of bloodstream infections caused by Acinetobacter baumannii and impact of drug resistance to both carbapenems and ampicillin-sulbactam on clinical outcomes, Antimicrob. Agents Chemother, vol.57, pp.6270-6275, 2013.

T. Chopra, D. Marchaim, P. C. Johnson, R. A. Awali, H. Doshi et al., Risk factors and outcomes for patients with bloodstream infection due to Acinetobacter baumannii-calcoaceticus complex, Antimicrob. Agents Chemother, vol.58, pp.4630-4635, 2014.

D. R. Chung, J. Song, S. H. Kim, V. Thamlikitkul, S. Huang et al., High prevalence of multidrug-resistant nonfermenters in hospital-acquired pneumonia in Asia, Am. J. Respir. Crit. Care Med, vol.184, pp.1409-1417, 2011.

R. T. Cirz, B. M. O'neill, J. A. Hammond, S. R. Head, and F. E. Romesberg, Defining the Pseudomonas aeruginosa SOS response and its role in the global response to the antibiotic ciprofloxacin, J. Bacteriol, vol.188, pp.7101-7110, 2006.

A. Ç. Ç?çek, A. Ö. Düzgün, A. Saral, T. Kayman, Z. Ç?zmec? et al., Detection of class 1 integron in Acinetobacter baumannii isolates collected from nine hospitals in Turkey, Asian Pac. J. Trop. Biomed, vol.3, pp.743-747, 2013.

C. A. Clark, L. Purins, P. Kaewrakon, T. Focareta, and P. A. Manning, The Vibrio cholerae O1 chromosomal integron, Microbiol. Read. Engl, vol.146, pp.2605-2612, 2000.

S. Cocchi, E. Grasselli, M. Gutacker, C. Benagli, M. Convert et al., Distribution and characterization of integrons in Escherichia coli strains of animal and human origin, FEMS Immunol. Med. Microbiol, vol.50, pp.126-132, 2007.

C. M. Collis, G. Grammaticopoulos, J. Briton, H. W. Stokes, and R. M. Hall, Site-specific insertion of gene cassettes into integrons, Mol. Microbiol, vol.9, pp.41-52, 1993.

C. M. Collis and R. M. Hall, Comparison of the structure-activity relationships of the integron-associated recombination sites attI3 and attI1 reveals common features, Microbiol. Read. Engl, vol.150, pp.1591-1601, 2004.

C. M. Collis and R. M. Hall, Expression of antibiotic resistance genes in the integrated cassettes of integrons, Antimicrob. Agents Chemother, vol.39, pp.155-162, 1995.

C. M. Collis and R. M. Hall, Gene cassettes from the insert region of integrons are excised as covalently closed circles, Mol. Microbiol, vol.6, pp.2875-2885, 1992.

C. M. Collis, M. Kim, S. R. Partridge, H. W. Stokes, and R. M. Hall, Characterization of the class 3 integron and the site-specific recombination system it determines, J. Bacteriol, vol.184, pp.3017-3026, 2002.

C. M. Collis, M. Kim, H. W. Stokes, and R. M. Hall, Integron-encoded IntI integrases preferentially recognize the adjacent cognate attI site in recombination with a 59-be site, Mol. Microbiol, vol.46, pp.1415-1427, 2002.

C. M. Collis, G. D. Recchia, M. J. Kim, H. W. Stokes, and R. M. Hall, Efficiency of recombination reactions catalyzed by class 1 integron integrase IntI1, J. Bacteriol, vol.183, pp.2535-2542, 2001.

M. Colomb-cotinat, J. Lacoste, C. Brun-buisson, V. Jarlier, B. Coignard et al., Estimating the morbidity and mortality associated with infections due to multidrugresistant bacteria (MDRB), Antimicrob. Resist. Infect. Control, vol.5, p.56, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01449337

M. Correia, F. Boavida, F. Grosso, M. J. Salgado, L. M. Lito et al., Molecular characterization of a new class 3 integron in Klebsiella pneumoniae, Antimicrob. Agents Chemother, vol.47, pp.2838-2843, 2003.

J. Courcelle, A. Khodursky, B. Peter, P. O. Brown, and P. C. Hanawalt, Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli, Genetics, vol.158, pp.41-64, 2001.

M. M. Cox, Regulation of bacterial RecA protein function, Crit. Rev. Biochem. Mol. Biol, vol.42, pp.41-63, 2007.

M. M. Cox, The bacterial RecA protein as a motor protein, Annu. Rev. Microbiol, vol.57, pp.551-577, 2003.

J. Cuñé, P. Cullen, G. Mazon, S. Campoy, B. Adler et al., The Leptospira interrogans lexA gene is not autoregulated, J. Bacteriol, vol.187, pp.5841-5845, 2005.

S. Da-re, F. Garnier, E. Guérin, S. Campoy, F. Denis et al., The SOS response promotes qnrB quinolone-resistance determinant expression, EMBO Rep, vol.10, pp.929-933, 2009.
URL : https://hal.archives-ouvertes.fr/inserm-00533078

S. Da-re and M. Ploy, , 2012.

, Med. Sci. MS, vol.28, pp.179-184

S. F. Dallo and T. Weitao, Insights into Acinetobacter war-wound infections, biofilms, and control, Adv. Skin Wound Care, vol.23, pp.169-174, 2010.

,

E. Darmon and D. R. Leach, Bacterial genome instability. Microbiol. Mol. Biol. Rev. MMBR, vol.78, pp.1-39, 2014.

Y. Deng, X. Bao, L. Ji, L. Chen, J. Liu et al., Resistance integrons: class 1, 2 and 3 integrons, Ann. Clin. Microbiol. Antimicrob, vol.14, p.45, 2015.

D. Salehi, M. Ferdosi-shahandashti, E. Yahyapour, Y. Khafri, S. Pournajaf et al., Integron-Mediated Antibiotic Resistance in Acinetobacter baumannii Isolated from Intensive Care Unit Patients, BioMed Res. Int, p.7157923, 2017.

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.5, 2010.

M. A. Díaz, R. K. Cooper, A. Cloeckaert, and R. J. Siebeling, Plasmid-mediated high-level gentamicin resistance among enteric bacteria isolated from pet turtles in Louisiana, Appl. Environ. Microbiol, vol.72, pp.306-312, 2006.

J. J. Díaz-mejía, C. F. Amábile-cuevas, I. Rosas, and V. Souza, An analysis of the evolutionary relationships of integron integrases, Escherichia coli isolates from clinical and environmental origins. Microbiol. Read. Engl, vol.154, pp.94-102, 2008.

L. Dijkshoorn, H. Aucken, P. Gerner-smidt, P. Janssen, M. E. Kaufmann et al., Comparison of outbreak and nonoutbreak Acinetobacter baumannii strains by genotypic and phenotypic methods, J. Clin. Microbiol, vol.34, pp.1519-1525, 1996.

Y. Doi, G. L. Murray, and A. Y. Peleg, Acinetobacter baumannii: evolution of antimicrobial resistance-treatment options, Semin. Respir. Crit. Care Med, vol.36, pp.85-98, 2015.

M. Dolejska, A. Cizek, and I. Literak, High prevalence of antimicrobial-resistant genes and integrons in Escherichia coli isolates from Black-headed Gulls in the Czech Republic, J. Appl. Microbiol, vol.103, pp.11-19, 2007.

S. Domingues, G. J. Da-silva, and K. M. Nielsen, Global dissemination patterns of common gene cassette arrays in class 1 integrons, Microbiol. Read. Engl, vol.161, pp.1313-1337, 2015.

M. S. Dorer, J. Fero, and N. R. Salama, DNA damage triggers genetic exchange in Helicobacter pylori, PLoS Pathog, vol.6, p.1001026, 2010.

R. C. Doten, K. L. Ngai, D. J. Mitchell, and L. N. Ornston, Cloning and genetic organization of the pca gene cluster from Acinetobacter calcoaceticus, J. Bacteriol, vol.169, pp.3168-3174, 1987.

F. Drabløs, E. Feyzi, P. A. Aas, C. B. Vaagbø, B. Kavli et al., Alkylation damage in DNA and RNA-repair mechanisms and medical significance, DNA Repair, vol.3, pp.1389-1407, 2004.

V. Dubois, M. Parizano, C. Arpin, L. Coulange, M. Bezian et al., High genetic stability of integrons in clinical isolates of Shigella spp. of worldwide origin, Antimicrob. Agents Chemother, vol.51, pp.1333-1340, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00166190

E. G. Dudley, C. Abe, J. Ghigo, P. Latour-lambert, J. C. Hormazabal et al., An IncI1 plasmid contributes to the adherence of the atypical enteroaggregative Escherichia coli strain C1096 to cultured cells and abiotic surfaces, Infect. Immun, vol.74, pp.2102-2114, 2006.

E. V. Duijkeren, A. T. Box, P. Schellen, D. J. Houwers, and A. C. Fluit, Class 1 integrons in Enterobacteriaceae isolated from clinical infections of horses and dogs in the Netherlands, Microb. Drug Resist. Larchmt. N, vol.11, pp.383-386, 2005.

S. I. Durbach, S. J. Andersen, and V. Mizrahi, SOS induction in mycobacteria: analysis of the DNA-binding activity of a LexA-like repressor and its role in DNA damage induction of the recA gene from Mycobacterium smegmatis, Mol. Microbiol, vol.26, pp.643-653, 1997.

M. R. Eber, M. Shardell, M. L. Schweizer, R. Laxminarayan, and E. N. Perencevich, Seasonal and temperature-associated increases in gram-negative bacterial bloodstream infections among hospitalized patients, PloS One, vol.6, 2011.

E. Joint, The bacterial challenge: time to react, 2009.

A. Endimiani, K. M. Hujer, A. M. Hujer, I. Bertschy, A. Rossano et al., Acinetobacter baumannii isolates from pets and horses in Switzerland: molecular characterization and clinical data, J. Antimicrob. Chemother, vol.66, pp.2248-2254, 2011.

J. Engelstädter, K. Harms, and P. J. Johnsen, The evolutionary dynamics of integrons in changing environments, ISME J, vol.10, pp.1296-1307, 2016.

, Enquête nationale de prévalence des infections nosocomiales et des traitements antiinfectieux en établissements de santé, France, mai-juin 2012 / 2013 / Maladies infectieuses / Rapports et synthèses / Publications et outils / Accueil [WWW Document, 2013.

I. Erill, S. Campoy, and J. Barbé, Aeons of distress: an evolutionary perspective on the bacterial SOS response, FEMS Microbiol. Rev, vol.31, pp.637-656, 2007.

J. A. Escudero, C. Loot, A. Nivina, and D. Mazel, The Integron: Adaptation On Demand. Microbiol. Spectr, vol.3, pp.3-0019, 2015.

M. Eveillard, M. Kempf, O. Belmonte, H. Pailhoriès, and M. Joly-guillou, Reservoirs of Acinetobacter baumannii outside the hospital and potential involvement in emerging human community-acquired infections, Int. J. Infect. Dis. IJID Off. Publ. Int. Soc. Infect. Dis, vol.17, pp.802-805, 2013.

C. Ewers, P. Klotz, U. Leidner, I. Stamm, E. Prenger-berninghoff et al., OXA-23 and ISAba1-OXA-66 class D ?-lactamases in Acinetobacter baumannii isolates from companion animals, Int. J. Antimicrob. Agents, vol.49, pp.37-44, 2017.

D. W. Eyre, T. Golubchik, N. C. Gordon, R. Bowden, P. Piazza et al., A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance, BMJ Open, vol.2, 2012.

M. E. Falagas, E. A. Karveli, I. I. Siempos, and K. Z. Vardakas, Acinetobacter infections: a growing threat for critically ill patients, Epidemiol. Infect, vol.136, pp.1009-1019, 2008.

A. R. Fernández-de-henestrosa, J. Cuñé, G. Mazón, B. L. Dubbels, D. A. Bazylinski et al., Characterization of a new LexA binding motif in the marine magnetotactic bacterium strain MC-1, J. Bacteriol, vol.185, pp.4471-4482, 2003.

A. R. Fernández-de-henestrosa, T. Ogi, S. Aoyagi, D. Chafin, J. J. Hayes et al., Identification of additional genes belonging to the LexA regulon in Escherichia coli, Mol. Microbiol, vol.35, pp.1560-1572, 2000.

A. R. Fernández-de-henestrosa, E. Rivera, A. Tapias, and J. Barbé, Identification of the Rhodobacter sphaeroides SOS box, Mol. Microbiol, vol.28, pp.991-1003, 1998.

M. Ferreira-da-silva, I. Vaz-moreira, M. Gonzalez-pajuelo, O. C. Nunes, and C. M. Manaia, Antimicrobial resistance patterns in Enterobacteriaceae isolated from an urban wastewater treatment plant, FEMS Microbiol. Ecol, vol.60, pp.166-176, 2007.

S. Ferreira, A. Paradela, J. Velez, E. Ramalheira, T. R. Walsh et al., Carriage of qnrA1 and qnrB2, blaCTX-M15, and complex class 1 integron in a clinical multiresistant Citrobacter freundii isolate, Diagn. Microbiol. Infect. Dis, vol.67, pp.188-190, 2010.

M. E. Fling and C. Richards, The nucleotide sequence of the trimethoprim-resistant dihydrofolate reductase gene harbored by Tn7, Nucleic Acids Res, vol.11, pp.5147-5158, 1983.

C. Flores, M. I. Qadri, and C. Lichtenstein, DNA sequence analysis of five genes; tnsA, B, C, D and E, required for Tn7 transposition, Nucleic Acids Res, vol.18, pp.901-911, 1990.

A. C. Fluit and F. Schmitz, Resistance integrons and super-integrons, Clin. Microbiol. Infect, vol.10, pp.272-288, 2004.
DOI : 10.1111/j.1198-743x.2004.00858.x

URL : https://doi.org/10.1111/j.1198-743x.2004.00858.x

É. L. Fonseca, S. Freitas, É. M. Scheidegger, T. Jacinto, and A. C. Vicente, Class 2 integrons in multidrug-resistant Acinetobacter baumannii circulating in different Brazilian geographic regions, Int. J. Antimicrob. Agents, vol.38, pp.95-96, 2011.

P. E. Fournier and H. Richet, The epidemiology and control of Acinetobacter baumannii in health care facilities, Clin. Infect. Dis, vol.42, pp.692-699, 2006.

P. Fournier, D. Vallenet, V. Barbe, S. Audic, H. Ogata et al., Comparative genomics of multidrug resistance in Acinetobacter baumannii, PLoS Genet, vol.2, p.7, 2006.

M. V. Francia, F. De-la-cruz, and J. M. García-lobo, Secondary-sites for integration mediated by the Tn21 integrase, Mol. Microbiol, vol.10, pp.823-828, 1993.

M. V. Francia, J. C. Zabala, F. De-la-cruz, and J. M. García-lobo, The IntI1 integron integrase preferentially binds single-stranded DNA of the attC site, J. Bacteriol, vol.181, pp.6844-6849, 1999.

M. P. Freire, . De-oliveira, D. Garcia, C. P. Garcia, C. Bueno et al., Bloodstream infection caused by extensively drug-resistant Acinetobacter baumannii in cancer patients: high mortality associated with delayed treatment rather than with the degree of neutropenia, Clin. Microbiol. Infect, vol.22, pp.352-358, 2016.

M. Friedman, Antibiotic-resistant bacteria: prevalence in food and inactivation by foodcompatible compounds and plant extracts, J. Agric. Food Chem, vol.63, pp.3805-3822, 2015.

N. Friedman, S. Vardi, M. Ronen, U. Alon, and J. Stavans, Precise Temporal Modulation in the Response of the SOS DNA Repair Network in Individual Bacteria, PLoS Biol, vol.3, 2005.

Y. Fukuta, L. G. Clarke, R. K. Shields, M. M. Wagener, A. W. Pasculle et al., Lack of seasonality in the occurrence of multidrug-resistant Acinectobacter baumannii complex, Infect. Control Hosp. Epidemiol, vol.33, pp.1051-1052, 2012.

A. C. Gales, R. N. Jones, and H. S. Sader, Global assessment of the antimicrobial activity of polymyxin B against 54 731 clinical isolates of Gram-negative bacilli: report from the SENTRY antimicrobial surveillance programme, Clin. Microbiol. Infect, vol.12, pp.315-321, 2001.

L. Gao, Y. Lyu, and Y. Li, Trends in Drug Resistance of Acinetobacter baumannii over a 10year Period: Nationwide Data from the China Surveillance of Antimicrobial Resistance Program, Chin. Med. J. (Engl.), vol.130, pp.659-664, 2017.

M. Garcia-garcera, M. Touchon, S. Brisse, and E. P. Rochaa, Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter, Environ. Microbiol, 2017.

A. M. Gasc, N. Sicard, J. P. Claverys, and A. M. Sicard, Lack of SOS repair in Streptococcus pneumoniae, Mutat. Res, vol.70, pp.157-165, 1980.

A. Gassama-sow, A. Aïdara-kane, O. Barraud, M. Gatet, F. Denis et al., High prevalence of trimethoprim-resistance cassettes in class 1 and 2 integrons in Senegalese Shigella spp isolates, J. Infect. Dev. Ctries, vol.4, pp.207-212, 2010.
URL : https://hal.archives-ouvertes.fr/inserm-00533209

A. Gassama-sow, M. H. Diallo, M. Gatet, F. Denis, A. Aïdara-kane et al., Description of an unusual class 2 integron in Shigella sonnei isolates in Senegal (subSaharan Africa), J. Antimicrob. Chemother, vol.62, pp.843-844, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00406911

K. C. Giese, C. B. Michalowski, and J. W. Little, RecA-dependent cleavage of LexA dimers, J. Mol. Biol, vol.377, pp.148-161, 2008.

M. Gillings, Y. Boucher, M. Labbate, A. Holmes, S. Krishnan et al., The evolution of class 1 integrons and the rise of antibiotic resistance, J. Bacteriol, vol.190, pp.5095-5100, 2008.

M. R. Gillings, Class 1 integrons as invasive species, Curr. Opin. Microbiol, vol.38, pp.10-15, 2017.
DOI : 10.1016/j.mib.2017.03.002

M. R. Gillings, Integrons: past, present, and future. Microbiol, Mol. Biol. Rev. MMBR, vol.78, pp.257-277, 2014.

M. R. Gillings, W. H. Gaze, A. Pruden, K. Smalla, J. M. Tiedje et al., Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution, ISME J, vol.9, pp.1269-1279, 2015.

M. R. Gillings, M. P. Holley, H. W. Stokes, and A. J. Holmes, Integrons in Xanthomonas: a source of species genome diversity, Proc. Natl. Acad. Sci. U. S. A, vol.102, pp.4419-4424, 2005.

M. R. Gillings, S. Krishnan, P. J. Worden, and S. A. Hardwick, Recovery of diverse genes for class 1 integron-integrases from environmental DNA samples, FEMS Microbiol. Lett, vol.287, pp.56-62, 2008.

D. Girlich, R. A. Bonnin, A. Jousset, and T. Naas, Promoter characterization and expression of the blaKPC-2 gene in Escherichia coli, Pseudomonas aeruginosa and Acinetobacter baumannii, J. Antimicrob. Chemother, vol.72, pp.1597-1601, 2017.

C. Goldstein, M. D. Lee, S. Sanchez, C. Hudson, B. Phillips et al., Incidence of class 1 and 2 integrases in clinical and commensal bacteria from livestock, companion animals, and exotics, Antimicrob. Agents Chemother, vol.45, pp.723-726, 2001.

G. Gonzalez, K. Sossa, H. Bello, M. Dominguez, S. Mella et al., Presence of integrons in isolates of different biotypes of Acinetobacter baumannii from Chilean hospitals, FEMS Microbiol. Lett, vol.161, pp.125-128, 1998.

D. N. Gopaul and G. D. Duyne, Structure and mechanism in site-specific recombination, Curr. Opin. Struct. Biol, vol.9, pp.14-20, 1999.

I. Grainge and M. Jayaram, The integrase family of recombinase: organization and function of the active site, Mol. Microbiol, vol.33, pp.449-456, 1999.

A. Gravel, B. Fournier, and P. H. Roy, DNA complexes obtained with the integron integrase IntI1 at the attI1 site, Nucleic Acids Res, vol.26, pp.4347-4355, 1998.

C. Greene, G. Vadlamudi, D. Newton, B. Foxman, and C. Xi, The influence of biofilm formation and multidrug resistance on environmental survival of clinical and environmental isolates of Acinetobacter baumannii, Am. J. Infect. Control, vol.44, pp.65-71, 2016.

A. Greener, S. M. Lehman, and D. R. Helinski, Promoters of the broad host range plasmid RK2: analysis of transcription (initiation) in five species of gram-negative bacteria, Genetics, vol.130, pp.27-36, 1992.

M. E. Griffith, J. M. Ceremuga, M. W. Ellis, C. H. Guymon, D. R. Hospenthal et al., Acinetobacter skin colonization of US Army Soldiers, Infect. Control Hosp. Epidemiol, vol.27, pp.659-661, 2006.

H. J. Grundmann, K. J. Towner, L. Dijkshoorn, P. Gerner-smidt, M. Maher et al., Multicenter study using standardized protocols and reagents for evaluation of reproducibility of PCR-based fingerprinting of Acinetobacter spp, J. Clin. Microbiol, vol.35, pp.3071-3077, 1997.

E. Guérin, G. Cambray, S. Da-re, D. Mazel, and M. Ploy, The SOS response controls antibiotic resistance by regulating the integrase of integrons, Med. Sci. MS, vol.26, pp.28-30, 2010.

E. Guerin, G. Cambray, N. Sanchez-alberola, S. Campoy, I. Erill et al., The SOS response controls integron recombination, Science, vol.324, p.1034, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00409031

E. Guérin, T. Jové, A. Tabesse, D. Mazel, and M. Ploy, High-level gene cassette transcription prevents integrase expression in class 1 integrons, J. Bacteriol, vol.193, pp.5675-5682, 2011.

B. Guerra, J. Fischer, and R. Helmuth, An emerging public health problem: acquired carbapenemase-producing microorganisms are present in food-producing animals, their environment, companion animals and wild birds, Vet. Microbiol, vol.171, pp.290-297, 2014.

E. Gullberg, S. Cao, O. G. Berg, C. Ilbäck, L. Sandegren et al., Selection of resistant bacteria at very low antibiotic concentrations, PLoS Pathog, vol.7, 2011.

R. M. Hall, D. E. Brookes, and H. W. Stokes, Site-specific insertion of genes into integrons: role of the 59-base element and determination of the recombination cross-over point, Mol. Microbiol, vol.5, pp.1941-1959, 1991.

R. M. Hall, H. J. Brown, D. E. Brookes, and H. W. Stokes, Integrons found in different locations have identical 5' ends but variable 3' ends, J. Bacteriol, vol.176, pp.6286-6294, 1994.
DOI : 10.1128/jb.176.20.6286-6294.1994

URL : https://jb.asm.org/content/176/20/6286.full.pdf

R. M. Hall and C. M. Collis, Mobile gene cassettes and integrons: capture and spread of genes by site-specific recombination, Mol. Microbiol, vol.15, pp.593-600, 1995.

R. M. Hall, C. M. Collis, M. J. Kim, S. R. Partridge, G. D. Recchia et al., Mobile gene cassettes and integrons in evolution, Ann. N. Y. Acad. Sci, vol.870, pp.68-80, 1999.

M. Hamidian and R. M. Hall, Origin of the AbGRI1 antibiotic resistance island found in the comM gene of Acinetobacter baumannii GC2 isolates, J. Antimicrob. Chemother, vol.72, pp.2944-2947, 2017.

M. Hamidian, S. J. Nigro, and R. M. Hall, Problems with the Oxford Multilocus Sequence Typing Scheme for Acinetobacter baumannii: Do Sequence Type 92 (ST92) and ST109 Exist?, J. Clin. Microbiol, vol.55, pp.2287-2289, 2017.

A. Hamouda, B. A. Evans, K. J. Towner, and S. G. Amyes, Characterization of epidemiologically unrelated Acinetobacter baumannii isolates from four continents by use of multilocus sequence typing, pulsed-field gel electrophoresis, and sequencebased typing of bla(OXA-51-like) genes, J. Clin. Microbiol, vol.48, pp.2476-2483, 2010.

A. Hamouda, J. Findlay, A. Hassan, L. Amyes, and S. G. , Epidemiology of Acinetobacter baumannii of animal origin, Int. J. Antimicrob. Agents, vol.38, pp.314-318, 2011.

B. Hanau-berçot, I. Podglajen, I. Casin, and E. Collatz, An intrinsic control element for translational initiation in class 1 integrons, Mol. Microbiol, vol.44, pp.119-130, 2002.

K. Hansson, L. Sundström, A. Pelletier, and P. H. Roy, IntI2 integron integrase in Tn7, J. Bacteriol, vol.184, pp.1712-1721, 2002.

J. M. Hare, S. Adhikari, K. V. Lambert, A. E. Hare, and A. N. Grice, The Acinetobacter regulatory UmuDAb protein cleaves in response to DNA damage with chimeric LexA/UmuD characteristics, FEMS Microbiol. Lett, vol.334, pp.57-65, 2012.

J. M. Hare, J. C. Ferrell, T. A. Witkowski, and A. N. Grice, Prophage induction and differential RecA and UmuDAb transcriptome regulation in the DNA damage responses of Acinetobacter baumannii and Acinetobacter baylyi, PloS One, vol.9, p.93861, 2014.

J. M. Hare, S. N. Perkins, and L. A. Gregg-jolly, A constitutively expressed, truncated umuDC operon regulates the recA-dependent DNA damage induction of a gene in Acinetobacter baylyi strain ADP1, Appl. Environ. Microbiol, vol.72, pp.4036-4043, 2006.

K. Harms, I. Starikova, and P. J. Johnsen, Costly Class-1 integrons and the domestication of the the functional integrase, Mob. Genet. Elem, vol.3, 2013.

I. S. Henriques, F. Fonseca, A. Alves, M. J. Saavedra, and A. Correia, Occurrence and diversity of integrons and beta-lactamase genes among ampicillin-resistant isolates from estuarine waters, Res. Microbiol, vol.157, pp.938-947, 2006.
DOI : 10.1016/j.resmic.2006.09.003

P. G. Higgins, C. Dammhayn, M. Hackel, and H. Seifert, Global spread of carbapenemresistant Acinetobacter baumannii, J. Antimicrob. Chemother, vol.65, pp.233-238, 2010.
DOI : 10.1093/jac/dkq123

URL : https://academic.oup.com/jac/article-pdf/65/6/1317/2097796/dkq123.pdf

B. Hochhut, Y. Lotfi, D. Mazel, S. M. Faruque, R. Woodgate et al., Molecular analysis of antibiotic resistance gene clusters in Vibrio cholerae O139 and O1 SXT constins, Antimicrob. Agents Chemother, vol.45, pp.2991-3000, 2001.

D. Hocquet, P. Berthelot, M. Roussel-delvallez, R. Favre, K. Jeannot et al., Pseudomonas aeruginosa may accumulate drug resistance mechanisms without losing its ability to cause bloodstream infections, Antimicrob. Agents Chemother, vol.51, pp.3531-3536, 2007.
DOI : 10.1128/aac.00503-07

URL : https://hal.archives-ouvertes.fr/hal-00464781

J. Hong, J. Ahn, B. C. Kim, and M. B. Gu, Construction of a functional network for common DNA damage responses in Escherichia coli, Genomics, vol.93, pp.514-524, 2009.

T. Horii, T. Ogawa, T. Nakatani, T. Hase, H. Matsubara et al., Regulation of SOS functions: purification of E. coli LexA protein and determination of its specific site cleaved by the RecA protein, Cell, vol.27, pp.515-522, 1981.

E. T. Houang, Y. W. Chu, C. M. Leung, K. Y. Chu, J. Berlau et al., Epidemiology and infection control implications of Acinetobacter spp. in Hong Kong, J. Clin. Microbiol, vol.39, pp.228-234, 2001.

E. T. Houang, R. T. Sormunen, L. Lai, C. Y. Chan, and A. S. Leong, Effect of desiccation on the ultrastructural appearances of Acinetobacter baumannii and Acinetobacter lwoffii, J. Clin. Pathol, vol.51, pp.786-788, 1998.

P. Hsueh, L. Teng, C. Chen, W. Chen, C. Yu et al., Pandrugresistant Acinetobacter baumannii causing nosocomial infections in a university hospital, Taiwan. Emerg. Infect. Dis, vol.8, pp.827-832, 2002.

H. Huang, Z. Yang, X. Wu, Y. Wang, Y. Liu et al., Complete genome sequence of Acinetobacter baumannii MDR-TJ and insights into its mechanism of antibiotic resistance, J. Antimicrob. Chemother, vol.67, pp.2825-2832, 2012.

K. M. Hujer, A. M. Hujer, E. A. Hulten, S. Bajaksouzian, J. M. Adams et al., Analysis of antibiotic resistance genes in multidrug-resistant Acinetobacter sp. isolates from military and civilian patients treated at the Walter Reed Army Medical Center, Antimicrob. Agents Chemother, vol.50, pp.4114-4123, 2006.

M. Hunger, R. Schmucker, V. Kishan, and W. Hillen, Analysis and nucleotide sequence of an origin of DNA replication in Acinetobacter calcoaceticus and its use for Escherichia coli shuttle plasmids, Gene, vol.87, pp.45-51, 1990.

G. Huys, K. Bartie, M. Cnockaert, D. T. Hoang-oanh, N. T. Phuong et al., Biodiversity of chloramphenicol-resistant mesophilic heterotrophs from Southeast Asian aquaculture environments, Res. Microbiol, vol.158, pp.228-235, 2007.

J. A. Imlay and S. Linn, Mutagenesis and stress responses induced in Escherichia coli by hydrogen peroxide, J. Bacteriol, vol.169, pp.2967-2976, 1987.
DOI : 10.1128/jb.169.7.2967-2976.1987

URL : https://jb.asm.org/content/169/7/2967.full.pdf

, White paper: recommendations on the conduct of superiority and organism-specific clinical trials of antibacterial agents for the treatment of infections caused by drug-resistant bacterial pathogens, Clin. Infect. Dis, vol.55, pp.1031-1046, 2012.

L. Jacobs and H. Y. Chenia, Characterization of integrons and tetracycline resistance determinants in Aeromonas spp. isolated from South African aquaculture systems, Int. J. Food Microbiol, vol.114, pp.295-306, 2007.

H. Jacquier, C. Zaoui, M. Sanson-le-pors, D. Mazel, and B. Berçot, Translation regulation of integrons gene cassette expression by the attC sites, Mol. Microbiol, vol.72, pp.1475-1486, 2009.

C. Janion, Inducible SOS response system of DNA repair and mutagenesis in Escherichia coli, Int. J. Biol. Sci, vol.4, pp.338-344, 2008.

M. Jara, C. Núñez, S. Campoy, A. R. Fernández-de-henestrosa, D. R. Lovley et al., Geobacter sulfurreducens has two autoregulated lexA genes whose products do not bind the recA promoter: differing responses of lexA and recA to DNA damage, J. Bacteriol, vol.185, pp.2493-2502, 2003.

Q. Jiang, K. Karata, R. Woodgate, M. M. Cox, and M. F. Goodman, The active form of DNA polymerase V is UmuD'(2)C-RecA-ATP, Nature, vol.460, pp.359-363, 2009.

N. Jochmann, A. Kurze, L. F. Czaja, K. Brinkrolf, I. Brune et al., Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays, Microbiol. Read. Engl, vol.155, pp.1459-1477, 2009.

C. Johansson, M. Kamali-moghaddam, and L. Sundström, Integron integrase binds to bulged hairpin DNA, Nucleic Acids Res, vol.32, pp.4033-4043, 2004.
DOI : 10.1093/nar/gkh730

URL : https://academic.oup.com/nar/article-pdf/32/13/4033/7037154/gkh730.pdf

M. Joly-guillou, Clinical impact and pathogenicity of Acinetobacter, Clin. Microbiol. Infect. Dis, vol.11, pp.868-873, 2005.

T. Jové, S. Da-re, F. Denis, D. Mazel, and M. Ploy, Inverse correlation between promoter strength and excision activity in class 1 integrons, PLoS Genet, vol.6, p.1000793, 2010.

T. Jové, S. Da-re, A. Tabesse, A. Gassama-sow, M. Ploy et al., Gene Expression in Class 2 Integrons Is SOS-Independent and Involves Two Pc Promoters, J. Antimicrob. Chemother, vol.69, pp.81-84, 2014.

K. Kadlec and S. Schwarz, Analysis and distribution of class 1 and class 2 integrons and associated gene cassettes among Escherichia coli isolates from swine, horses, cats and dogs collected in the BfT-GermVet monitoring study, J. Antimicrob. Chemother, vol.62, pp.469-473, 2008.

S. G. Kang, D. Y. Lee, S. J. Shin, J. M. Ahn, and H. S. Yoo, Changes in patterns of antimicrobial susceptibility and class 1 integron carriage among Escherichia coli isolates, J. Vet. Sci, vol.6, pp.201-205, 2005.

M. Kaushik, S. Kumar, R. K. Kapoor, J. S. Virdi, and P. Gulati, Integrons in enterobacteriaceae: diversity, distribution and epidemiology, Int. J. Antimicrob. Agents, 2017.
DOI : 10.1016/j.ijantimicag.2017.10.004

M. Kempf and J. Rolain, Emergence of resistance to carbapenems in Acinetobacter baumannii in Europe: clinical impact and therapeutic options, Int. J. Antimicrob. Agents, vol.39, pp.105-114, 2012.

M. L. Khaitsa, J. Oloya, D. Doetkott, and R. Kegode, Antimicrobial resistance and association with class 1 integrons in Escherichia coli isolated from turkey meat products, J. Food Prot, vol.71, pp.1679-1684, 2008.

P. P. Khil and R. D. Camerini-otero, Over 1000 genes are involved in the DNA damage response of Escherichia coli, Mol. Microbiol, vol.44, pp.89-105, 2002.

V. Kishan and W. Hillen, Molecular cloning, nucleotide sequence, and promoter structure of the Acinetobacter calcoaceticus trpFB operon, J. Bacteriol, vol.172, pp.6151-6155, 1990.

R. K. Kleppe and K. Kleppe, Preparations and properties of ribonucleic acid polymerase from Acinetobacter calcoaceticus, J. Bacteriol, vol.125, pp.435-443, 1976.

C. W. Knapp, J. Dolfing, P. A. Ehlert, and D. W. Graham, Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940, Environ. Sci. Technol, vol.44, pp.580-587, 2010.

R. Koczura, B. Przyszlakowska, J. Mokracka, and A. Kaznowski, Class 1 integrons and antibiotic resistance of clinical Acinetobacter calcoaceticus-baumannii complex in Pozna?, Curr. Microbiol, vol.69, pp.258-262, 2014.

M. A. Kohanski, M. A. Depristo, and J. J. Collins, Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis, Mol. Cell, vol.37, pp.311-320, 2010.
DOI : 10.1016/j.molcel.2010.01.003

URL : https://doi.org/10.1016/j.molcel.2010.01.003

K. N. Kreuzer, DNA damage responses in prokaryotes: regulating gene expression, modulating growth patterns, and manipulating replication forks, Cold Spring Harb. Perspect. Biol, vol.5, 2013.

L. Krizova, L. Dijkshoorn, and A. Nemec, Diversity and evolution of AbaR genomic resistance islands in Acinetobacter baumannii strains of European clone I, Antimicrob. Agents Chemother, vol.55, pp.3201-3206, 2011.

A. Kuzminov, Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol, Mol. Biol. Rev. MMBR, vol.63, pp.751-813, 1999.

Y. Lacotte, M. Ploy, and S. Raherison, Class 1 integrons are low-cost structures in Escherichia coli, ISME J, vol.11, pp.1535-1544, 2017.

E. Laroche, B. Pawlak, T. Berthe, D. Skurnik, and F. Petit, Occurrence of antibiotic resistance and class 1, 2 and 3 integrons in Escherichia coli isolated from a densely populated estuary, FEMS Microbiol. Ecol, vol.68, pp.118-130, 2009.

H. Lavakhamseh, P. Mohajeri, S. Rouhi, P. Shakib, R. Ramazanzadeh et al., Multidrug-Resistant Escherichia coli Strains Isolated from Patients Are Associated with Class 1 and 2 Integrons, Chemotherapy, vol.61, pp.72-76, 2016.

S. C. Leão, C. K. Matsumoto, A. Carneiro, R. T. Ramos, C. L. Nogueira et al., The detection and sequencing of a broad-host-range conjugative IncP-1? plasmid in an epidemic strain of Mycobacterium abscessus subsp. bolletii, PloS One, vol.8, p.60746, 2013.

C. Lee, J. H. Lee, M. Park, K. S. Park, I. K. Bae et al., Biology of Acinetobacter baumannii: Pathogenesis, Antibiotic Resistance Mechanisms, and Prospective Treatment Options, Front. Cell. Infect. Microbiol, vol.7, p.55, 2017.

M. Lee, C. Peng, H. Hsu, and H. Toh, Use of inverse PCR for analysis of class 1 integrons carrying an unusual 3' conserved segment structure, Antimicrob. Agents Chemother, vol.55, pp.943-945, 2011.

Y. Lee, R. Souza, D. Yong, and K. Lee, Prediction of Putative Resistance Islands in a Carbapenem-Resistant Acinetobacter baumannii Global Clone 2 Clinical Isolate, Ann. Lab. Med, vol.36, pp.320-324, 2016.

Y. Lee, L. Huang, T. Chen, L. Siu, C. Fung et al., Gene cassette arrays, antibiotic susceptibilities, and clinical characteristics of Acinetobacter baumannii bacteremic strains harboring class 1 integrons, J. Microbiol. Immunol. Infect. Wei Mian Yu Gan Ran Za Zhi, vol.42, pp.210-219, 2009.

G. C. Leite, M. S. Oliveira, L. V. Perdigão-neto, C. K. Rocha, T. Guimarães et al., Antimicrobial Combinations against Pan-Resistant Acinetobacter baumannii Isolates with Different Resistance Mechanisms, PloS One, vol.11, 2016.

G. Léon and P. H. Roy, Potential role of group IIC-attC introns in integron cassette formation, J. Bacteriol, vol.191, pp.6040-6051, 2009.

M. A. Leverstein-van-hall, H. E. Blok, A. R. Donders, A. Paauw, A. C. Fluit et al., Multidrug resistance among Enterobacteriaceae is strongly associated with the presence of integrons and is independent of species or isolate origin, J. Infect. Dis, vol.187, pp.251-259, 2003.

L. Hall, M. A. Paauw, A. Box, A. T. Blok, H. E. Verhoef et al., Presence of integron-associated resistance in the community is widespread and contributes to multidrug resistance in the hospital, J. Clin. Microbiol, vol.40, pp.3038-3040, 2002.

C. Lévesque, S. Brassard, J. Lapointe, and P. H. Roy, Diversity and relative strength of tandem promoters for the antibiotic-resistance genes of several integrons, Gene, vol.142, pp.49-54, 1994.

C. S. Lewin and S. G. Amyes, The role of the SOS response in bacteria exposed to zidovudine or trimethoprim, J. Med. Microbiol, vol.34, pp.329-332, 1991.

L. K. Lewis, G. R. Harlow, L. A. Gregg-jolly, and D. W. Mount, Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli, J. Mol. Biol, vol.241, pp.507-523, 1994.

L. Lin, B. Ling, and X. Li, Distribution of the multidrug efflux pump genes, adeABC, adeDE and adeIJK, and class 1 integron genes in multiple-antimicrobial-resistant clinical isolates of Acinetobacter baumannii-Acinetobacter calcoaceticus complex, Int. J. Antimicrob. Agents, vol.33, pp.27-32, 2009.

M. Lin and C. Lan, Antimicrobial resistance in Acinetobacter baumannii: From bench to bedside, World J. Clin. Cases, vol.2, pp.787-814, 2014.

J. W. Little, Mechanism of specific LexA cleavage: autodigestion and the role of RecA coprotease, Biochimie, vol.73, pp.411-421, 1991.

J. W. Little and D. W. Mount, The SOS regulatory system of Escherichia coli, Cell, vol.29, pp.11-22, 1982.

C. Liu, C. Y. Tang, K. Chang, H. Kuo, and M. Liou, A comparative study of class 1 integrons in Acinetobacter baumannii, Gene, vol.544, pp.75-82, 2014.

S. H. Lob, D. J. Hoban, D. F. Sahm, and R. E. Badal, Regional differences and trends in antimicrobial susceptibility of Acinetobacter baumannii, Int. J. Antimicrob. Agents, vol.47, pp.317-323, 2016.

N. J. Loman, R. V. Misra, T. J. Dallman, C. Constantinidou, S. E. Gharbia et al., Performance comparison of benchtop high-throughput sequencing platforms, Nat. Biotechnol, vol.30, pp.434-439, 2012.

C. Loot, M. Ducos-galand, J. A. Escudero, M. Bouvier, and D. Mazel, Replicative resolution of integron cassette insertion, Nucleic Acids Res, vol.40, pp.8361-8370, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01700782

C. Loot, V. Parissi, J. A. Escudero, J. Amarir-bouhram, D. Bikard et al., The integron integrase efficiently prevents the melting effect of Escherichia coli singlestranded DNA-binding protein on folded attC sites, J. Bacteriol, vol.196, pp.762-771, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01101080

Y. Luo, R. A. Pfuetzner, S. Mosimann, M. Paetzel, E. A. Frey et al., Crystal structure of LexA: a conformational switch for regulation of self-cleavage, Cell, vol.106, pp.585-594, 2001.

A. Lupo, D. Vogt, S. N. Seiffert, A. Endimiani, and V. Perreten, Antibiotic resistance and phylogenetic characterization of Acinetobacter baumannii strains isolated from commercial raw meat in Switzerland, J. Food Prot, vol.77, pp.1976-1981, 2014.

M. Maegele, S. Gregor, E. Steinhausen, B. Bouillon, M. M. Heiss et al., The long-distance tertiary air transfer and care of tsunami victims: injury pattern and microbiological and psychological aspects, Crit. Care Med, vol.33, pp.1136-1140, 2005.

E. Maiques, C. Ubeda, S. Campoy, N. Salvador, I. Lasa et al., beta-lactam antibiotics induce the SOS response and horizontal transfer of virulence factors in Staphylococcus aureus, J. Bacteriol, vol.188, pp.2726-2729, 2006.

J. K. Mak, M. Kim, J. Pham, J. Tapsall, and P. A. White, Antibiotic resistance determinants in nosocomial strains of multidrug-resistant Acinetobacter baumannii, J. Antimicrob. Chemother, vol.63, pp.47-54, 2009.

M. M. Malek, F. A. Amer, A. A. Allam, R. H. El-sokkary, T. Gheith et al., Occurrence of classes I and II integrons in Enterobacteriaceae collected from Zagazig University Hospitals, Egypt. Front. Microbiol, vol.6, p.601, 2015.

L. L. Maragakis, M. G. Tucker, R. G. Miller, K. C. Carroll, and T. M. Perl, Incidence and prevalence of multidrug-resistant acinetobacter using targeted active surveillance cultures, JAMA, vol.299, pp.2513-2514, 2008.
DOI : 10.1001/jama.299.21.2513

URL : https://jamanetwork.com/journals/jama/articlepdf/182015/jlt0604_2513_2514.pdf

C. Márquez, M. Labbate, A. J. Ingold, P. Roy-chowdhury, M. S. Ramírez et al., Recovery of a functional class 2 integron from an Escherichia coli strain mediating a urinary tract infection, Antimicrob. Agents Chemother, vol.52, pp.4153-4154, 2008.

C. Martin, J. Timm, J. Rauzier, R. Gomez-lus, J. Davies et al., Transposition of an antibiotic resistance element in mycobacteria, Nature, vol.345, pp.739-743, 1990.

T. Martinez, I. Martinez, G. J. Vazquez, E. E. Aquino, and I. E. Robledo, Genetic environment of the KPC gene in Acinetobacter baumannii ST2 clone from Puerto Rico and genomic insights into its drug resistance, J. Med. Microbiol, vol.65, pp.784-792, 2016.

D. Mazel, Integrons: agents of bacterial evolution, Nat. Rev. Microbiol, vol.4, pp.608-620, 2006.

D. Mazel, B. Dychinco, V. A. Webb, and J. Davies, A distinctive class of integron in the Vibrio cholerae genome, Science, vol.280, pp.605-608, 1998.

G. Mazón, J. M. Lucena, S. Campoy, A. R. Fernández-de-henestrosa, P. Candau et al., LexA-binding sequences in Gram-positive and cyanobacteria are closely related, Mol. Genet. Genomics MGG, vol.271, pp.40-49, 2004.

L. C. Mcdonald, S. N. Banerjee, and W. R. Jarvis, Seasonal variation of Acinetobacter infections: 1987-1996. Nosocomial Infections Surveillance System, Clin. Infect. Dis, vol.29, pp.1133-1137, 1999.

A. Mellmann, D. Harmsen, C. A. Cummings, E. B. Zentz, S. R. Leopold et al., Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology, PloS One, vol.6, p.22751, 2011.

R. E. Mendes, M. Castanheira, M. A. Toleman, H. S. Sader, R. N. Jones et al., Characterization of an integron carrying blaIMP-1 and a new aminoglycoside resistance gene, aac(6')-31, and its dissemination among genetically unrelated clinical isolates in a Brazilian hospital, Antimicrob. Agents Chemother, vol.51, pp.2611-2614, 2007.

N. Messier and P. H. Roy, Integron integrases possess a unique additional domain necessary for activity, J. Bacteriol, vol.183, pp.6699-6706, 2001.
DOI : 10.1128/jb.183.22.6699-6706.2001

URL : https://jb.asm.org/content/183/22/6699.full.pdf

B. Michel, After 30 years of study, the bacterial SOS response still surprises us, PLoS Biol, vol.3, p.255, 2005.

A. Miko, K. Pries, A. Schroeter, and R. Helmuth, Molecular mechanisms of resistance in multidrug-resistant serovars of Salmonella enterica isolated from foods in Germany, J. Antimicrob. Chemother, vol.56, pp.1025-1033, 2005.

C. Miller, H. Ingmer, L. E. Thomsen, K. Skarstad, and S. N. Cohen, DpiA binding to the replication origin of Escherichia coli plasmids and chromosomes destabilizes plasmid inheritance and induces the bacterial SOS response, J. Bacteriol, vol.185, pp.6025-6031, 2003.

C. Miller, L. E. Thomsen, C. Gaggero, R. Mosseri, H. Ingmer et al., SOS response induction by beta-lactams and bacterial defense against antibiotic lethality, Science, vol.305, pp.1629-1631, 2004.
DOI : 10.1126/science.1101630

V. Mizrahi and S. J. Andersen, DNA repair in Mycobacterium tuberculosis. What have we learnt from the genome sequence?, Mol. Microbiol, vol.29, pp.1331-1339, 1998.

C. Y. Mo, L. D. Birdwell, and R. M. Kohli, Specificity determinants for autoproteolysis of LexA, a key regulator of bacterial SOS mutagenesis, Biochemistry (Mosc.), vol.53, pp.3158-3168, 2014.

J. Mokracka, R. Koczura, and A. Kaznowski, Multiresistant Enterobacteriaceae with class 1 and class 2 integrons in a municipal wastewater treatment plant, Water Res, vol.46, pp.3353-3363, 2012.
DOI : 10.1016/j.watres.2012.03.037

A. Moura, I. Henriques, R. Ribeiro, and A. Correia, Prevalence and characterization of integrons from bacteria isolated from a slaughterhouse wastewater treatment plant, J. Antimicrob. Chemother, vol.60, pp.1243-1250, 2007.

F. Movahedzadeh, M. J. Colston, and E. O. Davis, Determination of DNA sequences required for regulated Mycobacterium tuberculosis RecA expression in response to DNAdamaging agents suggests that two modes of regulation exist, J. Bacteriol, vol.179, pp.3509-3518, 1997.

P. D. Mugnier, L. Poirel, T. Naas, and P. Nordmann, Worldwide dissemination of the blaOXA-23 carbapenemase gene of Acinetobacter baumannii, Emerg. Infect. Dis, vol.16, pp.35-40, 2010.

S. Mukherjee and R. Chakraborty, Incidence of class 1 integrons in multiple antibioticresistant Gram-negative copiotrophic bacteria from the River Torsa in India, Res. Microbiol, vol.157, pp.220-226, 2006.

T. Naas, F. Benaoudia, S. Massuard, and P. Nordmann, Integron-located VEB-1 extendedspectrum beta-lactamase gene in a Proteus mirabilis clinical isolate from Vietnam, J. Antimicrob. Chemother, vol.46, pp.703-711, 2000.
DOI : 10.1093/jac/46.5.703

URL : https://academic.oup.com/jac/article-pdf/46/5/703/9841343/703.pdf

T. Naas, L. Poirel, and P. Nordmann, Pyrosequencing for rapid identification of carbapenem-hydrolysing OXA-type beta-lactamases in Acinetobacter baumannii, Clin. Microbiol. Infect, vol.12, pp.1236-1240, 2006.

S. Nandi, J. J. Maurer, C. Hofacre, and A. O. Summers, Gram-positive bacteria are a major reservoir of Class 1 antibiotic resistance integrons in poultry litter, Proc. Natl. Acad. Sci. U. S. A, vol.101, pp.7118-7122, 2004.

E. L. Neidle, M. K. Shapiro, and L. N. Ornston, Cloning and expression in Escherichia coli of Acinetobacter calcoaceticus genes for benzoate degradation, J. Bacteriol, vol.169, pp.5496-5503, 1987.

A. Nemec, L. Dolzani, S. Brisse, P. Van-den-broek, and L. Dijkshoorn, Diversity of aminoglycoside-resistance genes and their association with class 1 integrons among strains of pan-European Acinetobacter baumannii clones, J. Med. Microbiol, vol.53, pp.1233-1240, 2004.

J. Nesvera, J. Hochmannová, and M. Pátek, An integron of class 1 is present on the plasmid pCG4 from gram-positive bacterium Corynebacterium glutamicum, FEMS Microbiol. Lett, vol.169, pp.391-395, 1998.

S. J. Nigro, D. N. Farrugia, I. T. Paulsen, and R. M. Hall, A novel family of genomic resistance islands, AbGRI2, contributing to aminoglycoside resistance in Acinetobacter baumannii isolates belonging to global clone 2, J. Antimicrob. Chemother, vol.68, pp.554-557, 2013.

S. J. Nigro and R. M. Hall, Loss and gain of aminoglycoside resistance in global clone 2 Acinetobacter baumannii in Australia via modification of genomic resistance islands and acquisition of plasmids, J. Antimicrob. Chemother, vol.71, pp.2432-2440, 2016.

S. J. Nigro, V. Post, and R. M. Hall, Aminoglycoside resistance in multiply antibiotic-resistant Acinetobacter baumannii belonging to global clone 2 from Australian hospitals, J. Antimicrob. Chemother, vol.66, pp.1504-1509, 2011.

A. Nivina, J. A. Escudero, C. Vit, D. Mazel, and C. Loot, Efficiency of integron cassette insertion in correct orientation is ensured by the interplay of the three unpaired features of attC recombination sites, Nucleic Acids Res, vol.44, pp.7792-7803, 2016.

M. D. Norton, A. J. Spilkia, and V. G. Godoy, Antibiotic resistance acquired through a DNA damage-inducible response in Acinetobacter baumannii, J. Bacteriol, vol.195, pp.1335-1345, 2013.

S. E. Nunes-düby, H. J. Kwon, R. S. Tirumalai, T. Ellenberger, and A. Landy, Similarities and differences among 105 members of the Int family of site-specific recombinases, Nucleic Acids Res, vol.26, pp.391-406, 1998.

B. W. Odetoyin, A. S. Labar, A. Lamikanra, A. O. Aboderin, and I. N. Okeke, Classes 1 and 2 integrons in faecal Escherichia coli strains isolated from mother-child pairs in Nigeria, PloS One, vol.12, 2017.

E. K. O'reilly and K. N. Kreuzer, Isolation of SOS constitutive mutants of Escherichia coli, J. Bacteriol, vol.186, pp.7149-7160, 2004.

M. Pagano, A. F. Martins, A. B. Machado, J. Barin, and A. L. Barth, Carbapenemsusceptible Acinetobacter baumannii carrying the ISAba1 upstream blaOXA-51-like gene in Porto Alegre, southern Brazil, Epidemiol. Infect, vol.141, pp.330-333, 2013.

H. Pailhoriès, O. Belmonte, M. Kempf, C. Lemarié, J. Cuziat et al., Diversity of Acinetobacter baumannii strains isolated in humans, companion animals, and the environment in Reunion Island: an exploratory study, Int. J. Infect. Dis, vol.37, pp.64-69, 2015.

C. Pal, J. Bengtsson-palme, E. Kristiansson, D. G. Larsson, J. Pan et al., Molecular characteristics of class 1 and class 2 integrons and their relationships to antibiotic resistance in clinical isolates of Shigella sonnei and Shigella flexneri, J. Antimicrob. Chemother, vol.58, pp.288-296, 2006.

C. C. Papagiannitsis, L. S. Tzouvelekis, and V. Miriagou, Relative strengths of the class 1 integron promoter hybrid 2 and the combinations of strong and hybrid 1 with an active p2 promoter, Antimicrob. Agents Chemother, vol.53, pp.277-280, 2009.

S. R. Partridge, Analysis of antibiotic resistance regions in Gram-negative bacteria, FEMS Microbiol. Rev, vol.35, pp.820-855, 2011.

S. R. Partridge, G. D. Recchia, C. Scaramuzzi, C. M. Collis, H. W. Stokes et al., Definition of the attI1 site of class 1 integrons, Microbiol. Read. Engl, vol.146, pp.2855-2864, 2000.

S. R. Partridge, G. D. Recchia, H. W. Stokes, and R. M. Hall, Family of Class 1 Integrons Related to In4 from Tn1696, Antimicrob. Agents Chemother, vol.45, pp.3014-3020, 2001.

S. R. Partridge, G. Tsafnat, E. Coiera, and J. R. Iredell, Gene cassettes and cassette arrays in mobile resistance integrons, FEMS Microbiol. Rev, vol.33, pp.757-784, 2009.

M. Patel, Q. Jiang, R. Woodgate, M. M. Cox, and M. F. Goodman, A new model for SOSinduced mutagenesis: how RecA protein activates DNA polymerase V, Crit. Rev. Biochem. Mol. Biol, vol.45, pp.171-184, 2010.

J. R. Patil and B. A. Chopade, Distribution and in vitro antimicrobial susceptibility of Acinetobacter species on the skin of healthy humans, Natl. Med. J. India, vol.14, pp.204-208, 2001.

R. Paton, R. S. Miles, J. Hood, S. G. Amyes, R. S. Miles et al., ARI 1: betalactamase-mediated imipenem resistance in Acinetobacter baumannii, Int. J. Antimicrob. Agents, vol.2, pp.81-87, 1993.

I. T. Paulsen, T. G. Littlejohn, P. Rådström, L. Sundström, O. Sköld et al., The 3' conserved segment of integrons contains a gene associated with multidrug resistance to antiseptics and disinfectants, Antimicrob. Agents Chemother, vol.37, pp.761-768, 1993.

A. Y. Peleg, H. Seifert, and D. L. Paterson, Acinetobacter baumannii: Emergence of a Successful Pathogen, Clin. Microbiol. Rev, vol.21, pp.538-582, 2008.

C. Peng, Z. Zong, and H. Fan, Acinetobacter baumannii isolates associated with communityacquired pneumonia in West China, Clin. Microbiol. Infect, vol.18, pp.491-493, 2012.

E. N. Perencevich, J. C. Mcgregor, M. Shardell, J. P. Furuno, A. D. Harris et al., Summer Peaks in the Incidences of Gram-Negative Bacterial Infection Among Hospitalized Patients, Infect. Control Hosp. Epidemiol, vol.29, pp.1124-1131, 2008.

F. Perez, A. M. Hujer, K. M. Hujer, B. K. Decker, P. N. Rather et al., Global challenge of multidrug-resistant Acinetobacter baumannii, Antimicrob. Agents Chemother, vol.51, pp.3471-3484, 2007.

A. Petersen, L. Guardabassi, A. Dalsgaard, and J. E. Olsen, Class I integrons containing a dhfrI trimethoprim resistance gene cassette in aquatic Acinetobacter spp, FEMS Microbiol. Lett, vol.182, pp.73-76, 2000.

M. Petrova, Z. Gorlenko, and S. Mindlin, Tn5045, a novel integron-containing antibiotic and chromate resistance transposon isolated from a permafrost bacterium, Res. Microbiol, vol.162, pp.337-345, 2011.

M. C. Ploy, F. Denis, P. Courvalin, and T. Lambert, Molecular characterization of integrons in Acinetobacter baumannii: description of a hybrid class 2 integron, Antimicrob. Agents Chemother, vol.44, pp.2684-2688, 2000.

J. R. Pohlhaus and K. N. Kreuzer, Norfloxacin-induced DNA gyrase cleavage complexes block Escherichia coli replication forks, causing double-stranded breaks in vivo, Mol. Microbiol, vol.56, pp.1416-1429, 2005.

L. Poirel, A. Carattoli, S. Bernabeu, T. Bruderer, R. Frei et al., A novel IncQ plasmid type harbouring a class 3 integron from Escherichia coli, J. Antimicrob. Chemother, vol.65, pp.1594-1598, 2010.

L. Poirel, O. Menuteau, N. Agoli, C. Cattoen, and P. Nordmann, Outbreak of extendedspectrum beta-lactamase VEB-1-producing isolates of Acinetobacter baumannii in a French hospital, J. Clin. Microbiol, vol.41, pp.3542-3547, 2003.

K. Poonsuk, C. Tribuddharat, and R. Chuanchuen, Class 1 integrons in Pseudomonas aeruginosa and Acinetobacter baumannii isolated from clinical isolates, Southeast Asian J. Trop. Med. Public Health, vol.43, pp.376-384, 2012.

V. Post and R. M. Hall, AbaR5, a large multiple-antibiotic resistance region found in Acinetobacter baumannii, Antimicrob. Agents Chemother, vol.53, pp.2667-2671, 2009.

V. Post, P. A. White, and R. M. Hall, Evolution of AbaR-type genomic resistance islands in multiply antibiotic-resistant Acinetobacter baumannii, J. Antimicrob. Chemother, vol.65, pp.1162-1170, 2010.

A. Potron, L. Poirel, and P. Nordmann, Emerging broad-spectrum resistance in Pseudomonas aeruginosa and Acinetobacter baumannii: Mechanisms and epidemiology, Int. J. Antimicrob. Agents, vol.45, pp.568-585, 2015.

E. Potvin, F. Sanschagrin, and R. C. Levesque, Sigma factors in Pseudomonas aeruginosa, FEMS Microbiol. Rev, vol.32, pp.38-55, 2008.

M. L. Power, A. Samuel, J. J. Smith, J. S. Stark, M. R. Gillings et al., Escherichia coli out in the cold: Dissemination of human-derived bacteria into the Antarctic microbiome, Environ. Pollut. Barking Essex, vol.215, pp.58-65, 1987.

L. Prakash, Lack of chemically induced mutation in repair-deficient mutants of yeast, Genetics, vol.78, pp.1101-1118, 1974.

M. Prudhomme, L. Attaiech, G. Sanchez, B. Martin, and J. Claverys, Antibiotic stress induces genetic transformability in the human pathogen Streptococcus pneumoniae, Science, vol.313, pp.89-92, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00086843

M. A. Quail, M. Smith, P. Coupland, T. D. Otto, S. R. Harris et al., A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers, BMC Genomics, vol.13, p.341, 2012.

P. Quillardet, M. Rouffaud, and P. Bouige, DNA array analysis of gene expression in response to UV irradiation in Escherichia coli, Res. Microbiol, vol.154, pp.559-572, 2003.

M. Radman, SOS repair hypothesis: phenomenology of an inducible DNA repair which is accompanied by mutagenesis, Basic Life Sci, vol.5, pp.355-367, 1975.

R. Rafei, M. Hamze, H. Pailhoriès, M. Eveillard, L. Marsollier et al., Extrahuman epidemiology of Acinetobacter baumannii in Lebanon. Appl. Environ. Microbiol, vol.81, pp.2359-2367, 2015.

M. S. Ramírez, S. Piñeiro, and D. Centrón, Novel insights about class 2 integrons from experimental and genomic epidemiology, Antimicrob. Agents Chemother, vol.54, pp.699-706, 2010.

M. S. Ramírez, C. Quiroga, and D. Centrón, Novel rearrangement of a class 2 integron in two non-epidemiologically related isolates of Acinetobacter baumannii, Antimicrob. Agents Chemother, vol.49, pp.5179-5181, 2005.

M. S. Ramírez, L. J. Vargas, V. Cagnoni, M. Tokumoto, and D. Centrón, Class 2 integron with a novel cassette array in a Burkholderia cenocepacia isolate, Antimicrob. Agents Chemother, vol.49, pp.4418-4420, 2005.

M. S. Ramirez and M. E. Tolmasky, Aminoglycoside modifying enzymes, Drug Resist. Updat. Rev. Comment. Antimicrob. Anticancer Chemother, vol.13, pp.151-171, 2010.

P. J. Rauch, R. Palmen, A. A. Burds, L. A. Gregg-jolly, J. R. Van-der-zee et al., The expression of the Acinetobacter calcoaceticus recA gene increases in response to DNA damage independently of RecA and of development of competence for natural transformation, Microbiol. Read. Engl, vol.142, pp.1025-1032, 1996.

A. Ravi, E. Avershina, S. L. Foley, J. Ludvigsen, O. Storrø et al., The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons, Sci. Rep, vol.5, p.15317, 2015.

A. Raymond-denise and N. Guillen, Expression of the Bacillus subtilis dinR and recA genes after DNA damage and during competence, J. Bacteriol, vol.174, pp.3171-3176, 1992.
URL : https://hal.archives-ouvertes.fr/pasteur-00166276

A. Raymond-denise and N. Guillen, Identification of dinR, a DNA damage-inducible regulator gene of Bacillus subtilis, J. Bacteriol, vol.173, pp.7084-7091, 1991.
URL : https://hal.archives-ouvertes.fr/hal-00016960

G. D. Recchia and R. M. Hall, Plasmid evolution by acquisition of mobile gene cassettes: plasmid pIE723 contains the aadB gene cassette precisely inserted at a secondary site in the incQ plasmid RSF1010, Mol. Microbiol, vol.15, pp.179-187, 1995.

G. D. Recchia, H. W. Stokes, and R. M. Hall, Characterisation of specific and secondary recombination sites recognised by the integron DNA integrase, Nucleic Acids Res, vol.22, pp.2071-2078, 1994.

H. F. Retailliau, A. W. Hightower, R. E. Dixon, and J. R. Allen, Acinetobacter calcoaceticus: a nosocomial pathogen with an unusual seasonal pattern, J. Infect. Dis, vol.139, pp.371-375, 1979.

V. B. Ribeiro, N. Lincopan, M. Landgraf, B. D. Franco, and M. T. Destro, Characterization of class 1 integrons and antibiotic resistance genes in multidrugresistant Salmonella enterica isolates from foodstuff and related sources, Braz. J. Microbiol. Publ. Braz. Soc. Microbiol, vol.42, pp.685-692, 2011.

L. B. Rice, Federal funding for the study of antimicrobial resistance in nosocomial pathogens: no ESKAPE, J. Infect. Dis, vol.197, pp.1079-1081, 2008.

D. E. Rizk and A. M. El-mahdy, Emergence of class 1 to 3 integrons among members of Enterobacteriaceae in Egypt, Microb. Pathog, 2017.

A. Robinson, A. J. Brzoska, K. M. Turner, R. Withers, E. J. Harry et al., Essential Biological Processes of an Emerging Pathogen: DNA Replication, Transcription, and Cell Division in Acinetobacter spp. Microbiol. Mol. Biol. Rev, vol.74, pp.273-297, 2010.

J. Rodríguez-baño, S. Martí, S. Soto, F. Fernández-cuenca, J. M. Cisneros et al., Biofilm formation in Acinetobacter baumannii: associated features and clinical implications, Clin. Microbiol. Infect, vol.14, pp.276-278, 2008.

C. M. Rodríguez-minguela, J. H. Apajalahti, B. Chai, J. R. Cole, and J. M. Tiedje, Worldwide prevalence of class 2 integrases outside the clinical setting is associated with human impact, Appl. Environ. Microbiol, vol.75, pp.5100-5110, 2009.

M. T. Roe, E. Vega, and S. D. Pillai, Antimicrobial resistance markers of class 1 and class 2 integron-bearing Escherichia coli from irrigation water and sediments, Emerg. Infect. Dis, vol.9, pp.822-826, 2003.

J. Rolain, Food and human gut as reservoirs of transferable antibiotic resistance encoding genes, p.173, 2013.

M. Ronen, R. Rosenberg, B. I. Shraiman, and U. Alon, Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics, Proc. Natl. Acad. Sci. U. S. A, vol.99, pp.10555-10560, 2002.

S. J. Rosser and H. K. Young, Identification and characterization of class 1 integrons in bacteria from an aquatic environment, J. Antimicrob. Chemother, vol.44, pp.11-18, 1999.

D. A. Rowe-magnus, A. Guerout, and D. Mazel, Bacterial resistance evolution by recruitment of super-integron gene cassettes, Mol. Microbiol, vol.43, pp.1657-1669, 2002.

D. A. Rowe-magnus, A. M. Guerout, P. Ploncard, B. Dychinco, J. Davies et al., The evolutionary history of chromosomal super-integrons provides an ancestry for multiresistant integrons, Proc. Natl. Acad. Sci. U. S. A, vol.98, pp.652-657, 2001.

J. Ruiz, M. M. Navia, C. Casals, J. M. Sierra, M. T. Jiménez-de-anta et al., Integronmediated antibiotic multiresistance in Acinetobacter baumannii clinical isolates from Spain, Clin. Microbiol. Infect, vol.9, pp.907-911, 2003.

L. Ruiz-martínez, L. López-jiménez, E. Fusté, T. Vinuesa, J. P. Martínez et al., Class 1 integrons in environmental and clinical isolates of Pseudomonas aeruginosa, Int. J. Antimicrob. Agents, vol.38, pp.398-402, 2011.

Y. Sáenz, L. Vinué, E. Ruiz, S. Somalo, S. Martínez et al., Class 1 integrons lacking qacEDelta1 and sul1 genes in Escherichia coli isolates of food, animal and human origins, Vet. Microbiol, vol.144, pp.493-497, 2010.

H. Salimizand, S. Menbari, R. Ramazanzadeh, M. Khonsha, and M. Saleh-vahedi, DNA fingerprinting and antimicrobial susceptibility pattern of clinical and environmental Acinetobacter baumannii isolates: a multicentre study, J. Chemother. Florence Italy, vol.28, pp.277-283, 2016.

B. Sallen, A. Rajoharison, S. Desvarenne, and C. Mabilat, Molecular epidemiology of integron-associated antibiotic resistance genes in clinical isolates of enterobacteriaceae, Microb. Drug Resist. Larchmt. N, vol.1, pp.195-202, 1995.

S. Santajit and N. Indrawattana, Mechanisms of Antimicrobial Resistance in ESKAPE Pathogens, BioMed Res. Int, p.2475067, 2016.

P. M. Sarma, D. Bhattacharya, S. Krishnan, and B. Lal, Assessment of intra-species diversity among strains of Acinetobacter baumannii isolated from sites contaminated with petroleum hydrocarbons, Can. J. Microbiol, vol.50, pp.405-414, 2004.

M. Sassanfar and J. W. Roberts, Nature of the SOS-inducing signal in Escherichia coli. The involvement of DNA replication, J. Mol. Biol, vol.212, pp.79-96, 1990.

M. Savari, A. Ekrami, S. Shoja, and A. Bahador, Acquisition of Tn6018-3' CS regions increases colistin MICs against Acinetobacter baumannii isolates harboring new variants of AbaRs, Folia Microbiol. (Praha), vol.62, pp.373-379, 2017.

K. Schlacher and M. F. Goodman, Lessons from 50 years of SOS DNA-damage-induced mutagenesis, Nat. Rev. Mol. Cell Biol, vol.8, pp.587-594, 2007.

K. Schlacher, P. Pham, M. M. Cox, and M. F. Goodman, Roles of DNA polymerase V and RecA protein in SOS damage-induced mutation, Chem. Rev, vol.106, pp.406-419, 2006.

A. Schlüter, R. Szczepanowski, A. Pühler, and E. M. Top, Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool, FEMS Microbiol. Rev, vol.31, pp.449-477, 2007.

A. S. Schmidt, M. S. Bruun, I. Dalsgaard, and J. L. Larsen, Incidence, distribution, and spread of tetracycline resistance determinants and integron-associated antibiotic resistance genes among motile aeromonads from a fish farming environment, Appl. Environ. Microbiol, vol.67, pp.5675-5682, 2001.

S. Schwarz, C. Kehrenberg, B. Doublet, and A. Cloeckaert, Molecular basis of bacterial resistance to chloramphenicol and florfenicol, FEMS Microbiol. Rev, vol.28, pp.519-542, 2004.

P. Scott, G. Deye, A. Srinivasan, C. Murray, K. Moran et al., An outbreak of multidrug-resistant Acinetobacter baumannii-calcoaceticus complex infection in the US military health care system associated with military operations in Iraq, Clin. Infect. Dis, vol.44, pp.1577-1584, 2007.

H. Segal and B. G. Elisha, Characterization of the Acinetobacter plasmid, pRAY, and the identification of regulatory sequences upstream of an aadB gene cassette on this plasmid, Plasmid, vol.42, pp.60-66, 1999.

H. Seifert, L. Dijkshoorn, P. Gerner-smidt, N. Pelzer, I. Tjernberg et al., Distribution of Acinetobacter species on human skin: comparison of phenotypic and genotypic identification methods, J. Clin. Microbiol, vol.35, pp.2819-2825, 1997.

H. Seifert, L. Dolzani, R. Bressan, T. Van-der-reijden, B. Van-strijen et al., Standardization and interlaboratory reproducibility assessment of pulsed-field gel electrophoresis-generated fingerprints of Acinetobacter baumannii, J. Clin. Microbiol, vol.43, pp.4328-4335, 2005.

E. Sepp, J. Stsepetova, K. Lõivukene, K. Truusalu, S. Kõljalg et al., The occurrence of antimicrobial resistance and class 1 integrons among commensal Escherichia coli isolates from infants and elderly persons, Ann. Clin. Microbiol. Antimicrob, vol.8, p.34, 2009.

V. Seputiene, J. Povilonis, and E. Suziedeliene, Novel variants of AbaR resistance islands with a common backbone in Acinetobacter baumannii isolates of European clone II, Antimicrob. Agents Chemother, vol.56, pp.1969-1973, 2012.

R. J. Seward, Detection of integrons in worldwide nosocomial isolates of Acinetobacter spp, Clin. Microbiol. Infect, vol.5, pp.308-318, 1999.

R. J. Seward, T. Lambert, and K. J. Towner, Molecular epidemiology of aminoglycoside resistance in Acinetobacter spp, J. Med. Microbiol, vol.47, pp.455-462, 1998.

B. W. Shaheen, O. A. Oyarzabal, and D. M. Boothe, The role of class 1 and 2 integrons in mediating antimicrobial resistance among canine and feline clinical E. coli isolates from the US, Vet. Microbiol, vol.144, pp.363-370, 2010.

N. Shibata, Y. Doi, K. Yamane, T. Yagi, H. Kurokawa et al., PCR typing of genetic determinants for metallo-beta-lactamases and integrases carried by gram-negative bacteria isolated in Japan, with focus on the class 3 integron, J. Clin. Microbiol, vol.41, pp.5407-5413, 2003.

P. L. Simo-tchuinte, T. Stalder, S. Venditti, A. Ngandjio, C. Dagot et al., Characterisation of class 3 integrons with oxacillinase gene cassettes in hospital sewage and sludge samples from France and Luxembourg, Int. J. Antimicrob. Agents, vol.48, pp.431-434, 2016.

C. C. Simonsen, E. Y. Chen, and A. D. Levinson, Identification of the type I trimethoprimresistant dihydrofolate reductase specified by the Escherichia coli R-plasmid R483: comparison with procaryotic and eucaryotic dihydrofolate reductases, J. Bacteriol, vol.155, pp.1001-1008, 1983.

D. Skurnik, D. Bonnet, C. Bernède-bauduin, R. Michel, C. Guette et al., Characteristics of human intestinal Escherichia coli with changing environments, Environ. Microbiol, vol.10, pp.2132-2137, 2008.

D. Skurnik, L. Menac'h, A. Zurakowski, D. Mazel, D. Courvalin et al., Integron-associated antibiotic resistance and phylogenetic grouping of Escherichia coli isolates from healthy subjects free of recent antibiotic exposure, Antimicrob. Agents Chemother, vol.49, pp.3062-3065, 2005.

D. Skurnik, R. Ruimy, A. Andremont, C. Amorin, P. Rouquet et al., Effect of human vicinity on antimicrobial resistance and integrons in animal faecal Escherichia coli, J. Antimicrob. Chemother, vol.57, pp.1215-1219, 2006.

S. N. Slilaty and J. W. Little, Lysine-156 and serine-119 are required for LexA repressor cleavage: a possible mechanism, Proc. Natl. Acad. Sci. U. S. A, vol.84, pp.3987-3991, 1987.

M. H. Smith, M. M. Cavenagh, and J. W. Little, Mutant LexA proteins with an increased rate of in vivo cleavage, Proc. Natl. Acad. Sci. U. S. A, vol.88, pp.7356-7360, 1991.

H. Sørum, M. C. Roberts, and J. H. Crosa, Identification and cloning of a tetracycline resistance gene from the fish pathogen Vibrio salmonicida, Antimicrob. Agents Chemother, vol.36, pp.611-615, 1992.

L. Soufi, M. S. Abbassi, Y. Sáenz, L. Vinué, S. Somalo et al., Prevalence and diversity of integrons and associated resistance genes in Escherichia coli isolates from poultry meat in Tunisia, Foodborne Pathog. Dis, vol.6, pp.1067-1073, 2009.

L. Soufi, Y. Sáenz, L. Vinué, M. S. Abbassi, E. Ruiz et al., Escherichia coli of poultry food origin as reservoir of sulphonamide resistance genes and integrons, Int. J. Food Microbiol, vol.144, pp.497-502, 2011.

F. J. Sousa, L. M. Lima, A. B. Pacheco, C. L. Oliveira, I. Torriani et al., Tetramerization of the LexA repressor in solution: implications for gene regulation of the E.coli SOS system at acidic pH, J. Mol. Biol, vol.359, pp.1059-1074, 2006.

B. Spellberg and R. A. Bonomo, Airborne assault": a new dimension in Acinetobacter baumannii transmission, Crit. Care Med, vol.41, pp.2042-2044, 2013.

B. Spellberg and J. H. Rex, The value of single-pathogen antibacterial agents, Nat. Rev. Drug Discov, vol.12, p.963, 2013.

T. Stalder, O. Barraud, M. Casellas, C. Dagot, and M. Ploy, Integron involvement in environmental spread of antibiotic resistance, Front. Microbiol, vol.3, p.119, 2012.

C. Stange, J. P. Sidhu, A. Tiehm, and S. Toze, Antibiotic resistance and virulence genes in coliform water isolates, Int. J. Hyg. Environ. Health, vol.219, pp.823-831, 2016.

I. Starikova, K. Harms, P. Haugen, T. T. Lunde, R. Primicerio et al., A trade-off between the fitness cost of functional integrases and long-term stability of integrons, PLoS Pathog, vol.8, p.1003043, 2012.

H. W. Stokes and M. R. Gillings, Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens, FEMS Microbiol. Rev, vol.35, pp.790-819, 2011.

H. W. Stokes and R. M. Hall, A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons, Mol. Microbiol, vol.3, pp.1669-1683, 1989.

H. W. Stokes, C. L. Nesbø, M. Holley, M. I. Bahl, M. R. Gillings et al., Class 1 integrons potentially predating the association with tn402-like transposition genes are present in a sediment microbial community, J. Bacteriol, vol.188, pp.5722-5730, 2006.

H. W. Stokes, D. B. O'gorman, G. D. Recchia, M. Parsekhian, and R. M. Hall, Structure and function of 59-base element recombination sites associated with mobile gene cassettes, Mol. Microbiol, vol.26, pp.731-745, 1997.

R. M. Story, I. T. Weber, and T. A. Steitz, The structure of the E. coli RecA protein monomer and polymer, Nature, vol.355, pp.318-325, 1992.

G. Storz and R. Hengge, Bacterial Stress Responses, Second Edition, 2011.

E. Strugeon, V. Tilloy, M. Ploy, and S. Da-re, The Stringent Response Promotes Antibiotic Resistance Dissemination by Regulating Integron Integrase Expression in Biofilms, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01500749

, Eur. Cent. Dis. Prev. Control. URL

M. Sun, M. Ye, A. P. Schwab, X. Li, J. Wan et al., Human migration activities drive the fluctuation of ARGs: Case study of landfills in Nanjing, eastern, China. J. Hazard. Mater, vol.315, pp.93-101, 2016.

M. Sunde, Prevalence and characterization of class 1 and class 2 integrons in Escherichia coli isolated from meat and meat products of Norwegian origin, J. Antimicrob. Chemother, vol.56, pp.1019-1024, 2005.

M. Sunde, H. Solheim, and J. S. Slettemeås, Genetic linkage between class 1 integrons with the dfrA12-orfF-aadA2 cassette array and sul3 in Escherichia coli, Vet. Microbiol, vol.130, pp.422-425, 2008.

F. Taddei, I. Matic, and M. Radman, cAMP-dependent SOS induction and mutagenesis in resting bacterial populations, Proc. Natl. Acad. Sci. U. S. A, vol.92, pp.11736-11740, 1995.

C. R. Taitt, T. A. Leski, M. G. Stockelman, D. W. Craft, D. V. Zurawski et al., Antimicrobial resistance determinants in Acinetobacter baumannii isolates taken from military treatment facilities, Antimicrob. Agents Chemother, vol.58, pp.767-781, 2014.
DOI : 10.1128/aac.01897-13

URL : https://aac.asm.org/content/58/2/767.full.pdf

G. H. Talbot, J. Bradley, J. E. Edwards, D. Gilbert, M. Scheld et al., Bad bugs need drugs: an update on the development pipeline from the Antimicrobial Availability Task Force of the Infectious Diseases Society of America, Clin. Infect. Dis, vol.42, pp.657-668, 2006.

A. Tauch, S. Götker, A. Pühler, J. Kalinowski, and G. Thierbach, The 27.8-kb R-plasmid pTET3 from Corynebacterium glutamicum encodes the aminoglycoside adenyltransferase gene cassette aadA9 and the regulated tetracycline efflux system Tet 33 flanked by active copies of the widespread insertion sequence IS6100, Plasmid, vol.48, pp.117-129, 2002.

A. T. Thliveris, J. W. Little, and D. W. Mount, Repression of the E coli recA gene requires at least two LexA protein monomers, Biochimie, vol.73, pp.449-456, 1991.

M. A. Toleman, H. Vinodh, U. Sekar, V. Kamat, and T. R. Walsh, blaVIM-2-harboring integrons isolated in India, Russia, and the United States arise from an ancestral class 1 integron predating the formation of the 3' conserved sequence, Antimicrob. Agents Chemother, vol.51, pp.2636-2638, 2007.

M. E. Tolmasky, Bacterial resistance to aminoglycosides and beta-lactams: the Tn1331 transposon paradigm, Front. Biosci. J. Virtual Libr, vol.5, pp.20-29, 2000.
DOI : 10.2741/a493

URL : https://www.bioscience.org/2000/v5/d/tolmasky/tolmasky.pdf

K. J. Towner, Acinetobacter: an old friend, but a new enemy, J. Hosp. Infect, vol.73, pp.355-363, 2009.
DOI : 10.1016/j.jhin.2009.03.032

A. Tsakris, A. Ikonomidis, N. Spanakis, A. Poulou, and S. Pournaras, Characterization of In3Mor, a new integron carrying VIM-1 metallo-beta-lactamase and sat1 gene, from Morganella morganii, J. Antimicrob. Chemother, vol.59, pp.739-741, 2007.

G. Turabelidze, S. J. Lawrence, H. Gao, E. Sodergren, G. M. Weinstock et al., Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis, J. Clin. Microbiol, vol.51, pp.3950-3954, 2013.

J. F. Turton, M. E. Kaufmann, J. Glover, J. M. Coelho, M. Warner et al., Detection and typing of integrons in epidemic strains of Acinetobacter baumannii found in the United Kingdom, J. Clin. Microbiol, vol.43, pp.3074-3082, 2005.

C. Ubeda, E. Maiques, M. A. Tormo, S. Campoy, I. Lasa et al., SaPI operon I is required for SaPI packaging and is controlled by LexA, Mol. Microbiol, vol.65, pp.41-50, 2007.

D. Vallenet, P. Nordmann, V. Barbe, L. Poirel, S. Mangenot et al., Comparative analysis of Acinetobacters: three genomes for three lifestyles, PloS One, vol.3, p.1805, 2008.

A. S. Vangnai and W. Petchkroh, Biodegradation of 4-chloroaniline by bacteria enriched from soil, FEMS Microbiol. Lett, vol.268, pp.209-216, 2007.
DOI : 10.1111/j.1574-6968.2006.00579.x

URL : https://academic.oup.com/femsle/article-pdf/268/2/209/19428351/268-2-209.pdf

E. Varhimo, K. Savijoki, H. Jefremoff, J. Jalava, A. Sukura et al., Ciprofloxacin induces mutagenesis to antibiotic resistance independent of UmuC in Streptococcus uberis, Environ. Microbiol, vol.10, pp.2179-2183, 2008.

A. Vasilakopoulou, M. Psichogiou, L. Tzouvelekis, P. T. Tassios, C. Kosmidis et al., Prevalence and characterization of class 1 integrons in Escherichia coli of poultry and human origin, Foodborne Pathog. Dis, vol.6, pp.1211-1218, 2009.

S. Vaux, E. Nguyen, S. Alleaume, K. Blanckaert, M. Galas et al., Signalement des infections nosocomiales à Acinetobacter baumannii résistant à l'imipénème, 2001.

J. Vila, S. Martí, and J. Sánchez-céspedes, Porins, efflux pumps and multidrug resistance in Acinetobacter baumannii, J. Antimicrob. Chemother, vol.59, pp.1210-1215, 2007.

J. Vila, M. Navia, J. Ruiz, and C. Casals, Cloning and nucleotide sequence analysis of a gene encoding an OXA-derived beta-lactamase in Acinetobacter baumannii, Antimicrob. Agents Chemother, vol.41, pp.2757-2759, 1997.

J. Vincent, J. Rello, J. Marshall, E. Silva, A. Anzueto et al., International study of the prevalence and outcomes of infection in intensive care units, JAMA, vol.302, pp.2323-2329, 2009.

L. Vinué, T. Jové, C. Torres, and M. Ploy, Diversity of class 1 integron gene cassette Pc promoter variants in clinical Escherichia coli strains and description of a new P2 promoter variant, Int. J. Antimicrob. Agents, vol.38, pp.526-529, 2011.

L. Vinué, Y. Sáenz, S. Somalo, E. Escudero, M. A. Moreno et al., Prevalence and diversity of integrons and associated resistance genes in faecal Escherichia coli isolates of healthy humans in Spain, J. Antimicrob. Chemother, vol.62, pp.934-937, 2008.

A. T. Vo, E. Van-duijkeren, A. C. Fluit, and W. Gaastra, Characteristics of extendedspectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates from horses, Vet. Microbiol, vol.124, pp.248-255, 2007.

M. R. Volkert, F. H. Gately, and L. I. Hajec, Expression of DNA damage-inducible genes of Escherichia coli upon treatment with methylating, ethylating and propylating agents, Mutat. Res, vol.217, pp.109-115, 1989.

A. C. Vollmer, S. Kwakye, M. Halpern, and E. C. Everbach, Bacterial stress responses to 1megahertz pulsed ultrasound in the presence of microbubbles, Appl. Environ. Microbiol, vol.64, pp.3927-3931, 1998.

J. T. Wade, N. B. Reppas, G. M. Church, and K. Struhl, Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites, Genes Dev, vol.19, pp.2619-2630, 2005.

G. C. Walker, Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli, Microbiol. Rev, vol.48, pp.60-93, 1984.

Y. Wang, P. Hao, B. Lu, H. Yu, W. Huang et al., Causes of infection after earthquake, China, Emerg. Infect. Dis, vol.16, pp.974-975, 2008.

B. S. Weber, C. M. Harding, and M. F. Feldman, Pathogenic Acinetobacter: from the Cell Surface to Infinity and Beyond, J. Bacteriol, vol.198, pp.880-887, 2015.

Q. Wei, Q. Hu, S. Li, H. Lu, G. Chen et al., A novel functional class 2 integron in clinical Proteus mirabilis isolates, J. Antimicrob. Chemother, vol.69, pp.973-976, 2014.

L. M. Weiner, A. K. Webb, B. Limbago, M. A. Dudeck, J. Patel et al., Antimicrobial-Resistant Pathogens Associated With HealthcareAssociated Infections: Summary of Data Reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, Infect. Control Hosp. Epidemiol, vol.37, pp.1288-1301, 2011.

C. Wendt, B. Dietze, E. Dietz, and H. Rüden, Survival of Acinetobacter baumannii on dry surfaces, J. Clin. Microbiol, vol.35, pp.1394-1397, 1997.

D. G. White, S. Zhao, R. Sudler, S. Ayers, S. Friedman et al., The isolation of antibiotic-resistant Salmonella from retail ground meats, N. Engl. J. Med, vol.345, pp.1147-1154, 2001.

, WHO | Antimicrobial resistance: global report on surveillance, 2014.

, WHO | Global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics, 2017.

K. W. Winterling, D. Chafin, J. J. Hayes, J. Sun, A. S. Levine et al., The Bacillus subtilis DinR binding site: redefinition of the consensus sequence, J. Bacteriol, vol.180, pp.2201-2211, 1998.

T. A. Witkowski, A. N. Grice, D. B. Stinnett, W. K. Wells, M. A. Peterson et al., UmuDAb: An Error-Prone Polymerase Accessory Homolog Whose N-Terminal Domain Is Required for Repression of DNA Damage Inducible Gene Expression in Acinetobacter baylyi, PloS One, vol.11, 2016.

D. Wong, T. B. Nielsen, R. A. Bonomo, P. Pantapalangkoor, B. Luna et al., Clinical and Pathophysiological Overview of Acinetobacter Infections: a Century of Challenges, Clin. Microbiol. Rev, vol.30, pp.409-447, 2017.

H. Xu, J. Davies, and V. Miao, Molecular characterization of class 3 integrons from Delftia spp, J. Bacteriol, vol.189, pp.6276-6283, 2007.

M. Yamamoto, M. Nagao, Y. Matsumura, A. Matsushima, Y. Ito et al., Interspecies dissemination of a novel class 1 integron carrying blaIMP-19 among Acinetobacter species in Japan, J. Antimicrob. Chemother, vol.66, pp.2480-2483, 2011.

H. Yang, S. Chen, D. G. White, S. Zhao, P. Mcdermott et al., Characterization of multiple-antimicrobial-resistant Escherichia coli isolates from diseased chickens and swine in China, J. Clin. Microbiol, vol.42, pp.3483-3489, 2004.

M. Yang, S. Su, and V. Sung, Identification and characterization of a second lexA gene of Xanthomonas axonopodis Pathovar citri, Appl. Environ. Microbiol, vol.71, pp.3589-3598, 2005.

E. Yoon, V. Balloy, L. Fiette, M. Chignard, P. Courvalin et al., Contribution of the Ade Resistance-Nodulation-Cell Division-Type Efflux Pumps to Fitness and Pathogenesis of Acinetobacter baumannii, vol.7, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01382765

E. Zander, A. Fernández-gonzález, X. Schleicher, C. Dammhayn, W. Kamolvit et al., Worldwide dissemination of acquired carbapenem-hydrolysing class D ?-lactamases in Acinetobacter spp. other than Acinetobacter baumannii, Int. J. Antimicrob. Agents, vol.43, pp.375-377, 2014.

E. Zander, H. Seifert, and P. G. Higgins, Insertion sequence IS18 mediates overexpression of blaOXA-257 in a carbapenem-resistant Acinetobacter bereziniae isolate, J. Antimicrob. Chemother, vol.69, pp.270-271, 2014.

R. Zarrilli, S. Pournaras, M. Giannouli, and A. Tsakris, Global evolution of multidrugresistant Acinetobacter baumannii clonal lineages, Int. J. Antimicrob. Agents, vol.41, pp.11-19, 2013.

A. P. Zhang, Y. Z. Pigli, and P. A. Rice, Structure of the LexA-DNA complex and implications for SOS box measurement, Nature, vol.466, pp.883-886, 2010.

B. Zhang, Z. Liu, Z. Lin, X. Zhang, and W. Fu, Microbiologic characteristics of pathogenic bacteria from hospitalized trauma patients who survived Wenchuan earthquake, Eur. J. Clin. Microbiol. Infect. Dis, vol.31, pp.2529-2535, 2012.

J. Zhang, W. Zhu, Y. Chu, S. Tian, and B. Chen, Molecular epidemiological study of multidrug resistant Acinetobacter baumannii, Zhonghua Nei Ke Za Zhi, vol.49, pp.657-661, 2010.

W. Zhang, Z. Lu, S. Schwarz, R. Zhang, X. Wang et al., Complete sequence of the bla(NDM-1)-carrying plasmid pNDM-AB from Acinetobacter baumannii of food animal origin, J. Antimicrob. Chemother, vol.68, pp.1681-1682, 2013.

X. Zhang, T. Zhang, M. Zhang, H. H. Fang, and S. Cheng, Characterization and quantification of class 1 integrons and associated gene cassettes in sewage treatment plants, Appl. Microbiol. Biotechnol, vol.82, pp.1169-1177, 2009.

Y. Zhang, A. Z. Gu, M. He, D. Li, and J. Chen, Subinhibitory Concentrations of Disinfectants Promote the Horizontal Transfer of Multidrug Resistance Genes within and across Genera, Environ. Sci. Technol, vol.51, pp.570-580, 2017.

Q. Zhong, W. Xu, Y. Wu, and H. Xu, Clonal spread of carbapenem non-susceptible Acinetobacter baumannii in an intensive care unit in a teaching hospital in China, Ann. Lab. Med, vol.32, pp.413-419, 2012.

Y. Zhu, Y. Yi, F. Liu, N. Lv, X. Yang et al., Distribution and molecular profiling of class 1 integrons in MDR Acinetobacter baumannii isolates and whole genome-based analysis of antibiotic resistance mechanisms in a representative strain, Microbiol. Res, vol.169, pp.811-816, 2014.

M. D. Zilberberg, B. H. Nathanson, K. Sulham, W. Fan, and A. F. Shorr, Multidrug resistance, inappropriate empiric therapy, and hospital mortality in Acinetobacter baumannii pneumonia and sepsis, Crit. Care Lond. Engl, vol.20, p.221, 2016.
DOI : 10.1186/s13054-016-1392-4

URL : https://ccforum.biomedcentral.com/track/pdf/10.1186/s13054-016-1392-4

S. Zordan, E. Prenger-berninghoff, R. Weiss, T. Van-der-reijden, P. Van-den-broek et al., Multidrug-resistant Acinetobacter baumannii in veterinary clinics, Germany. Emerg. Infect. Dis, vol.17, pp.1751-1754, 2011.

V. V. Zverlov and W. H. Schwarz, Organization of the chromosomal region containing the genes lexA and topA in Thermotoga neapolitana. Primary structure of LexA reveals phylogenetic relevance, Syst. Appl. Microbiol, vol.22, pp.174-178, 1999.

, Communications scientifiques sur le travail de thèse ? Communications orales : o Nationale : Diversité des séquences promotrices : le modèle intégron. E. CouveDeacon, conférence invitée, « Section des Anti-Microbiens-Société Française de Microbiologie, vol.2, 2013.

. Locale, Etude des promoteurs des intégrons de classe 1 chez Acinetobacter baumannii. E. Couvé-Deacon, F. Garnier, MC Ploy. « Journée Scientifique GEIST, 2014.

, ? Communications affichées : o Internationale : Strength and diversity of the gene cassettes promoter Pc of class 1 integrons in Acinetobacter baumannii. E. Couvé-Deacon

M. C. Burucoa, F. Ploy, and . Garnier, , 2013.

T. Jové, O. Barraud, C. Burucoa, M. C. Ploy, and F. Garnier, Etude des promoteurs des cassettes des intégrons chez Acinetobacter baumannii. E. Couvé-Deacon, 2013.

, Annexe, vol.3

E. Couvé-deacon, A. Tristan, N. Pestourie, C. Faure, V. Doffoel-hantz et al., occasion de publier les articles qui sont listés ci-dessous :-PVL-producing Methicillin-Susceptible Staphylococcus aureus outbreak in a French rugby team

Q. Ballouhey, L. Fourcade, E. Couve-deacon, J. Cros, V. Lescure et al., Urine contamination in non-toilet-trained and uncircumcised boys, 2016.

P. Loubet, N. Samih-lenzi, F. Galtier, P. Vanhems, P. Loulergue et al., Factors associated with poor outcomes among adults hospitalized for influenza in France: A three-year prospective multicenter study, vol.79, pp.68-73, 2016.

J. R. Zahar, P. Lesprit, S. Ruckly, A. Eden, H. Hikombo et al., Predominance of healthcare-associated cases among episodes of community-onset bacteraemia due to extended-spectrum ?-lactamase-producing Enterobacteriaceae, Int J Antimicrob Agents, vol.49, issue.1, pp.67-73, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01897836

P. Loubet, N. Lenzi, M. Valette, V. Foulongne, A. Krivine et al., Clinical characteristics and outcome of respiratory syncytial virus infection among adults hospitalized with influenza-like illness in France, Clin Microbiol Infect, vol.23, issue.4, pp.253-259, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01518888

E. Couvé-deacon, F. Mons, F. Garnier, P. Leduc, L. Ponthier et al., Neonatal Outbreak of Methicillin-Resistant Staphylococcus aureus Clone Geraldine: A Bundle of Measures to Halt Transmission, Infect Control Hosp Epidemiol, vol.38, issue.6, pp.749-751, 2017.

E. Couvé-deacon, D. Postil, O. Barraud, C. Duchiron, D. Chainier et al., Crosssectional Study, Staphylococcus Aureus Carriage in French Athletes at Risk of CA-MRSA Infection: a Prospective, vol.3, p.28, 2017.

F. A. Stressmann, E. Couve-deacon, D. Chainier, A. Chauhan, A. Wessel et al., Comparative Analysis of Bacterial Community Composition and Structure in Clinically Symptomatic and Asymptomatic Central Venous Catheters, vol.2, pp.146-163, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01689523

D. Chainier, O. Barraud, G. Masson, E. Couve-deacon, B. François et al., Cultivation-Independent Approach, Integron Digestive Carriage in Human and Cattle: A "One Health, vol.8, p.1891, 2017.

E. De-classe-1 and C. Baumannii,