C. M. Collis, M. J. Kim, H. W. Stokes, and R. M. Hall, Binding of the purified integron DNA integrase IntI1 to integron- and cassette-associated recombination sites, Molecular Microbiology, vol.29, issue.2, pp.477-490, 1998.
DOI : 10.1007/BF02464882

L. Biskri, M. Bouvier, A. M. Guerout, S. Boisnard, and D. Mazel, Comparative Study of Class 1 Integron and Vibrio cholerae Superintegron Integrase Activities, Journal of Bacteriology, vol.187, issue.5, pp.1740-1750, 2005.
DOI : 10.1128/JB.187.5.1740-1750.2005

M. Bouvier, G. Demarre, and D. Mazel, Integron cassette insertion: a recombination process involving a folded single strand substrate, The EMBO Journal, vol.91, issue.24, pp.4356-4367, 2005.
DOI : 10.1038/sj.emboj.7600434

T. Jove, S. Da-re, F. Denis, D. Mazel, and M. C. Ploy, Inverse Correlation between Promoter Strength and Excision Activity in Class 1 Integrons, PLoS Genetics, vol.314, issue.1, 2010.
DOI : 10.1371/journal.pgen.1000793.s004

URL : https://hal.archives-ouvertes.fr/inserm-00533193

D. Mazel, Integrons: agents of bacterial evolution, Nature Reviews Microbiology, vol.91, issue.8, pp.608-620, 2006.
DOI : 10.1073/pnas.91.20.9218

D. A. Rowe-magnus and D. Mazel, Resistance gene capture, Current Opinion in Microbiology, vol.2, issue.5, pp.483-488, 1999.
DOI : 10.1016/S1369-5274(99)00004-1

P. Martinez-freijo, A. C. Fluit, F. J. Schmitz, V. S. Grek, J. Verhoef et al., Class I integrons in Gram-negative isolates from different European hospitals and association with decreased susceptibility to multiple antibiotic compounds, Journal of Antimicrobial Chemotherapy, vol.42, issue.6, pp.689-696, 1998.
DOI : 10.1093/jac/42.6.689

H. W. Stokes and R. M. Hall, A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons, Molecular Microbiology, vol.9, issue.12, pp.1669-1683, 1989.
DOI : 10.1007/BF00337818

C. A. Liebert, R. M. Hall, and A. Summers, Transposon Tn21, flagship of the floating genome, Microbiol. Mol. Biol. Rev, vol.63, pp.507-522, 1999.

L. Poirel, O. Menuteau, N. Agoli, C. Cattoen, and P. Nordmann, Outbreak of Extended-Spectrum ??-Lactamase VEB-1-Producing Isolates of Acinetobacter baumannii in a French Hospital, Journal of Clinical Microbiology, vol.41, issue.8, pp.3542-3547, 2003.
DOI : 10.1128/JCM.41.8.3542-3547.2003

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, Journal of Antimicrobial Chemotherapy, vol.57, issue.6, pp.1215-1219, 2006.
DOI : 10.1093/jac/dkl122

A. C. Fluit and F. J. Schmitz, Resistance integrons and super-integrons, Clinical Microbiology and Infection, vol.10, issue.4, 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

D. A. Rowe-magnus, A. M. Guerout, and D. Mazel, Bacterial resistance evolution by recruitment of super-integron gene cassettes, Molecular Microbiology, vol.43, issue.6, pp.1657-1669, 2002.
DOI : 10.1099/00222615-46-5-398

S. R. Partridge, G. Tsafnat, E. Coiera, and J. R. Iredell, Gene cassettes and cassette arrays in mobile resistance integrons, FEMS Microbiology Reviews, vol.16, issue.4, pp.757-784, 2009.
DOI : 10.1128/AAC.01313-08

D. Mazel, B. Dychinco, V. A. Webb, and J. Davies, A Distinctive Class of Integron in the Vibrio cholerae Genome, Science, vol.280, issue.5363, pp.605-608, 1998.
DOI : 10.1126/science.280.5363.605

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, pp.652-657, 2001.
DOI : 10.1073/pnas.96.5.2192

Y. W. Wu, M. Rho, T. G. Doak, and Y. Ye, ABSTRACT, Applied and Environmental Microbiology, vol.78, issue.15, pp.5288-5296, 2012.
DOI : 10.1128/AEM.00564-12

URL : https://hal.archives-ouvertes.fr/hal-00953003

E. Martinez, C. Marquez, A. Ingold, J. Merlino, S. P. Djordjevic et al., ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.56, issue.4, pp.2169-2172, 2012.
DOI : 10.1128/AAC.06048-11

URL : https://hal.archives-ouvertes.fr/hal-00462315

E. Ruiz, Y. Saenz, M. Zarazaga, R. Rocha-gracia, L. Martinez-martinez et al., qnr, aac(6???)-Ib-cr and qepA genes in Escherichia coli and Klebsiella spp.: genetic environments and plasmid and chromosomal location, Journal of Antimicrobial Chemotherapy, vol.63, issue.4, pp.886-897, 2012.
DOI : 10.1093/jac/dkn474

N. Coleman, S. Tetu, N. Wilson, and A. Holmes, An unusual integron in Treponema denticola, Microbiology, vol.150, issue.11, pp.3524-3526, 2004.
DOI : 10.1099/mic.0.27569-0

M. Gillings, Y. Boucher, M. Labbate, A. Holmes, S. Krishnan et al., The Evolution of Class 1 Integrons and the Rise of Antibiotic Resistance, Journal of Bacteriology, vol.190, issue.14, pp.5095-5100, 2008.
DOI : 10.1128/JB.00152-08

L. Roux, F. Zouine, M. Chakroun, N. Binesse, J. Saulnier et al., Genome sequence of Vibrio splendidus: An abundant planctonic marine species with a large genotypic diversity, Environ. Microbiol, vol.11, 1959.

A. Rossi and M. Galas, New carbenicillin-hydrolyzing beta-lactamase (carb-7) from Vibrio cholerae non-O1, non-O139 strains encoded by the vcr region of the V. cholerae genome, Antimicrob. Agents Chemother, vol.46, pp.2162-2168, 2002.

A. Petroni, R. G. Melano, H. A. Saka, A. Garutti, L. Mange et al., CARB-9, a Carbenicillinase Encoded in the VCR Region of Vibrio cholerae Non-O1, Non-O139 Belongs to a Family of Cassette-Encoded ??-Lactamases, Antimicrobial Agents and Chemotherapy, vol.48, issue.10
DOI : 10.1128/AAC.48.10.4042-4046.2004

E. L. Fonseca, S. Freitas, F. Vieira, V. V. Vicente, and A. , O1, Emerging Infectious Diseases, vol.14, issue.7, pp.1129-1131, 2008.
DOI : 10.3201/eid1407.080132

URL : https://hal.archives-ouvertes.fr/hal-00399254

G. Sow, A. Aidara-kane, A. Barraud, O. Gatet, M. 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

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 & Development, vol.19, issue.21, pp.2619-2630, 2005.
DOI : 10.1101/gad.1355605

E. Guerin, G. Cambray, N. Sanchez-alberola, S. Campoy, I. Erill et al., The SOS Response Controls Integron Recombination, Science, vol.9, issue.5, p.1034, 2009.
DOI : 10.1016/j.mib.2006.07.002

URL : https://hal.archives-ouvertes.fr/hal-00409031

G. Cambray, N. Sanchez-alberola, S. Campoy, E. Guerin, S. Da-re et al., Prevalence of SOS-mediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons, Mobile DNA, vol.2, issue.1, p.6, 2011.
DOI : 10.1101/gr.849004

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

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, Journal of Bacteriology, vol.194, issue.7, pp.1005982-1005993, 1128.
DOI : 10.1128/JB.05982-11

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, mBio, vol.2, issue.2, pp.335-345, 2011.
DOI : 10.1128/mBio.00335-10

URL : http://mbio.asm.org/content/2/2/e00335-10.full.pdf

Z. Baharoglu, D. Bikard, and D. Mazel, Conjugative DNA Transfer Induces the Bacterial SOS Response and Promotes Antibiotic Resistance Development through Integron Activation, PLoS Genetics, vol.310, issue.Pt 9, 2010.
DOI : 10.1371/journal.pgen.1001165.s006

URL : https://doi.org/10.1371/journal.pgen.1001165

I. Matic, C. Rayssiguier, and M. Radman, Interspecies gene exchange in bacteria: The role of SOS and mismatch repair systems in evolution of species, Cell, vol.80, issue.3, pp.507-515, 1995.
DOI : 10.1016/0092-8674(95)90501-4

I. Matic, F. Taddei, and M. Radman, No Genetic Barriers between Salmonella enterica Serovar Typhimurium and Escherichia coli in SOS-Induced Mismatch Repair-Deficient Cells, Journal of Bacteriology, vol.182, issue.20, pp.5922-5924, 2000.
DOI : 10.1128/JB.182.20.5922-5924.2000

S. Delmas, Cellular response to horizontally transferred DNA in Escherichia coli is tuned by DNA repair systems, DNA Repair, vol.4, issue.2, pp.221-229, 2005.
DOI : 10.1016/j.dnarep.2004.09.008

M. Smorawinska, M. Szuplewska, P. Zaleski, P. Wawrzyniak, A. Maj et al., Mobilizable narrow host range plasmids as natural suicide vectors enabling horizontal gene transfer among distantly related bacterial species, FEMS Microbiology Letters, vol.11, issue.1, pp.76-82, 2012.
DOI : 10.1007/s10126-008-9160-3

URL : https://academic.oup.com/femsle/article-pdf/326/1/76/19120782/326-1-76.pdf

R. R. Colwell, A Global and Historical Perspective of the Genus Vibrio, In The Biology, 2006.
DOI : 10.1128/9781555815714.ch1

H. Urakawa and I. N. Rivera, Aquatic Environment, In The Biology, 2006.
DOI : 10.1128/9781555815714.ch12

L. E. Bryan, M. S. Shahrabadi, and H. M. Van-den-elzen, Gentamicin Resistance in Pseudomonas aeruginosa: R-Factor-Mediated Resistance, Antimicrobial Agents and Chemotherapy, vol.6, issue.2, pp.191-199, 1974.
DOI : 10.1128/AAC.6.2.191

URL : http://aac.asm.org/content/6/2/191.full.pdf

P. Kontomichalou, M. Mitani, and R. C. Clowes, Circular R-factor molecules controlling penicillinase synthesis, replicating in Escherichia coli under either relaxed or stringent control, J. Bacteriol, vol.104, pp.34-44, 1970.

A. Moura, I. Henriques, K. Smalla, and A. Correia, Wastewater bacterial communities bring together broad-host range plasmids, integrons and a wide diversity of uncharacterized gene cassettes, Research in Microbiology, vol.161, issue.1, pp.58-66, 2010.
DOI : 10.1016/j.resmic.2009.11.004

A. Moura, C. Oliveira, I. Henriques, K. Smalla, and A. Correia, Broad diversity of conjugative plasmids in integron-carrying bacteria from wastewater environments, FEMS Microbiology Letters, vol.19, issue.103, pp.157-164, 2012.
DOI : 10.1093/nar/19.24.6823

B. Stecher, R. Denzler, L. Maier, F. Bernet, M. J. Sanders et al., Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae, Proc. Natl. Acad. Sci. USA 2012, pp.1269-1274
DOI : 10.1111/j.1462-5822.2008.01118.x

URL : http://www.pnas.org/content/109/4/1269.full.pdf

D. Dubnau, DNA Uptake in Bacteria, Annual Review of Microbiology, vol.53, issue.1, pp.217-244, 1999.
DOI : 10.1146/annurev.micro.53.1.217

J. P. Claverys, B. Martin, and P. Polard, The genetic transformation machinery: composition, localization, and mechanism, FEMS Microbiology Reviews, vol.140, issue.3, pp.643-656, 2009.
DOI : 10.1073/pnas.90.9.3875

URL : https://hal.archives-ouvertes.fr/hal-00407190

R. E. Yasbin, G. A. Wilson, and F. Young, Transformation and transfection in lysogenic strains of Bacillus subtilis: Evidence for selective induction of prophage in competent cells, J. Bacteriol, vol.121, pp.296-304, 1975.

P. Seitz and M. Blokesch, Cues and regulatory pathways involved in natural competence and transformation in pathogenic and environmental Gram-negative bacteria, FEMS Microbiology Reviews, vol.121, issue.Pt 12, pp.336-363, 2012.
DOI : 10.1073/pnas.92.8.3616

X. Charpentier, P. Polard, and J. P. Claverys, Induction of competence for genetic transformation by antibiotics: convergent evolution of stress responses in distant bacterial species lacking SOS?, Current Opinion in Microbiology, vol.15, issue.5, pp.570-576, 2012.
DOI : 10.1016/j.mib.2012.08.001

URL : https://hal.archives-ouvertes.fr/hal-00787606

K. L. Meibom, M. Blokesch, N. A. Dolganov, C. Y. Wu, and G. K. Schoolnik, Chitin Induces Natural Competence in Vibrio cholerae, Chitin induces natural competence in Vibrio cholerae, pp.1824-1827, 2005.
DOI : 10.1126/science.1120096

L. Scrudato, M. Blokesch, and M. , The Regulatory Network of Natural Competence and Transformation of Vibrio cholerae, PLoS Genetics, vol.2, issue.6, p.1002778, 2012.
DOI : 10.1371/journal.pgen.1002778.s009

J. J. Zulty and G. J. Barcak, Identification of a DNA transformation gene required for com101A+ expression and supertransformer phenotype in Haemophilus influenzae., Proc. Natl. Acad. Sci, pp.3616-3620, 1995.
DOI : 10.1073/pnas.92.8.3616

S. Yamamoto, M. Morita, H. Izumiya, and H. Watanabe, Chitin disaccharide (GlcNAc)2 induces natural competence in Vibrio cholerae through transcriptional and translational activation of a positive regulatory gene tfoXVC, Gene, vol.457, issue.1-2, pp.42-49, 2010.
DOI : 10.1016/j.gene.2010.03.003

S. Karudapuram and G. J. Barcak, The Haemophilus influenzae dprABC genes constitute a competence-inducible operon that requires the product of the tfoX (sxy) gene for transcriptional activation., Journal of Bacteriology, vol.179, issue.15, pp.4815-4820, 1997.
DOI : 10.1128/jb.179.15.4815-4820.1997

A. D. Cameron, M. Volar, L. A. Bannister, and R. J. Redfield, RNA secondary structure regulates the translation of sxy and competence development in Haemophilus influenzae, Nucleic Acids Research, vol.175, issue.1, pp.10-20, 2008.
DOI : 10.1128/jb.175.22.7142-7149.1993

R. J. Redfield, A. D. Cameron, Q. Qian, J. Hinds, T. R. Ali et al., A Novel CRP-dependent Regulon Controls Expression of Competence Genes in Haemophilus influenzae, Journal of Molecular Biology, vol.347, issue.4, pp.735-747, 2005.
DOI : 10.1016/j.jmb.2005.01.012

K. L. Meibom, X. B. Li, A. T. Nielsen, C. Y. Wu, S. Roseman et al., The Vibrio cholerae chitin utilization program, Proc. Natl. Acad. Sci, pp.2524-2529, 2004.
DOI : 10.1126/science.280.5364.694

M. Blokesch and G. K. Schoolnik, The Extracellular Nuclease Dns and Its Role in Natural Transformation of Vibrio cholerae, Journal of Bacteriology, vol.190, issue.21, pp.7232-7240, 2008.
DOI : 10.1128/JB.00959-08

S. Domingues, K. Harms, W. F. Fricke, P. J. Johnsen, G. J. Da-silva et al., Natural Transformation Facilitates Transfer of Transposons, Integrons and Gene Cassettes between Bacterial Species, PLoS Pathogens, vol.8, issue.8, p.1002837, 2012.
DOI : 10.1371/journal.ppat.1002837.s005

L. A. Singletary, J. L. Gibson, E. J. Tanner, G. J. Mckenzie, P. L. Lee et al., An SOS-Regulated Type 2 Toxin-Antitoxin System, Journal of Bacteriology, vol.191, issue.24, pp.7456-7465, 2009.
DOI : 10.1128/JB.00963-09

D. P. Pandey and K. Gerdes, Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes, Nucleic Acids Research, vol.33, issue.3, pp.966-976, 2005.
DOI : 10.1093/nar/gki201

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, Antimicrobial Agents and Chemotherapy, vol.45, issue.11, pp.2991-3000, 2001.
DOI : 10.1128/AAC.45.11.2991-3000.2001

R. A. Wozniak, D. E. Fouts, M. Spagnoletti, M. M. Colombo, D. Ceccarelli et al., Comparative ICE Genomics: Insights into the Evolution of the SXT/R391 Family of ICEs, PLoS Genetics, vol.40, issue.12, p.1000786, 2009.
DOI : 10.1371/journal.pgen.1000786.s002

M. A. Toleman, P. M. Bennett, and T. R. Walsh, ISCR Elements: Novel Gene-Capturing Systems of the 21st Century?, Microbiology and Molecular Biology Reviews, vol.70, issue.2, pp.296-316, 2006.
DOI : 10.1128/MMBR.00048-05

Z. Baharoglu and D. Mazel, ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.55, issue.5, pp.2438-2441, 2011.
DOI : 10.1128/AAC.01549-10

R. A. Wozniak and M. K. Waldor, Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow, Nature Reviews Microbiology, vol.5, issue.8, pp.552-563, 2010.
DOI : 10.1128/jb.173.22.7136-7141.1991

G. Garriss and V. Burrus, Integrating Conjugative Elements of the SXT/R391 Family, Bacterial Integrative Mobile Genetic Elements, 2013.

R. A. Wozniak and M. K. Waldor, A Toxin???Antitoxin System Promotes the Maintenance of an Integrative Conjugative Element, PLoS Genetics, vol.53, issue.1, p.1000439, 2009.
DOI : 10.1371/journal.pgen.1000439.t004

L. Dziewit, M. Jazurek, L. Drewniak, J. Baj, and D. Bartosik, The SXT Conjugative Element and Linear Prophage N15 Encode Toxin-Antitoxin-Stabilizing Systems Homologous to the tad-ata Module of the Paracoccus aminophilus Plasmid pAMI2, Journal of Bacteriology, vol.189, issue.5, pp.1983-1997, 2007.
DOI : 10.1128/JB.01610-06

S. M. Faruque, K. Biswas, S. M. Udden, Q. S. Ahmad, D. A. Sack et al., Transmissibility of cholera: In vivo-formed biofilms and their relationship to infectivity and persistence in the environment, Proc. Natl. Acad. Sci, pp.6350-6355, 2006.
DOI : 10.1016/0035-9203(61)90090-6

S. M. Butler and A. Camilli, Both chemotaxis and net motility greatly influence the infectivity of Vibrio cholerae, Proc. Natl. Acad. Sci, pp.5018-5023, 2004.
DOI : 10.1016/0378-1119(91)90007-X

J. W. Beaber, B. Hochhut, and M. K. Waldor, SOS response promotes horizontal dissemination of antibiotic resistance genes, Nature, vol.53, issue.6969, pp.72-74, 2004.
DOI : 10.1073/pnas.120163297

V. Burrus and M. K. Waldor, Control of SXT Integration and Excision, Journal of Bacteriology, vol.185, issue.17, pp.5045-5054, 2003.
DOI : 10.1128/JB.185.17.5045-5054.2003

G. Cambray, A. M. Guerout, D. Mazel, and . Integrons, Integrons, Annual Review of Genetics, vol.44, issue.1, pp.141-166, 2010.
DOI : 10.1146/annurev-genet-102209-163504

URL : https://hal.archives-ouvertes.fr/hal-00535771

G. Garriss, M. K. Waldor, and V. Burrus, Mobile Antibiotic Resistance Encoding Elements Promote Their Own Diversity, PLoS Genetics, vol.53, issue.12, 2009.
DOI : 10.1371/journal.pgen.1000775.s003

URL : https://doi.org/10.1371/journal.pgen.1000775

G. Garriss, D. Poulin-laprade, and V. Burrus, DNA-Damaging Agents Induce the RecA-Independent Homologous Recombination Functions of Integrating Conjugative Elements of the SXT/R391 Family, Journal of Bacteriology, vol.195, issue.9, 1991.
DOI : 10.1128/JB.02090-12

B. Hochhut, J. W. Beaber, R. Woodgate, and M. K. Waldor, Formation of Chromosomal Tandem Arrays of the SXT Element and R391, Two Conjugative Chromosomally Integrating Elements That Share an Attachment Site, Journal of Bacteriology, vol.183, issue.4, pp.1124-1132, 2001.
DOI : 10.1128/JB.183.4.1124-1132.2001

V. Burrus and M. K. Waldor, Formation of SXT Tandem Arrays and SXT-R391 Hybrids, Journal of Bacteriology, vol.186, issue.9, pp.2636-2645, 2004.
DOI : 10.1128/JB.186.9.2636-2645.2004

M. Galimand, A. Guiyoule, G. Gerbaud, B. Rasoamanana, S. Chanteau et al., Mediated by a Transferable Plasmid, New England Journal of Medicine, vol.337, issue.10, pp.677-680, 1997.
DOI : 10.1056/NEJM199709043371004

R. L. Lindsey, P. J. Fedorka-cray, J. G. Frye, and R. J. Meinersmann, Inc A/C Plasmids Are Prevalent in Multidrug-Resistant Salmonella enterica Isolates, Applied and Environmental Microbiology, vol.75, issue.7, pp.1908-1915, 2009.
DOI : 10.1128/AEM.02228-08

W. F. Fricke, T. J. Welch, P. F. Mcdermott, M. K. Mammel, J. E. Leclerc et al., Comparative Genomics of the IncA/C Multidrug Resistance Plasmid Family, Journal of Bacteriology, vol.191, issue.15, pp.4750-4757, 2009.
DOI : 10.1128/JB.00189-09

J. C. Pan, R. Ye, H. Q. Wang, H. Q. Xiang, W. Zhang et al., Vibrio cholerae O139 Multiple-Drug Resistance Mediated by Yersinia pestis pIP1202-Like Conjugative Plasmids, Antimicrobial Agents and Chemotherapy, vol.52, issue.11, pp.3829-3836, 2008.
DOI : 10.1128/AAC.00375-08

URL : http://aac.asm.org/content/52/11/3829.full.pdf

T. J. Welch, W. F. Fricke, P. F. Mcdermott, D. G. White, M. L. Rosso et al., Multiple Antimicrobial Resistance in Plague: An Emerging Public Health Risk, PLoS ONE, vol.189, issue.1, p.309, 2007.
DOI : 10.1371/journal.pone.0000309.s001

A. Carattoli, L. Villa, L. Poirel, R. A. Bonnin, and P. Nordmann, ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.56, issue.2, pp.783-786, 2011.
DOI : 10.1128/AAC.05116-11

T. J. Johnson, K. S. Lang, /. Inca, and . Plasmids, IncA/C plasmids, Mobile Genetic Elements, vol.176, issue.1, pp.55-58, 2012.
DOI : 10.1128/AEM.02788-10

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3383451/pdf

R. Bruckner and F. Titgemeyer, Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization, FEMS Microbiology Letters, vol.209, issue.2, pp.141-148, 2002.
DOI : 10.1016/S0378-1097(02)00559-1

A. Kolb, S. Busby, H. Buc, S. Garges, and S. Adhya, Transcriptional Regulation by cAMP and Its Receptor Protein, Annual Review of Biochemistry, vol.62, issue.1, pp.749-795, 1993.
DOI : 10.1146/annurev.bi.62.070193.003533

J. Stulke and W. Hillen, Carbon catabolite repression in bacteria, Current Opinion in Microbiology, vol.2, issue.2, pp.195-201, 1999.
DOI : 10.1016/S1369-5274(99)80034-4

A. D. Cameron and R. J. Redfield, Non-canonical CRP sites control competence regulons in Escherichia coli and many other ??-proteobacteria, Nucleic Acids Research, vol.II, issue.20, pp.6001-6014, 2006.
DOI : 10.1101/gr.849004

B. De-crombrugghe, S. Busby, and H. Buc, Cyclic AMP receptor protein: role in transcription activation, Science, vol.224, issue.4651, pp.831-838, 1984.
DOI : 10.1126/science.6372090

F. Rojo, : optimizing metabolic versatility and interactions with the environment, FEMS Microbiology Reviews, vol.180, issue.5, pp.658-684, 2010.
DOI : 10.1128/JB.00817-08

B. Gorke and J. Stulke, Carbon catabolite repression in bacteria: many ways to make the most out of nutrients, Nature Reviews Microbiology, vol.280, issue.8, pp.613-624, 2008.
DOI : 10.1111/j.1365-2958.2007.06071.x

G. Gosset, Z. Zhang, S. Nayyar, W. A. Cuevas, M. H. Saier et al., Transcriptome Analysis of Crp-Dependent Catabolite Control of Gene Expression in Escherichia coli, Journal of Bacteriology, vol.186, issue.11, pp.3516-3524, 2004.
DOI : 10.1128/JB.186.11.3516-3524.2004

W. Liang, A. Pascual-montano, A. J. Silva, and J. A. Benitez, The cyclic AMP receptor protein modulates quorum sensing, motility and multiple genes that affect intestinal colonization in Vibrio cholerae, Microbiology, vol.153, issue.9, pp.2964-2975, 2007.
DOI : 10.1099/mic.0.2007/006668-0

D. Zheng, C. Constantinidou, J. L. Hobman, and S. D. Minchin, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling, Nucleic Acids Research, vol.32, issue.19, pp.5874-5893, 2004.
DOI : 10.1093/nar/gkh908

S. Kumar and S. Srivastava, Cyclic AMP and its receptor protein are required for expression of transfer genes of conjugative plasmid F in Escherichia coli, MGG Molecular & General Genetics, vol.112, issue.1, pp.27-34, 1983.
DOI : 10.1007/BF00330320

K. Skorupski and R. K. Taylor, Cyclic AMP and its receptor protein negatively regulate the coordinate expression of cholera toxin and toxin-coregulated pilus in Vibrio cholerae, Proc. Natl. Acad. Sci, pp.265-270, 1997.
DOI : 10.1126/science.8073279

A. J. Silva and J. A. Benitez, Transcriptional Regulation of Vibrio cholerae Hemagglutinin/Protease by the Cyclic AMP Receptor Protein and RpoS, Journal of Bacteriology, vol.186, issue.19, pp.6374-6382, 2004.
DOI : 10.1128/JB.186.19.6374-6382.2004

S. Sinha, A. D. Cameron, and R. J. Redfield, Sxy Induces a CRP-S Regulon in Escherichia coli, Journal of Bacteriology, vol.191, issue.16, pp.5180-5195, 2009.
DOI : 10.1128/JB.00476-09

S. Sinha, J. C. Mell, and R. J. Redfield, Seventeen Sxy-Dependent Cyclic AMP Receptor Protein Site-Regulated Genes Are Needed for Natural Transformation in Haemophilus influenzae, Journal of Bacteriology, vol.194, issue.19
DOI : 10.1128/JB.00671-12

M. Blokesch, Chitin colonization, chitin degradation and chitin-induced natural competence of Vibrio cholerae are subject to catabolite repression, Environmental Microbiology, vol.76, issue.8, pp.1898-1912, 2012.
DOI : 10.1128/AEM.00008-10

J. L. Botsford and J. G. Harman, Cyclic AMP in prokaryotes, Microbiol. Rev, vol.56, pp.100-122, 1992.

Y. C. Liu, W. K. Huang, T. S. Huang, and C. M. Kunin, Detection of Antimicrobial Activity in Urine for Epidemiologic Studies of Antibiotic Use, Journal of Clinical Epidemiology, vol.52, issue.6, pp.539-545, 1999.
DOI : 10.1016/S0895-4356(99)00027-X

B. E. Haggard and L. D. Bartsch, Net Changes in Antibiotic Concentrations Downstream from an Effluent Discharge, Journal of Environment Quality, vol.38, issue.1, pp.343-352, 2009.
DOI : 10.2134/jeq2007.0540

J. Fick, H. Soderstrom, R. H. Lindberg, C. Phan, M. Tysklind et al., CONTAMINATION OF SURFACE, GROUND, AND DRINKING WATER FROM PHARMACEUTICAL PRODUCTION, Environmental Toxicology and Chemistry, vol.28, issue.12, pp.2522-2527, 2009.
DOI : 10.1897/09-073.S1

K. Kummerer, Antibiotics in the aquatic environment ??? A review ??? Part I, Chemosphere, vol.75, issue.4, pp.417-434, 2009.
DOI : 10.1016/j.chemosphere.2008.11.086

K. Kummerer, Antibiotics in the aquatic environment ??? A review ??? Part II, Chemosphere, vol.75, issue.4, pp.435-441, 2009.
DOI : 10.1016/j.chemosphere.2008.12.006

D. Hughes and D. I. Andersson, Selection of resistance at lethal and non-lethal antibiotic concentrations, Current Opinion in Microbiology, vol.15, issue.5, pp.555-560, 2012.
DOI : 10.1016/j.mib.2012.07.005

E. B. Goh, G. Yim, W. Tsui, J. Mcclure, M. G. Surette et al., Transcriptional modulation of bacterial gene expression by subinhibitory concentrations of antibiotics, Proc. Natl. Acad. Sci. USA 2002, pp.17025-17030
DOI : 10.7164/antibiotics.53.979

S. P. Bernier and M. G. Surette, Concentration-dependent activity of antibiotics in natural environments. Front, 2013.

J. Davies, G. B. Spiegelman, and G. Yim, The world of subinhibitory antibiotic concentrations, Current Opinion in Microbiology, vol.9, issue.5, pp.445-453, 2006.
DOI : 10.1016/j.mib.2006.08.006

G. Yim, F. De-la-cruz, G. B. Spiegelman, and J. Davies, Transcription Modulation of Salmonella enterica Serovar Typhimurium Promoters by Sub-MIC Levels of Rifampin, Journal of Bacteriology, vol.188, issue.22, pp.7988-7991, 2006.
DOI : 10.1128/JB.00791-06

G. Yim, J. Mcclure, M. G. Surette, and J. Davies, Modulation of Salmonella gene expression by subinhibitory concentrations of quinolones, The Journal of Antibiotics, vol.8, issue.1, pp.73-78, 2011.
DOI : 10.1371/journal.pbio.0060280

W. H. Tsui, G. Yim, H. H. Wang, J. E. Mcclure, M. G. Surette et al., Dual Effects of MLS Antibiotics, Chemistry & Biology, vol.11, issue.9, pp.1307-1316, 2004.
DOI : 10.1016/j.chembiol.2004.07.010

J. F. Linares, I. Gustafsson, F. Baquero, and J. L. Martinez, Antibiotics as intermicrobial signaling agents instead of weapons, Proc. Natl. Acad. Sci, pp.19484-19489, 2006.
DOI : 10.1128/JB.00791-06

J. B. Kaplan, Antibiotic-induced biofilm formation, The International Journal of Artificial Organs, vol.34, issue.9, pp.737-751, 2011.
DOI : 10.5301/ijao.5000027

J. B. Kaplan and S. Jabbouri, Extracellular DNA-dependent biofilm formation by Staphylococcus epidermidis RP62A in response to subminimal inhibitory concentrations of antibiotics, Research in Microbiology, vol.162, issue.5, pp.535-541, 2011.
DOI : 10.1016/j.resmic.2011.03.008

R. N. Haddadin, S. Saleh, I. S. Al-adham, T. E. Buultjens, and P. J. Collier, biofilms, Journal of Applied Microbiology, vol.57, issue.Pt 5, pp.1281-1291, 2010.
DOI : 10.1080/1120009X.1993.11739246

L. R. Hoffman, D. A. Argenio, M. J. Maccoss, Z. Zhang, R. A. Jones et al., Aminoglycoside antibiotics induce bacterial biofilm formation, Nature, vol.171, issue.7054, pp.1171-1175, 2005.
DOI : 10.1128/jb.171.12.6649-6655.1989

S. A. Rogers, R. W. Huigens, J. Cavanagh, and C. Melander, Synergistic Effects between Conventional Antibiotics and 2-Aminoimidazole-Derived Antibiofilm Agents, Antimicrobial Agents and Chemotherapy, vol.54, issue.5, pp.2112-2118, 2010.
DOI : 10.1128/AAC.01418-09

URL : http://aac.asm.org/content/54/5/2112.full.pdf

S. P. Bernier, D. Lebeaux, A. S. Defrancesco, A. Valomon, G. Soubigou et al., Starvation, Together with the SOS Response, Mediates High Biofilm-Specific Tolerance to the Fluoroquinolone Ofloxacin, PLoS Genetics, vol.73, issue.1, p.1003144
DOI : 10.1371/journal.pgen.1003144.s008

URL : https://hal.archives-ouvertes.fr/pasteur-01385427

R. S. Mueller, B. D. Dill, C. Pan, C. P. Belnap, B. C. Thomas et al., Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community, Environmental Microbiology, vol.71, issue.8, pp.2279-2292, 2011.
DOI : 10.1128/AEM.71.1.227-239.2005

H. Gotoh, N. Kasaraneni, N. Devineni, S. F. Dallo, and T. Weitao, SOS involvement in stress-inducible biofilm formation, Biofouling, vol.48, issue.5, pp.603-611, 2010.
DOI : 10.1038/35101627

S. Molin and T. Tolker-nielsen, Gene transfer occurs with enhanced efficiency in biofilms and induces enhanced stabilisation of the biofilm structure, Current Opinion in Biotechnology, vol.14, issue.3, pp.255-261, 2003.
DOI : 10.1016/S0958-1669(03)00036-3

C. Hennequin, C. Aumeran, F. Robin, O. Traore, and C. Forestier, Antibiotic resistance and plasmid transfer capacity in biofilm formed with a CTX-M-15-producing Klebsiella pneumoniae isolate, Journal of Antimicrobial Chemotherapy, vol.67, issue.1, pp.2123-2130, 2012.
DOI : 10.1093/jac/dkr405

URL : https://hal.archives-ouvertes.fr/hal-00815869

P. Ysern, B. Clerch, M. Castano, I. Gibert, J. Barbe et al., by fluoroquinolones, Mutagenesis, vol.5, issue.1, pp.63-66, 1990.
DOI : 10.1093/mutage/5.1.63

C. Miller, L. E. Thomsen, C. Gaggero, R. Mosseri, H. Ingmer et al., SOS Response Induction by ??-Lactams and Bacterial Defense Against Antibiotic Lethality, Science, vol.305, issue.5690, pp.1629-1631, 2004.
DOI : 10.1126/science.1101630

T. Perez-capilla, M. R. Baquero, J. M. Gomez-gomez, A. Ionel, S. Martin et al., SOS-Independent Induction of dinB Transcription by ??-Lactam-Mediated Inhibition of Cell Wall Synthesis in Escherichia coli, Journal of Bacteriology, vol.187, issue.4, pp.1515-1518, 2005.
DOI : 10.1128/JB.187.4.1515-1518.2005

K. J. Shaw, N. Miller, X. Liu, D. Lerner, J. Wan et al., Comparison of the Changes in Global Gene Expression of <i>Escherichia coli</i> Induced by Four Bactericidal Agents, Journal of Molecular Microbiology and Biotechnology, vol.5, issue.2, pp.105-122, 2003.
DOI : 10.1159/000069981

L. R. Mesak and J. Davies, Phenotypic changes in ciprofloxacin-resistant Staphylococcus aureus, Research in Microbiology, vol.160, issue.10, pp.785-791, 2009.
DOI : 10.1016/j.resmic.2009.09.013

L. R. Mesak, V. Miao, and J. Davies, Effects of Subinhibitory Concentrations of Antibiotics on SOS and DNA Repair Gene Expression in Staphylococcus aureus, Antimicrobial Agents and Chemotherapy, vol.52, issue.9, pp.3394-3397, 2008.
DOI : 10.1128/AAC.01599-07

E. Lopez and J. Blazquez, Effect of Subinhibitory Concentrations of Antibiotics on Intrachromosomal Homologous Recombination in Escherichia coli, Antimicrobial Agents and Chemotherapy, vol.53, issue.8, pp.3411-3415, 2009.
DOI : 10.1128/AAC.00358-09

R. T. Cirz and F. Romesberg, Induction and Inhibition of Ciprofloxacin Resistance-Conferring Mutations in Hypermutator Bacteria, Antimicrobial Agents and Chemotherapy, vol.50, issue.1, pp.220-225, 2006.
DOI : 10.1128/AAC.50.1.220-225.2006

J. P. Didier, R. Villet, E. Huggler, D. P. Lew, D. C. Hooper et al., ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.55, issue.5, pp.1946-1952, 2011.
DOI : 10.1128/AAC.01407-10

S. E. Cohen and G. C. Walker, The Transcription Elongation Factor NusA Is Required for Stress-Induced Mutagenesis in Escherichia coli, Current Biology, vol.20, issue.1, pp.80-85, 2010.
DOI : 10.1016/j.cub.2009.11.039

Z. Baharoglu, E. Krin, and D. Mazel, RpoS Plays a Central Role in the SOS Induction by Sub-Lethal Aminoglycoside Concentrations in Vibrio cholerae, PLoS Genetics, vol.336, issue.4, p.1003421
DOI : 10.1371/journal.pgen.1003421.t002

URL : https://hal.archives-ouvertes.fr/pasteur-01691109

D. Hocquet, C. Llanes, M. Thouverez, H. D. Kulasekara, X. Bertrand et al., Evidence for Induction of Integron-Based Antibiotic Resistance by the SOS Response in a Clinical Setting, PLoS Pathogens, vol.47, issue.6, p.1002778, 2012.
DOI : 10.1371/journal.ppat.1002778.s008

URL : https://hal.archives-ouvertes.fr/hal-00802793

I. Erill, S. Campoy, and J. Barbe, Aeons of distress: an evolutionary perspective on the bacterial SOS response, FEMS Microbiology Reviews, vol.31, issue.6, pp.31-637, 2007.
DOI : 10.1016/S0723-2020(99)80063-0

A. Gutierrez, L. Laureti, S. Crussard, H. Abida, A. Rodrí-guez-rojas et al., ??-lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity, Nature Communications, vol.22, 1610.
DOI : 10.1111/j.1365-2958.1996.tb02664.x

E. Denamur, O. Tenaillon, C. Deschamps, D. Skurnik, E. Ronco et al., Intermediate Mutation Frequencies Favor Evolution of Multidrug Resistance in Escherichia coli, Genetics, vol.171, issue.2, pp.825-827, 2005.
DOI : 10.1534/genetics.105.045526

S. Da-re, F. Garnier, E. Guerin, S. Campoy, F. Denis et al., The SOS response promotes qnrB quinolone-resistance determinant expression, EMBO reports, vol.112, issue.8, pp.929-933, 2009.
DOI : 10.1128/AAC.00339-07

URL : https://hal.archives-ouvertes.fr/inserm-00533078

C. Ubeda, E. Maiques, E. Knecht, I. Lasa, R. P. Novick et al., Antibiotic-induced SOS response promotes horizontal dissemination of pathogenicity island-encoded virulence factors in staphylococci, Molecular Microbiology, vol.181, issue.3, pp.836-844, 2005.
DOI : 10.1086/315239

E. Maiques, C. Ubeda, S. Campoy, N. Salvador, I. Lasa et al., ??-Lactam Antibiotics Induce the SOS Response and Horizontal Transfer of Virulence Factors in Staphylococcus aureus, Journal of Bacteriology, vol.188, issue.7, pp.2726-2729, 2006.
DOI : 10.1128/JB.188.7.2726-2729.2006

E. Gullberg, S. Cao, O. G. Berg, C. Ilback, L. Sandegren et al., Andersson, D.I. Selection of resistant bacteria at very low antibiotic concentrations, PLoS Pathog, 2011.

I. Gustafsson, M. Sjolund, E. Torell, M. Johannesson, L. Engstrand et al., Bacteria with increased mutation frequency and antibioticresistance are enriched in the commensal flora of patients with high antibiotic usage, Journal of Antimicrobial Chemotherapy, vol.52, issue.4, pp.645-650, 2003.
DOI : 10.1093/jac/dkg427

A. Liu, A. Fong, E. Becket, J. Yuan, C. Tamae et al., ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.55, issue.3, pp.1204-1210, 2011.
DOI : 10.1128/AAC.01182-10

URL : https://hal.archives-ouvertes.fr/hal-01105217

T. Dorr, K. Lewis, and M. Vulic, SOS Response Induces Persistence to Fluoroquinolones in Escherichia coli, PLoS Genetics, vol.178, issue.12, 2009.
DOI : 10.1371/journal.pgen.1000760.t001

T. Dorr, M. Vulic, and K. Lewis, Ciprofloxacin Causes Persister Formation by Inducing the TisB toxin in Escherichia coli, PLoS Biology, vol.183, issue.2, p.1000317, 2010.
DOI : 10.1371/journal.pbio.1000317.s001

K. Lewis, Persister Cells, Annual Review of Microbiology, vol.64, issue.1, pp.357-372, 2010.
DOI : 10.1146/annurev.micro.112408.134306

A. M. Guerout, N. Iqbal, N. Mine, M. Ducos-galand, L. Van-melderen et al., Characterization of the phd-doc and ccd Toxin-Antitoxin Cassettes from Vibrio Superintegrons, Journal of Bacteriology, vol.195, issue.10, pp.2270-2283, 2013.
DOI : 10.1128/JB.01389-12

URL : https://hal.archives-ouvertes.fr/pasteur-01692120

M. A. Kohanski, M. A. Depristo, and J. J. Collins, Sublethal Antibiotic Treatment Leads to Multidrug Resistance via Radical-Induced Mutagenesis, Molecular Cell, vol.37, issue.3, pp.311-320, 2010.
DOI : 10.1016/j.molcel.2010.01.003

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

T. J. Mcbride, B. D. Preston, and L. A. Loeb, Mutagenic spectrum resulting from DNA damage by oxygen radicals, Biochemistry, vol.30, issue.1, pp.207-213, 1991.
DOI : 10.1021/bi00215a030

S. Fraud and K. Poole, ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.55, issue.3, pp.1068-1074, 2011.
DOI : 10.1128/AAC.01495-10

V. Aiassa, A. I. Barnes, and A. M. Smania, Sublethal ciprofloxacin treatment leads to resistance via antioxidant systems in Proteus mirabilis, FEMS Microbiology Letters, vol.161, issue.1, pp.25-32, 2012.
DOI : 10.1128/AAC.46.8.2582-2587.2002

D. J. Dwyer, M. A. Kohanski, and J. J. Collins, Role of reactive oxygen species in antibiotic action and resistance, Current Opinion in Microbiology, vol.12, issue.5, pp.482-489, 2009.
DOI : 10.1016/j.mib.2009.06.018

D. J. Dwyer, M. A. Kohanski, B. Hayete, and J. J. Collins, Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli, Molecular Systems Biology, vol.273, issue.1, p.91, 2007.
DOI : 10.1016/0968-0004(96)20008-8

W. Y. Wholey and U. Jakob, Hsp33 confers bleach resistance by protecting elongation factor Tu against oxidative degradation in Vibrio cholerae, Molecular Microbiology, vol.1050, issue.5, pp.981-991, 2012.
DOI : 10.1016/0167-4781(90)90188-8

D. Nguyen, A. Joshi-datar, F. Lepine, E. Bauerle, O. Olakanmi et al., Active Starvation Responses Mediate Antibiotic Tolerance in Biofilms and Nutrient-Limited Bacteria, Science, vol.148, issue.1, pp.982-986, 2011.
DOI : 10.1016/0378-1119(94)90237-2

URL : https://hal.archives-ouvertes.fr/pasteur-00722468

K. Shatalin, E. Shatalina, A. Mironov, and E. Nudler, H2S: A Universal Defense Against Antibiotics in Bacteria, Science, vol.284, issue.5, pp.986-990, 2011.
DOI : 10.1074/jbc.M805459200

P. Belenky, J. J. Collins, and . Microbiology, Antioxidant Strategies to Tolerate Antibiotics, Science, vol.57, issue.10, pp.915-916, 2011.
DOI : 10.1016/j.addr.2005.04.002

K. J. Allen and M. W. Griffiths, Impact of hydroxyl- and superoxide anion-based oxidative stress on logarithmic and stationary phase Escherichia coli O157:H7 stress and virulence gene expression, Food Microbiology, vol.29, issue.1, pp.141-147
DOI : 10.1016/j.fm.2011.09.014

H. Merrikh, A. E. Ferrazzoli, A. Bougdour, A. Olivier-mason, and S. T. Lovett, A DNA damage response in Escherichia coli involving the alternative sigma factor, RpoS, Proc. Natl. Acad. Sci. USA 2009, pp.611-616
DOI : 10.1111/j.1365-2958.2006.05093.x

H. Merrikh, A. E. Ferrazzoli, and S. T. Lovett, Growth Phase and (p)ppGpp Control of IraD, a Regulator of RpoS Stability, in Escherichia coli, Journal of Bacteriology, vol.191, issue.24, pp.7436-7446, 2009.
DOI : 10.1128/JB.00412-09

A. Battesti, Y. M. Tsegaye, D. G. Packer, N. Majdalani, and S. Gottesman, H-NS Regulation of IraD and IraM Antiadaptors for Control of RpoS Degradation, Journal of Bacteriology, vol.194, issue.10, pp.2470-2478, 2012.
DOI : 10.1128/JB.00132-12

URL : https://hal.archives-ouvertes.fr/hal-01556019

R. Hengge-aronis, Signal Transduction and Regulatory Mechanisms Involved in Control of the ??S (RpoS) Subunit of RNA Polymerase, Microbiology and Molecular Biology Reviews, vol.66, issue.3, pp.373-395, 2002.
DOI : 10.1128/MMBR.66.3.373-395.2002

E. Barth, K. V. Gora, K. M. Gebendorfer, F. Settele, U. Jakob et al., Interplay of cellular cAMP levels, {sigma}S activity and oxidative stress resistance in Escherichia coli, pp.1680-1689, 2009.

M. J. Daly, A new perspective on radiation resistance based on Deinococcus radiodurans, Nature Reviews Microbiology, vol.26, issue.3, pp.237-245, 2009.
DOI : 10.1099/00221287-147-7-1709

E. S. Henle and S. Linn, Formation, Prevention, and Repair of DNA Damage by Iron/Hydrogen Peroxide, Journal of Biological Chemistry, vol.263, issue.6 suppl., pp.19095-19098, 1997.
DOI : 10.1074/jbc.271.44.27536

K. Keyer and J. A. Imlay, Superoxide accelerates DNA damage by elevating free-iron levels, Proc. Natl. Acad. Sci, pp.13635-13640, 1996.
DOI : 10.1016/0003-9861(92)90513-V

URL : http://www.pnas.org/content/93/24/13635.full.pdf

S. Hansen, K. Lewis, and M. Vulic, Role of Global Regulators and Nucleotide Metabolism in Antibiotic Tolerance in Escherichia coli, Antimicrobial Agents and Chemotherapy, vol.52, issue.8, pp.2718-2726, 2008.
DOI : 10.1128/AAC.00144-08

R. Miyazaki, M. Minoia, N. Pradervand, S. Sulser, F. Reinhard et al., Cellular Variability of RpoS Expression Underlies Subpopulation Activation of an Integrative and Conjugative Element, PLoS Genetics, vol.55, issue.7, 2012.
DOI : 10.1371/journal.pgen.1002818.s012

A. Santos-zavaleta, S. Gama-castro, and E. Perez-rueda, A comparative genome analysis of the RpoS sigmulon shows a high diversity of responses and origins, Microbiology, vol.157, issue.5, pp.1393-1401, 2011.
DOI : 10.1099/mic.0.042937-0

S. M. Chiang and H. Schellhorn, Evolution of the RpoS Regulon: Origin of RpoS and the Conservation of RpoS-Dependent Regulation in Bacteria, Journal of Molecular Evolution, vol.97, issue.Pt 4, pp.557-571, 2010.
DOI : 10.1016/S0168-6445(98)00011-4

T. King, S. Seeto, and T. Ferenci, Genotype-by-Environment Interactions Influencing the Emergence of rpoS Mutations in Escherichia coli Populations, Genetics, vol.172, issue.4, pp.2071-2079, 2006.
DOI : 10.1534/genetics.105.053892

M. M. Zambrano, D. A. Siegele, M. Almiron, A. Tormo, and R. Kolter, Microbial competition: Escherichia coli mutants that take over stationary phase cultures, Science, vol.259, issue.5102, pp.1757-1760, 1993.
DOI : 10.1126/science.7681219

Y. Zhang, C. Shi, J. Yu, J. Ren, and D. Sun, RpoS Regulates a Novel Type of Plasmid DNA Transfer in Escherichia coli, PLoS ONE, vol.96, issue.3, 2012.
DOI : 10.1371/journal.pone.0033514.s006

A. Joelsson, B. Kan, and J. Zhu, Quorum Sensing Enhances the Stress Response in Vibrio cholerae, Applied and Environmental Microbiology, vol.73, issue.11, pp.3742-3746, 2007.
DOI : 10.1128/AEM.02804-06

K. R. Allison, M. P. Brynildsen, and J. J. Collins, Metabolite-enabled eradication of bacterial persisters by aminoglycosides, Nature, vol.31, issue.7346, pp.216-220, 2011.
DOI : 10.1093/nar/gng015

M. A. Farha and E. Brown, Discovery of antibiotic adjuvants, Nature Biotechnology, vol.31, issue.2, pp.31-120, 2013.
DOI : 10.1038/nrmicro2474

M. P. Brynildsen, J. A. Winkler, C. S. Spina, I. C. Macdonald, and J. J. Collins, Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production, Nature Biotechnology, vol.178, issue.2, pp.31-160, 2013.
DOI : 10.1038/nprot.2007.99

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3568245/pdf

T. K. Lu and J. J. Collins, Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy, Proc. Natl. Acad. Sci, pp.4629-4634, 2009.
DOI : 10.1371/journal.pbio.0060010