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

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, 2012.
DOI : 10.1128/JB.05982-11

Z. Baharoglu and D. Mazel, Vibrio cholerae triggers SOS and mutagenesis in response to a wide range of antibiotics, a route towards multi-resistance, Antimicrob Agents Chemother, 2011.

G. Walker, The SOS Response of Escherichia coli. Escherichia coli and Salmonella, American Society of Microbiology, vol.1, pp.1400-1416, 1996.

J. Fick, H. Soderstrom, R. Lindberg, C. Phan, and M. Tysklind, 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

D. Hughes and D. 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

Y. Liu, W. Huang, T. Huang, and C. 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. Haggard and L. 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. Davies, G. 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

M. Kohanski, M. Depristo, and 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

N. Jena, DNA damage by reactive species: Mechanisms, mutation and repair, Journal of Biosciences, vol.439, issue.3, pp.503-517, 2012.
DOI : 10.1038/nature04561

M. 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

K. Keyer and J. Imlay, Superoxide accelerates DNA damage by elevating free-iron levels, Proceedings of the National Academy of Sciences, vol.295, issue.2, pp.13635-13640, 1996.
DOI : 10.1016/0003-9861(92)90513-V
URL : http://www.pnas.org/content/93/24/13635.full.pdf

D. Touati, Iron and Oxidative Stress in Bacteria, Archives of Biochemistry and Biophysics, vol.373, issue.1, pp.1-6, 2000.
DOI : 10.1006/abbi.1999.1518

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

A. Lu, X. Li, Y. Gu, P. Wright, and D. Chang, Repair of Oxidative DNA Damage: Mechanisms and Functions, Cell Biochemistry and Biophysics, vol.35, issue.2, pp.141-170, 2001.
DOI : 10.1385/CBB:35:2:141

J. Foti, B. Devadoss, J. Winkler, J. Collins, and G. Walker, Oxidation of the Guanine Nucleotide Pool Underlies Cell Death by Bactericidal Antibiotics, Science, vol.2, issue.7073, pp.315-319, 2012.
DOI : 10.1016/j.molcel.2005.01.012

S. Dukan, A. Farewell, M. Ballesteros, F. Taddei, and M. Radman, Protein oxidation in response to increased transcriptional or translational errors, Proceedings of the National Academy of Sciences, vol.440, issue.3, pp.5746-5749, 2000.
DOI : 10.1016/S0014-5793(98)01495-1

A. Mamun, A. Gautam, S. Humayun, and M. , Hypermutagenesis in mutA cells is mediated by mistranslational corruption of polymerase, and is accompanied by replication fork collapse, Molecular Microbiology, vol.148, issue.6, pp.1752-1763, 2006.
DOI : 10.1128/JB.183.5.1796-1800.2001

A. Krisko and M. Radman, Protein damage and death by radiation in Escherichia coli and Deinococcus radiodurans, Proceedings of the National Academy of Sciences, vol.193, issue.1, pp.14373-14377, 2010.
DOI : 10.1038/ismej.2007.116

K. Allen and M. 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, 2012.
DOI : 10.1016/j.fm.2011.09.014

H. Weber, T. Polen, J. Heuveling, V. Wendisch, and R. Hengge, Genome-Wide Analysis of the General Stress Response Network in Escherichia coli: ??S-Dependent Genes, Promoters, and Sigma Factor Selectivity, Journal of Bacteriology, vol.187, issue.5, pp.1591-1603, 2005.
DOI : 10.1128/JB.187.5.1591-1603.2005

H. Merrikh, A. Ferrazzoli, A. Bougdour, A. Olivier-mason, and S. Lovett, A DNA damage response in Escherichia coli involving the alternative sigma factor, RpoS, Proceedings of the National Academy of Sciences, vol.60, issue.1, pp.611-616, 2009.
DOI : 10.1111/j.1365-2958.2006.05093.x

H. Merrikh, A. Ferrazzoli, and S. 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. Tsegaye, D. Packer, N. Majdalani, and S. Gottesman, H-NS Regulation of IraD and IraM Anti-adaptors for Control of RpoS Degradation, 2012.

E. Barth, K. Gora, K. Gebendorfer, F. Settele, and U. Jakob, Interplay of cellular cAMP levels, ??S activity and oxidative stress resistance in Escherichia coli, Microbiology, vol.155, issue.5, pp.1680-1689, 2009.
DOI : 10.1099/mic.0.026021-0

E. 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. Park, M. Kang, S. Kim, H. Lee, and J. Lim, Isolation and Characterization of rpoS from a Pathogenic Bacterium, Vibrio vulnificus: Role of ??S in Survival of Exponential-Phase Cells under Oxidative Stress, Journal of Bacteriology, vol.186, issue.11, pp.3304-3312, 2004.
DOI : 10.1128/JB.186.11.3304-3312.2004

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

C. Mccullen, J. Benhammou, N. Majdalani, and S. Gottesman, Mechanism of Positive Regulation by DsrA and RprA Small Noncoding RNAs: Pairing Increases Translation and Protects rpoS mRNA from Degradation, Journal of Bacteriology, vol.192, issue.21, pp.5559-5571, 2010.
DOI : 10.1128/JB.00464-10

A. Bougdour, C. Cunning, P. Baptiste, T. Elliott, and S. Gottesman, Multiple pathways for regulation of ??S (RpoS) stability in Escherichia coli via the action of multiple anti-adaptors, Molecular Microbiology, vol.102, issue.2, pp.298-313, 2008.
DOI : 10.1128/jb.178.2.470-476.1996

A. Bougdour, S. Wickner, and S. Gottesman, Modulating RssB activity: IraP, a novel regulator of ??S stability in Escherichia coli, Genes & Development, vol.20, issue.7, pp.884-897, 2006.
DOI : 10.1101/gad.1400306

C. Webb, M. Moreno, M. Wilmes-riesenberg, R. Curtiss, and J. Foster, Effects of DksA and ClpP protease on sigma S production and virulence in Salmonella typhimurium, Molecular Microbiology, vol.24, issue.1, pp.112-123, 1999.
DOI : 10.1006/jmbi.1995.0178

J. Wilhelm, R. Vytasek, I. Ostadalova, and L. Vajner, Evaluation of different methods detecting intracellular generation of free radicals, Molecular and Cellular Biochemistry, vol.26, issue.1-2, pp.167-176, 2009.
DOI : 10.1177/27.1.220325

L. Henderson and J. Chappell, Dihydrorhodamine 123: a fluorescent probe for superoxide generation?, European Journal of Biochemistry, vol.272, issue.3, pp.973-980, 1993.
DOI : 10.1042/bj2720743

K. Au, S. Clark, J. Miller, and P. Modrich, Escherichia coli mutY gene encodes an adenine glycosylase active on G-A mispairs., Proceedings of the National Academy of Sciences, vol.86, issue.22, pp.8877-8881, 1989.
DOI : 10.1073/pnas.86.22.8877

M. Flores, N. Sanchez, and B. Michel, A fork-clearing role for UvrD, Molecular Microbiology, vol.73, issue.6, pp.1664-1675, 2005.
DOI : 10.1016/0300-9084(91)90196-8

K. Igarashi and K. Kashiwagi, Polyamine Modulon in Escherichia coli: Genes Involved in the Stimulation of Cell Growth by Polyamines, The Journal of Biochemistry, vol.139, issue.1, pp.11-16, 2006.
DOI : 10.1042/bj3250289

I. Jung and I. Kim, Transcription of ahpC, katG, and katE genes in Escherichia coli is regulated by polyamines: polyamine-deficient mutant sensitive to H2O2-induced oxidative damage, Biochemical and Biophysical Research Communications, vol.301, issue.4, pp.915-922, 2003.
DOI : 10.1016/S0006-291X(03)00064-0

A. Tkachenko, A. Akhova, M. Shumkov, and L. Nesterova, Polyamines reduce oxidative stress in Escherichia coli cells exposed to bactericidal antibiotics, Research in Microbiology, vol.163, issue.2, pp.83-91, 2012.
DOI : 10.1016/j.resmic.2011.10.009

S. Huang, Y. Chen, G. Kong, S. Chen, and J. Besemer, A novel genetic island of meningitic Escherichia coli K1 containing the ibeA invasion gene (GimA): functional annotation and carbon-source-regulated invasion of human brain microvascular endothelial cells, Functional & Integrative Genomics, vol.1, issue.5, pp.312-322, 2001.
DOI : 10.1007/s101420100039

M. Guillemet and P. Moreau, Fur-Dependent Detoxification of Organic Acids by rpoS Mutants during Prolonged Incubation under Aerobic, Phosphate Starvation Conditions, Journal of Bacteriology, vol.190, issue.16, pp.5567-5575, 2008.
DOI : 10.1128/JB.00577-08

A. Sikora, S. Beyhan, M. Bagdasarian, F. Yildiz, and M. Sandkvist, Cell Envelope Perturbation Induces Oxidative Stress and Changes in Iron Homeostasis in Vibrio cholerae, Journal of Bacteriology, vol.191, issue.17, pp.5398-5408, 2009.
DOI : 10.1128/JB.00092-09

W. Wholey and J. U. , 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

A. Mey, E. Wyckoff, V. Kanukurthy, C. Fisher, and S. Payne, Iron and Fur Regulation in Vibrio cholerae and the Role of Fur in Virulence, Infection and Immunity, vol.73, issue.12, pp.8167-8178, 2005.
DOI : 10.1128/IAI.73.12.8167-8178.2005

F. Mika, S. Busse, A. Possling, J. Berkholz, and N. Tschowri, Targeting of csgD by the small regulatory RNA RprA links stationary phase, biofilm formation and cell envelope stress in Escherichia coli, Molecular Microbiology, vol.31, issue.1, 2012.
DOI : 10.1093/nar/gkg595

M. Laubacher and S. Ades, The Rcs Phosphorelay Is a Cell Envelope Stress Response Activated by Peptidoglycan Stress and Contributes to Intrinsic Antibiotic Resistance, Journal of Bacteriology, vol.190, issue.6, pp.2065-2074, 2008.
DOI : 10.1128/JB.01740-07

L. Calhoun and Y. Kwon, The ferritin-like protein Dps protects Salmonella enterica serotype Enteritidis from the Fenton-mediated killing mechanism of bactericidal antibiotics, International Journal of Antimicrobial Agents, vol.37, issue.3, pp.261-265, 2011.
DOI : 10.1016/j.ijantimicag.2010.11.034

T. Dong and H. Schellhorn, Role of RpoS in Virulence of Pathogens, Infection and Immunity, vol.78, issue.3, pp.887-897, 2010.
DOI : 10.1128/IAI.00882-09

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

M. Levert, O. Zamfir, O. Clermont, O. Bouvet, and S. Lespinats, Molecular and evolutionary bases of within-patient genotypic and phenotypic diversity in Escherichia coli extraintestinal infections, PLoS Pathog, vol.6, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-01414730

D. Rozen, P. N. Arjan-de-visser, J. Lenski, R. Schneider, and D. , Death and cannibalism in a seasonal environment facilitate bacterial coexistence, Ecology Letters, vol.155, issue.1, pp.34-44, 2009.
DOI : 10.1111/j.1461-0248.2008.01257.x
URL : https://hal.archives-ouvertes.fr/hal-00342476

L. Ma, J. Chen, R. Liu, X. Zhang, and Y. Jiang, Mutation of rpoS gene decreased resistance to environmental stresses, synthesis of extracellular products and virulence of Vibrio anguillarum, FEMS Microbiol Ecol, vol.70, pp.130-136, 2009.

D. Merrell, A. Tischler, S. Lee, and A. Camilli, Vibrio cholerae Requires rpoS for Efficient Intestinal Colonization, Infection and Immunity, vol.68, issue.12, pp.6691-6696, 2000.
DOI : 10.1128/IAI.68.12.6691-6696.2000

A. Nielsen, N. Dolganov, G. Otto, M. Miller, and C. Wu, RpoS Controls the Vibrio cholerae Mucosal Escape Response, PLoS Pathogens, vol.18, issue.10, 2006.
DOI : 10.1371/journal.ppat.0020109.st006

S. 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

D. Mazel, B. Dychinco, V. 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. Rowe-magnus, A. Guerout, L. Biskri, P. Bouige, and D. Mazel, Comparative Analysis of Superintegrons: Engineering Extensive Genetic Diversity in the Vibrionaceae, Genome Research, vol.13, issue.3, pp.428-442, 2003.
DOI : 10.1101/gr.617103

D. Rowe-magnus, A. Guerout, P. Ploncard, B. Dychinco, and J. Davies, The evolutionary history of chromosomal super-integrons provides an ancestry for multiresistant integrons, Proceedings of the National Academy of Sciences, vol.96, issue.5, pp.652-657, 2001.
DOI : 10.1073/pnas.96.5.2192

D. Rowe-magnus, A. 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

T. Jove, S. Da-re, F. Denis, D. Mazel, and M. 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

G. Cambray, N. Sanchez-alberola, S. Campoy, E. Guerin, and S. Da-re, 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

E. Guerin, G. Cambray, N. Sanchez-alberola, S. Campoy, and I. Erill, 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

S. Partridge, G. Tsafnat, E. Coiera, and J. 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
URL : https://academic.oup.com/femsre/article-pdf/33/4/757/18141700/33-4-757.pdf

D. Hocquet, C. Llanes, M. Thouverez, H. Kulasekara, and X. Bertrand, Evidence for Induction of Integron-Based Antibiotic Resistance by the SOS Response in a Clinical Setting, PLoS Pathogens, vol.47, issue.6, 2012.
DOI : 10.1371/journal.ppat.1002778.s008
URL : https://hal.archives-ouvertes.fr/hal-00802793

H. Bennett and D. Clarke, The pbgPE operon in Photorhabdus luminescens Is Required for Pathogenicity and Symbiosis, Journal of Bacteriology, vol.187, issue.1, pp.77-84, 2005.
DOI : 10.1128/JB.187.1.77-84.2005

N. Ruiz and T. Silhavy, Constitutive Activation of the Escherichia coli Pho Regulon Upregulates rpoS Translation in an Hfq-Dependent Fashion, Journal of Bacteriology, vol.185, issue.20, pp.5984-5992, 2003.
DOI : 10.1128/JB.185.20.5984-5992.2003

C. Coynault, V. Robbe-saule, and F. Norel, ) regulon, Molecular Microbiology, vol.63, issue.1, pp.149-160, 1996.
DOI : 10.1016/0264-410X(92)90392-W

T. Tajiri, H. Maki, and M. Sekiguchi, Functional cooperation of MutT, MutM and MutY proteins in preventing mutations caused by spontaneous oxidation of guanine nucleotide in Escherichia coli, Mutation Research/DNA Repair, vol.336, issue.3, pp.257-267, 1995.
DOI : 10.1016/0921-8777(94)00062-B