O. Tenaillon, D. Skurnik, B. Picard, and E. Denamur, The population genetics of commensal Escherichia coli, Nature Reviews Microbiology, vol.75, issue.3, pp.207-217, 2010.
DOI : 10.1038/nrmicro2298

T. Russo and J. Johnson, Medical and economic impact of extraintestinal infections due to Escherichia coli: focus on an increasingly important endemic problem, Microbes and Infection, vol.5, issue.5, pp.449-456, 2003.
DOI : 10.1016/S1286-4579(03)00049-2

D. Gordon, O. Clermont, H. Tolley, and E. Denamur, Assigning Escherichia coli strains to phylogenetic groups: multi-locus sequence typing versus the PCR triplex method, Environmental Microbiology, vol.60, issue.10, pp.2484-2496, 2008.
DOI : 10.1111/j.1462-2920.2008.01669.x

T. Wirth, D. Falush, R. Lan, F. Colles, P. Mensa et al., Sex and virulence in Escherichia coli:a n evolutionary perspective, Mol Microbiol, issue.5, pp.601136-1151, 2006.

P. Desjardins, B. Picard, B. Kaltenböck, J. Elion, and E. Denamur, Sex in Escherichia coli does not disrupt the clonal structure of the population: evidence from random amplified polymorphic DNA and restriction-fragment-length polymorphism, Journal of Molecular Evolution, vol.18, issue.4, pp.440-448, 1995.
DOI : 10.1007/BF00160315

B. Picard, J. Garcia, S. Gouriou, P. Duriez, N. Brahimi et al., The link between phylogeny and virulence in Escherichia coli extraintestinal infection, Infect Immun, vol.67, issue.2, pp.546-553, 1999.

P. Duriez, O. Clermont, S. Bonacorsi, E. Bingen, A. Chaventre et al., Commensal Escherichia coli isolates are phylogenetically distributed among geographically distinct human populations, Microbiology, vol.147, issue.6, pp.1671-1676, 2001.
DOI : 10.1099/00221287-147-6-1671

W. Stamm and S. Norrby, Urinary Tract Infections: Disease Panorama and Challenges, The Journal of Infectious Diseases, vol.183, issue.s1, pp.1-4, 2001.
DOI : 10.1086/318850

C. Svanborg and G. Godaly, BACTERIAL VIRULENCE IN URINARY TRACT INFECTION, Infectious Disease Clinics of North America, vol.11, issue.3, pp.513-529, 1997.
DOI : 10.1016/S0891-5520(05)70371-8

L. Emody, M. Kerenyi, and G. Nagy, Virulence factors of uropathogenic Escherichia coli, International Journal of Antimicrobial Agents, vol.22, issue.2, pp.29-33, 2003.
DOI : 10.1016/S0924-8579(03)00236-X

V. Roos, G. Ulett, M. Schembri, and P. Klemm, The Asymptomatic Bacteriuria Escherichia coli Strain 83972 Outcompetes Uropathogenic E. coli Strains in Human Urine, Infection and Immunity, vol.74, issue.1, pp.615-624, 2006.
DOI : 10.1128/IAI.74.1.615-624.2006

A. Anfora, B. Haugen, P. Roesch, R. P. Welch, and R. , Roles of Serine Accumulation and Catabolism in the Colonization of the Murine Urinary Tract by Escherichia coli CFT073, Infection and Immunity, vol.75, issue.11, pp.755298-5304, 2007.
DOI : 10.1128/IAI.00652-07

S. Farr and T. Kogoma, Oxidative stress responses in Escherichia coli and Salmonella typhimurium, Microbiol Rev, vol.55, pp.561-585, 1991.

O. Carmel-harel and G. Storz, Responses to Oxidative Stress, Annual Review of Microbiology, vol.54, issue.1, pp.439-461, 2000.
DOI : 10.1146/annurev.micro.54.1.439

D. Jenkins, J. Schultz, and A. Matin, Starvation-induced cross protection against heat or H2O2 challenge in Escherichia coli., Journal of Bacteriology, vol.170, issue.9, pp.3910-3914, 1988.
DOI : 10.1128/jb.170.9.3910-3914.1988

P. Moreau, Diversion of the Metabolic Flux from Pyruvate Dehydrogenase to Pyruvate Oxidase Decreases Oxidative Stress during Glucose Metabolism in Nongrowing Escherichia coli Cells Incubated under Aerobic, Phosphate Starvation Conditions, Journal of Bacteriology, vol.186, issue.21, pp.7364-7368, 2004.
DOI : 10.1128/JB.186.21.7364-7368.2004

S. Saby, P. Leroy, and J. Block, Escherichia coli resistance to chlorine and glutathione synthesis in response to oxygenation and starvation, Appl Environ Microbiol, vol.65, issue.12, pp.5600-5603, 1999.

J. Snyder, B. Haugen, E. Buckles, C. Lockatell, D. Johnson et al., Transcriptome of Uropathogenic Escherichia coli during Urinary Tract Infection, Infection and Immunity, vol.72, issue.11, pp.726373-6381, 2004.
DOI : 10.1128/IAI.72.11.6373-6381.2004

D. Gordon and M. Riley, A theoretical and experimental analysis of bacterial growth in the bladder, Molecular Microbiology, vol.43, issue.4, pp.555-562, 1992.
DOI : 10.1016/S0140-6736(77)92111-0

R. Hull and S. Hull, Nutritional requirements for growth of uropathogenic Escherichia coli in human urine, Infect Immun, vol.65, issue.5, pp.1960-1961, 1997.

T. Russo, U. Carlino, A. Mong, and S. Jodush, Identification of genes in an extraintestinal isolate of Escherichia coli with increased expression after exposure to human urine, Infect Immun, vol.67, issue.10, pp.5306-5314, 1999.

H. Mobley, D. Green, A. Trifillis, D. Johnson, G. Chippendale et al., Pyelonephritogenic Escherichia coli and killing of cultured human renal proximal tubular epithelial cells: role of hemolysin in some strains, Infect Immun, issue.5, pp.581281-1289, 1990.

S. Chen, C. Hung, J. Xu, C. Reigstad, V. Magrini et al., Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: A comparative genomics approach, Proceedings of the National Academy of Sciences, vol.103, issue.15, pp.5977-5982, 2006.
DOI : 10.1073/pnas.0600938103

M. Touchon, C. Hoede, O. Tenaillon, V. Barbe, S. Baeriswyl et al., Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths, PLoS Genetics, vol.68, issue.1, p.1000344, 2009.
DOI : 10.1371/journal.pgen.1000344.s016

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

L. Gall, T. Clermont, O. Gouriou, S. Picard, B. Nassif et al., Extraintestinal Virulence Is a Coincidental By-Product of Commensalism in B2 Phylogenetic Group Escherichia coli Strains, Molecular Biology and Evolution, vol.24, issue.11, pp.242373-2384, 2007.
DOI : 10.1093/molbev/msm172

URL : https://hal.archives-ouvertes.fr/hal-00554748

P. Andersson, I. Engberg, G. Lidin-janson, K. Lincoln, R. Hull et al., Persistence of Escherichia coli bacteriuria is not determined by bacterial adherence, Infect Immun, vol.59, issue.9, pp.2915-2921, 1991.

J. Zdziarski, C. Svanborg, B. Wullt, J. Hacker, and U. Dobrindt, Molecular Basis of Commensalism in the Urinary Tract: Low Virulence or Virulence Attenuation?, Infection and Immunity, vol.76, issue.2, pp.695-703, 2008.
DOI : 10.1128/IAI.01215-07

F. Blattner, G. Plunkett, C. Bloch, N. Perna, V. Burland et al., The Complete Genome Sequence of Escherichia coli K-12, Science, vol.277, issue.5331, pp.2771453-1474, 1997.
DOI : 10.1126/science.277.5331.1453

O. Clermont, M. Lescat, O. Brien, C. Gordon, D. Tenaillon et al., Evidence for a human-specific Escherichia coli clone, Environmental Microbiology, vol.65, issue.4, pp.1000-1006, 2008.
DOI : 10.1111/j.1365-2958.2006.05172.x

H. Watanabe, A. Wada, Y. Inagaki, K. Itoh, and K. Tamura, Outbreaks of enterohaemorrhagic Escherichia colt O157:H7 infection by two different genotype strains in Japan, 1996, The Lancet, vol.348, issue.9030, pp.831-832, 1996.
DOI : 10.1016/S0140-6736(05)65257-9

J. Mccord and I. Fridovich, Superoxide dismutase. An enzymic function for erythrocuprein (hemocuprein), J Biol Chem, vol.244, issue.22, pp.6049-6055, 1969.

E. Bleuter, In Red Cell Metabolism: A Manual of Biochemical Methods: Grune and Startton, pp.67-69

E. Bleuter, In Red cell Metabolism: A Manual of Biochemical Methods: Grune and Startton, pp.105-106

C. Huang, L. Chang, M. Anderson, and A. Meister, Catalytic and regulatory properties of the heavy subunit of rat kidney gamma-glutamylcysteine synthetase, J Biol Chem, vol.268, issue.26, pp.19675-19680, 1993.

P. Krien, V. Margou, and M. Kermici, Electrochemical determination of femtomole amounts of free reduced and oxidized glutathione, Journal of Chromatography B: Biomedical Sciences and Applications, vol.576, issue.2, pp.255-261, 1992.
DOI : 10.1016/0378-4347(92)80199-Z

M. Bradford, A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding, Analytical Biochemistry, vol.72, issue.1-2, pp.248-254, 1976.
DOI : 10.1016/0003-2697(76)90527-3

B. Gonzalez-flecha and B. Demple, Homeostatic regulation of intracellular hydrogen peroxide concentration in aerobically growing Escherichia coli., Journal of Bacteriology, vol.179, issue.2, pp.382-388, 1997.
DOI : 10.1128/jb.179.2.382-388.1997

R. Raskoda, . Myersgs, . Mongodinef, . Frickewf, . Gajerp et al., The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates, pp.6881-6893

M. Cha, W. Kim, C. Lim, K. Kim, and I. Kim, Escherichia coli Periplasmic Thiol Peroxidase Acts as Lipid Hydroperoxide Peroxidase and the Principal Antioxidative Function during Anaerobic Growth, Journal of Biological Chemistry, vol.279, issue.10, pp.2798769-8778, 2004.
DOI : 10.1074/jbc.M312388200

T. Stamey and G. Mihara, Observations on the growth of urethral and vaginal bacteria in sterile urine, J Urol, vol.124, issue.4, pp.461-463, 1980.

C. Alteri and H. Mobley, Quantitative Profile of the Uropathogenic Escherichia coli Outer Membrane Proteome during Growth in Human Urine, Infection and Immunity, vol.75, issue.6, pp.2679-2688, 2007.
DOI : 10.1128/IAI.00076-06

L. Notley-mcrobb, T. King, and T. Ferenci, rpoS Mutations and Loss of General Stress Resistance in Escherichia coli Populations as a Consequence of Conflict between Competing Stress Responses, Journal of Bacteriology, vol.184, issue.3
DOI : 10.1128/JB.184.3.806-811.2002

M. Levert, O. Zamfir, O. Clermont, O. Bouvet, S. Lespinats et al., Molecular and Evolutionary Bases of Within-Patient Genotypic and Phenotypic Diversity in Escherichia coli Extraintestinal Infections, PLoS Pathogens, vol.54, issue.9, p.1001125, 2010.
DOI : 10.1371/journal.ppat.1001125.s008

URL : https://hal.archives-ouvertes.fr/pasteur-01414730

V. Roos and P. Klemm, Global Gene Expression Profiling of the Asymptomatic Bacteriuria Escherichia coli Strain 83972 in the Human Urinary Tract, Infection and Immunity, vol.74, issue.6, pp.3565-3575, 2006.
DOI : 10.1128/IAI.01959-05

S. Alexeeva, B. De-kort, G. Sawers, K. Hellingwerf, and M. De-mattos, Effects of Limited Aeration and of the ArcAB System on Intermediary Pyruvate Catabolism in Escherichia coli, Journal of Bacteriology, vol.182, issue.17, pp.4934-4940, 2000.
DOI : 10.1128/JB.182.17.4934-4940.2000

V. Sabarly, O. Bouvet, J. Glodt, O. Clermont, D. Skurnik et al., The decoupling between genetic structure and metabolic phenotypes in Escherichia coli leads to continuous phenotypic diversity, Journal of Evolutionary Biology, vol.37, issue.7, pp.241559-1571, 2011.
DOI : 10.1111/j.1420-9101.2011.02287.x

V. Hancock, R. Vejborg, and P. Klemm, Functional genomics of probiotic Escherichia coli Nissle 1917 and 83972, and UPEC strain CFT073: comparison of transcriptomes, growth and biofilm formation, Molecular Genetics and Genomics, vol.189, issue.6, pp.437-454, 2010.
DOI : 10.1007/s00438-010-0578-8

R. Vejborg, V. Hancock, M. Schembri, and P. Klemm, Comparative Genomics of Escherichia coli Strains Causing Urinary Tract Infections, Applied and Environmental Microbiology, vol.77, issue.10, pp.773268-3278, 2011.
DOI : 10.1128/AEM.02970-10

V. Roos, E. Nielsen, and P. Klemm, strains: adhesins, growth and competition, FEMS Microbiology Letters, vol.262, issue.1, pp.22-30, 2006.
DOI : 10.1111/j.1574-6968.2006.00355.x

V. Hancock, A. Seshasayee, D. Ussery, N. Luscombe, and P. Klemm, Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972, Molecular Genetics and Genomics, vol.76, issue.Suppl 1A, pp.523-534, 2008.
DOI : 10.1007/s00438-008-0330-9

J. Johnson, C. Clabots, and H. Rosen, Effect of Inactivation of the Global Oxidative Stress Regulator oxyR on the Colonization Ability of Escherichia coli O1:K1:H7 in a Mouse Model of Ascending Urinary Tract Infection, Infection and Immunity, vol.74, issue.1, pp.461-468, 2006.
DOI : 10.1128/IAI.74.1.461-468.2006

P. Klemm, V. Hancock, and M. Schembri, Mellowing Out: Adaptation to Commensalism by Escherichia coli Asymptomatic Bacteriuria Strain 83972, Infection and Immunity, vol.75, issue.8, pp.753688-3695, 2007.
DOI : 10.1128/IAI.01730-06

B. Boles and P. Singh, Endogenous oxidative stress produces diversity and adaptability in biofilm communities, Proceedings of the National Academy of Sciences, vol.105, issue.34, pp.12503-12508, 2008.
DOI : 10.1073/pnas.0801499105

I. Bjedov, O. Tenaillon, B. Gerard, V. Souza, E. Denamur et al., Stress-Induced Mutagenesis in Bacteria, Science, vol.300, issue.5624, pp.1404-1409, 2003.
DOI : 10.1126/science.1082240