B. Foxman, The epidemiology of urinary tract infection, Nature Reviews Urology, vol.8, issue.12, pp.653-660, 2010.
DOI : 10.3201/eid1307.070094

A. Hartstein, S. Garber, T. Ward, S. Jones, and V. Morthland, Abstract, Infection Control, vol.2, issue.05, pp.380-386, 1981.
DOI : 10.1016/0002-9343(81)90591-X

T. Hooton, Diagnosis, Prevention, and Treatment of Catheter-Associated Urinary Tract Infection in Adults: 2009 International Clinical Practice Guidelines from the Infectious Diseases Society of America, Clinical Infectious Diseases, vol.103, issue.Suppl 1, pp.625-663, 2010.
DOI : 10.1073/pnas.0605399103

S. Saint, Preventing Hospital-Acquired Urinary Tract Infection in the United States: A National Study, Clinical Infectious Diseases, vol.355, issue.26, pp.243-250, 2008.
DOI : 10.1056/NEJMoa061115

S. Saint, Clinical and economic consequences of nosocomial catheter-related bacteriuria, American Journal of Infection Control, vol.28, issue.1, pp.68-75, 2000.
DOI : 10.1016/S0196-6553(00)90015-4

R. Platt, B. Polk, B. Murdock, and B. Rosner, Mortality Associated with Nosocomial Urinary-Tract Infection, New England Journal of Medicine, vol.307, issue.11, pp.637-642, 1982.
DOI : 10.1056/NEJM198209093071101

C. Givens and R. Wenzel, Catheter-Associated Urinary Tract Infections in Surgical Patients, Survey of Anesthesiology, vol.25, issue.6, pp.646-648, 1980.
DOI : 10.1097/00132586-198112000-00064

P. Tambyah, V. Knasinski, and D. Maki, Conclusions:, Infection Control & Hospital Epidemiology, vol.124, issue.01, pp.27-31, 2002.
DOI : 10.1093/oxfordjournals.aje.a114487

R. Klevens, Estimating Health Care-Associated Infections and Deaths in U.S. Hospitals, 2002, Public Health Reports, vol.51, issue.53, pp.160-166, 2002.
DOI : 10.3201/eid0403.980320

P. Tambyah, V. Knasinski, and D. Maki, Conclusions:, Infection Control & Hospital Epidemiology, vol.124, issue.01, pp.27-31, 2002.
DOI : 10.1093/oxfordjournals.aje.a114487

L. Peychl and R. Zalud, Changes in the urinary bladder caused by short-term permanent catheter insertion], Cas Lek Cesk, vol.147, issue.6, pp.325-329, 2008.

K. Delnay, W. Stonehill, H. Goldman, A. Jukkola, and R. Dmochowski, BLADDER HISTOLOGICAL CHANGES ASSOCIATED WITH CHRONIC INDWELLING URINARY CATHETER, The Journal of Urology, vol.161, issue.4, pp.1106-1108, 1999.
DOI : 10.1016/S0022-5347(01)61601-X

P. Guiton, T. Hannan, B. Ford, M. Caparon, and S. Hultgren, Enterococcus faecalis Overcomes Foreign Body-Mediated Inflammation To Establish Urinary Tract Infections, Infection and Immunity, vol.81, issue.1, pp.329-339, 2013.
DOI : 10.1128/IAI.00856-12

URL : http://iai.asm.org/content/81/1/329.full.pdf

P. Guiton, C. Hung, L. Hancock, M. Caparon, and S. Hultgren, Enterococcal Biofilm Formation and Virulence in an Optimized Murine Model of Foreign Body-Associated Urinary Tract Infections, Infection and Immunity, vol.78, issue.10, pp.4166-4175, 2010.
DOI : 10.1128/IAI.00711-10

A. Flores-mireles, J. Walker, M. Caparon, and S. Hultgren, Urinary tract infections: epidemiology, mechanisms of infection and treatment options, Nature Reviews Microbiology, vol.78, issue.5, pp.269-284, 2015.
DOI : 10.1128/IAI.01235-09

D. Maki and P. Tambyah, Engineering out the Risk of Infection with Urinary Catheters, Emerging Infectious Diseases, vol.7, issue.2, pp.342-347, 2001.
DOI : 10.3201/eid0702.010240

A. Flores-mireles, J. Pinkner, M. Caparon, and S. Hultgren, EbpA vaccine antibodies block binding of Enterococcus faecalis to fibrinogen to prevent catheter-associated bladder infection in mice, Science Translational Medicine, vol.3, issue.9, pp.254-127, 2014.
DOI : 10.1128/IAI.00219-09

K. Rock, E. Latz, F. Ontiveros, and H. Kono, The Sterile Inflammatory Response, Annual Review of Immunology, vol.28, issue.1, pp.321-342, 2010.
DOI : 10.1146/annurev-immunol-030409-101311

V. Jojic, Identification of transcriptional regulators in the mouse immune system, Nature Immunology, vol.95, issue.6, pp.633-643, 2013.
DOI : 10.1016/j.devcel.2009.02.008

T. Heng and M. Painter, The Immunological Genome Project: networks of gene expression in immune cells, Nature Immunology, vol.171, issue.10, pp.1091-1094, 2008.
DOI : 10.1038/nri2252

G. Mora-bau, A. Platt, N. Van-rooijen, G. Randolph, M. Albert et al., Macrophages Subvert Adaptive Immunity to Urinary Tract Infection, PLOS Pathogens, vol.54, issue.7, p.1005044, 2015.
DOI : 10.1371/journal.ppat.1005044.s008

URL : https://hal.archives-ouvertes.fr/pasteur-01380952

K. Futamura, Novel full-spectral flow cytometry with multiple spectrally-adjacent fluorescent proteins and fluorochromes and visualization of in vivo cellular movement, Cytometry Part A, vol.3, issue.9, pp.830-842, 2015.
DOI : 10.1186/scrt108

C. Nathan, Points of control in inflammation, Nature, vol.17, issue.6917, pp.846-852, 2002.
DOI : 10.1073/pnas.94.20.10919

G. Randolph, K. Inaba, D. Robbiani, R. Steinman, and W. Muller, Differentiation of Phagocytic Monocytes into Lymph Node Dendritic Cells In Vivo, Immunity, vol.11, issue.6, pp.753-761, 1999.
DOI : 10.1016/S1074-7613(00)80149-1

C. Varol, Monocytes give rise to mucosal, but not splenic, conventional dendritic cells, The Journal of Experimental Medicine, vol.21, issue.1, pp.171-180, 2007.
DOI : 10.4049/jimmunol.178.4.2000

URL : http://europepmc.org/articles/pmc2118434?pdf=render

F. Ginhoux, Langerhans cells arise from monocytes in vivo, Nature Immunology, vol.174, issue.3, pp.265-273, 2006.
DOI : 10.1016/0022-1759(94)90012-4

M. Ingersoll, K. Kline, H. Nielsen, and S. Hultgren, infection of the urinary tract modulates host immunity, Cellular Microbiology, vol.9, issue.Suppl. 1, pp.2568-2578, 2008.
DOI : 10.1086/515643

D. Rosen, C. Hung, K. Kline, and S. Hultgren, Streptozocin-Induced Diabetic Mouse Model of Urinary Tract Infection, Infection and Immunity, vol.76, issue.9, pp.4290-4298, 2008.
DOI : 10.1128/IAI.00255-08

A. Kau, S. Martin, W. Lyon, E. Hayes, M. Caparon et al., Enterococcus faecalis Tropism for the Kidneys in the Urinary Tract of C57BL/6J Mice, Infection and Immunity, vol.73, issue.4, pp.2461-2468, 2005.
DOI : 10.1128/IAI.73.4.2461-2468.2005

A. Barber, J. Norton, A. Spivak, and M. Mulvey, Urinary Tract Infections: Current and Emerging Management Strategies, Clinical Infectious Diseases, vol.2010, issue.20, pp.719-724, 2013.
DOI : 10.1073/pnas.0915077107

URL : https://academic.oup.com/cid/article-pdf/57/5/719/17852835/cit284.pdf

Z. Tavakkol, Resident bacterial flora in the skin of C57BL/6 mice housed under SPF conditions, J Am Assoc Lab Anim Sci, vol.49, issue.5, pp.588-591, 2010.

A. Gozalo, V. Hoffmann, L. Brinster, W. Elkins, L. Ding et al., Spontaneous Staphylococcus xylosus infection in mice deficient in NADPH oxidase and comparison with other laboratory mouse strains, J Am Assoc Lab Anim Sci, vol.49, issue.4, pp.480-486, 2010.

K. Kline, Characterization of a Novel Murine Model of Staphylococcus saprophyticus Urinary Tract Infection Reveals Roles for Ssp and SdrI in Virulence, Infection and Immunity, vol.78, issue.5, pp.1943-1951, 2010.
DOI : 10.1128/IAI.01235-09

URL : https://hal.archives-ouvertes.fr/pasteur-01662518

W. Fiedelman, Carbenicillin therapy of urinary tract infections due to difficult uropathogens. III. Enterococcus s suppl), Curr Ther Res Clin Exp, vol.18, issue.1, pp.249-256, 1975.

S. Vaidyanathan, B. Soni, J. Bingley, E. Brown, and S. Markey, Prevention of pressure sore caused by indwelling urinary catheters, Spinal Cord, vol.39, issue.9, p.489, 2002.
DOI : 10.1038/sj.sc.3101212

J. Kadurugamuwa, K. Modi, J. Yu, K. Francis, T. Purchio et al., Noninvasive Biophotonic Imaging for Monitoring of Catheter-Associated Urinary Tract Infections and Therapy in Mice, Infection and Immunity, vol.73, issue.7, pp.3878-3887, 2005.
DOI : 10.1128/IAI.73.7.3878-3887.2005

P. Guiton, ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.56, issue.9, pp.4738-4745, 2012.
DOI : 10.1128/AAC.00447-12

H. Zowawi, The emerging threat of multidrug-resistant Gram-negative bacteria in urology, Nature Reviews Urology, vol.12, issue.10, pp.570-584, 2015.
DOI : 10.1371/journal.ppat.1000586

E. Singlas, Pharmacokinetics of sulfamethoxazole - trimethoprim combination during chronic peritoneal dialysis: Effect of peritonitis, European Journal of Clinical Pharmacology, vol.14, issue.5, pp.409-415, 1982.
DOI : 10.1159/000220651

M. Bartlett, M. Shaw, J. Smith, and S. Meshnick, Efficacy of sulfamethoxypyridazine in a murine model of Pneumocystis carinii pneumonia, Antimicrob Agents Chemother, vol.42, issue.4, pp.934-935, 1998.

C. Smith and M. Finland, Carbenicillin: activity in vitro and absorption and excretion in normal young men, Appl Microbiol, vol.16, issue.11, pp.1753-1760, 1968.

K. Schelling, Reducing catheter-associated urinary tract infections in a neuro???spine intensive care unit, American Journal of Infection Control, vol.43, issue.8, pp.892-894, 2015.
DOI : 10.1016/j.ajic.2015.04.184

K. Kline and D. Bowdish, Infection in an aging population, Current Opinion in Microbiology, vol.29, pp.63-67, 2016.
DOI : 10.1016/j.mib.2015.11.003

S. Chen, 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.13, issue.5, pp.5977-5982, 2006.
DOI : 10.1093/bioinformatics/13.5.555

M. Mulvey, J. Schilling, and S. Hultgren, Establishment of a Persistent Escherichia coli Reservoir during the Acute Phase of a Bladder Infection, Infection and Immunity, vol.69, issue.7, pp.4572-4579, 2001.
DOI : 10.1128/IAI.69.7.4572-4579.2001

G. Dunny, B. Brown, and D. Clewell, Induced cell aggregation and mating in Streptococcus faecalis: evidence for a bacterial sex pheromone., Proceedings of the National Academy of Sciences, vol.75, issue.7, pp.3479-3483, 1978.
DOI : 10.1073/pnas.75.7.3479

D. Kim, G. Pertea, C. Trapnell, H. Pimentel, R. Kelley et al., TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biology, vol.14, issue.4, p.36, 2013.
DOI : 10.1186/gb-2009-10-3-r25

S. Anders, P. Pyl, and W. Huber, HTSeq--a Python framework to work with high-throughput sequencing data, Bioinformatics, vol.13, issue.1, pp.166-169, 2015.
DOI : 10.1093/bioinformatics/btp616

R. Development and C. Team, R Project for Statistical Computing. https://www.r-project.org. Accessed, 2016.

Y. Benita, Z. Cao, C. Giallourakis, C. Li, A. Gardet et al., Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor, Blood, vol.115, issue.26, pp.5376-5384, 2010.
DOI : 10.1182/blood-2010-01-263855

V. Carey, Ontology concepts and tools for statistical genomics, Journal of Multivariate Analysis, vol.90, issue.1, pp.213-228, 2004.
DOI : 10.1016/j.jmva.2004.02.001

URL : https://doi.org/10.1016/j.jmva.2004.02.001

J. Wall and C. Jenkins, Practical statistics for astronomers, 2003.
DOI : 10.1017/cbo9780511536618

Y. Benjamini and Y. Hochberg, Controlling the False Discovery Rate -a Practical and Powerful Approach to Multiple Testing, J Roy Stat Soc B Met, vol.57, issue.1, pp.289-300, 1995.

G. Alterovitz, M. Xiang, M. Mohan, and M. Ramoni, GO PaD: the Gene Ontology Partition Database, Nucleic Acids Research, vol.33, issue.suppl_1, pp.322-327, 2007.
DOI : 10.1093/nar/gki108

URL : https://academic.oup.com/nar/article-pdf/35/suppl_1/D322/16746708/gkl799.pdf