E. Alix and A. B. Blanc-potard, MgtC: a key player in intramacrophage survival, Trends in Microbiology, vol.15, issue.6, pp.252-256, 2007.
DOI : 10.1016/j.tim.2007.03.007

P. Amavisit, D. Lightfoot, G. F. Browning, and P. F. Markham, Variation between Pathogenic Serovars within Salmonella Pathogenicity Islands, Journal of Bacteriology, vol.185, issue.12, pp.3624-3635, 2003.
DOI : 10.1128/JB.185.12.3624-3635.2003

M. F. Anjum, C. Marooney, M. Fookes, S. Baker, G. Dougan et al., Identification of Core and Variable Components of the Salmonella enterica Subspecies I Genome by Microarray, Infection and Immunity, vol.73, issue.12, pp.7894-7905, 2005.
DOI : 10.1128/IAI.73.12.7894-7905.2005

S. Bekal, R. Brousseau, L. Masson, G. Prefontaine, J. Fairbrother et al., Rapid Identification of Escherichia coli Pathotypes by Virulence Gene Detection with DNA Microarrays, Journal of Clinical Microbiology, vol.41, issue.5, pp.2113-2125, 2003.
DOI : 10.1128/JCM.41.5.2113-2125.2003

G. Bergsten, B. Wullt, and C. Svanborg, Escherichia coli, fimbriae, bacterial persistence and host response induction in the human urinary tract, International Journal of Medical Microbiology, vol.295, issue.6-7, pp.487-502, 2005.
DOI : 10.1016/j.ijmm.2005.07.008

M. Bielaszewska, U. Dobrindt, J. Gartner, I. Gallitz, J. Hacker et al., Aspects of genome plasticity in pathogenic Escherichia coli, International Journal of Medical Microbiology, vol.297, issue.7-8, pp.625-639, 2007.
DOI : 10.1016/j.ijmm.2007.03.001

J. Bispham, B. N. Tripathi, P. R. Watson, and T. S. Wallis, Salmonella Pathogenicity Island 2 Influences Both Systemic Salmonellosis and Salmonella-Induced Enteritis in Calves, Infection and Immunity, vol.69, issue.1, pp.367-377, 2001.
DOI : 10.1128/IAI.69.1.367-377.2001

A. B. Blanc-potard and E. A. Groisman, The Salmonella selC locus contains a pathogenicity island mediating intramacrophage survival, The EMBO Journal, vol.16, issue.17, pp.5376-5385, 1997.
DOI : 10.1093/emboj/16.17.5376

A. B. Blanc-potard, F. Solomon, J. Kayser, and E. A. Groisman, The SPI-3 pathogenicity island of Salmonella enterica, J. Bacteriol, vol.181, pp.998-1004, 1999.

F. R. Blattner, G. Plunkett, C. A. Bloch, N. T. Perna, V. Burland et al., The Complete Genome Sequence of Escherichia coli K-12, Science, vol.277, issue.5331, pp.1453-1474, 1997.
DOI : 10.1126/science.277.5331.1453

G. Blum, V. Falbo, A. Caprioli, and J. Hacker, Gene clusters encoding the cytotoxic necrotizing factor type 1, Prs-fimbriae and alpha-hemolysin form the pathogenicity island II of the uropathogenic Escherichia coli strain J96, FEMS Microbiol. Lett, vol.126, pp.189-195, 1995.

E. F. Boyd and H. Brüssow, Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved, Trends in Microbiology, vol.10, issue.11, pp.521-529, 2002.
DOI : 10.1016/S0966-842X(02)02459-9

C. Branger, O. Zamfir, S. Geoffroy, G. Laurans, G. Arlet et al., and Extended-spectrum ??-Lactamase Type, Emerging Infectious Diseases, vol.11, issue.1, pp.54-61, 2005.
DOI : 10.3201/eid1101.040257

G. Bruant, C. Maynard, S. Bekal, I. Gaucher, L. Masson et al., Development and Validation of an Oligonucleotide Microarray for Detection of Multiple Virulence and Antimicrobial Resistance Genes in Escherichia coli, Applied and Environmental Microbiology, vol.72, issue.5, pp.3780-3784, 2006.
DOI : 10.1128/AEM.72.5.3780-3784.2006

W. Brunder, H. Schmidt, and H. Karch, KatP, a novel catalase-peroxidase encoded by the large plasmid of enterohaemorrhagic Escherichia coli O157:H7, Microbiology, vol.142, issue.11, pp.3305-3315, 1996.
DOI : 10.1099/13500872-142-11-3305

W. Brunder, H. Schmidt, and H. Karch, EspP, a novel extracellular serine protease of enterohaemorrhagic Escherichia coli O157:H7 cleaves human coagulation factor V, Molecular Microbiology, vol.24, issue.4, pp.767-778, 1997.
DOI : 10.1046/j.1365-2958.1997.3871751.x

E. Brzuszkiewicz, H. Bruggemann, H. Liesegang, M. Emmerth, T. Olschlager et al., How to become a uropathogen: Comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains, Proc. Natl. Acad. Sci. U.S.A. 103, pp.12879-12884, 2006.
DOI : 10.1073/pnas.0603038103

V. Burland, Y. Shao, N. T. Perna, G. Plunkett, H. J. Sofia et al., The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7, Nucleic Acids Research, vol.26, issue.18, pp.4196-4204, 1998.
DOI : 10.1093/nar/26.18.4196

K. G. Campellone, D. Robbins, and J. M. Leong, EspFU Is a Translocated EHEC Effector that Interacts with Tir and N-WASP and Promotes Nck-Independent Actin Assembly, Developmental Cell, vol.7, issue.2, pp.217-228, 2004.
DOI : 10.1016/j.devcel.2004.07.004

E. Caron, V. F. Crepin, N. Simpson, S. Knutton, J. Garmendia et al., Subversion of actin dynamics by EPEC and EHEC, Current Opinion in Microbiology, vol.9, issue.1, pp.40-45, 2006.
DOI : 10.1016/j.mib.2005.12.008

B. Coburn, Y. Li, D. Owen, B. A. Vallance, and B. B. Finlay, Salmonella enterica Serovar Typhimurium Pathogenicity Island 2 Is Necessary for Complete Virulence in a Mouse Model of Infectious Enterocolitis, Infection and Immunity, vol.73, issue.6, pp.3219-3227, 2005.
DOI : 10.1128/IAI.73.6.3219-3227.2005

B. K. Coombes, B. A. Coburn, A. A. Potter, S. Gomis, K. Mirakhur et al., Analysis of the Contribution of Salmonella Pathogenicity Islands 1 and 2 to Enteric Disease Progression Using a Novel Bovine Ileal Loop Model and a Murine Model of Infectious Enterocolitis, Infection and Immunity, vol.73, issue.11, pp.7161-7169, 2005.
DOI : 10.1128/IAI.73.11.7161-7169.2005

S. Dahan, S. Wiles, R. M. La-ragione, A. Best, M. J. Woodward et al., EspJ Is a Prophage-Carried Type III Effector Protein of Attaching and Effacing Pathogens That Modulates Infection Dynamics, Infection and Immunity, vol.73, issue.2, pp.679-686, 2005.
DOI : 10.1128/IAI.73.2.679-686.2005

E. A. Dean-nystrom, L. J. Gansheroff, M. Mills, H. W. Moon, and A. D. O-'brien, Vaccination of Pregnant Dams with IntiminO157 Protects Suckling Piglets from Escherichia coli O157:H7 Infection, Infection and Immunity, vol.70, issue.5, pp.2414-2418, 2002.
DOI : 10.1128/IAI.70.5.2414-2418.2002

M. Diard, S. Baeriswyl, O. Clermont, S. Gouriou, B. Picard et al., Caenorhabditis elegans as a simple model to study phenotypic and genetic virulence determinants of extraintestinal pathogenic Escherichia coli. Microbes Infect, pp.214-223, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00554711

U. Dobrindt, (Patho-)Genomics of Escherichia coli, International Journal of Medical Microbiology, vol.295, issue.6-7, pp.357-371, 2005.
DOI : 10.1016/j.ijmm.2005.07.009

U. Dobrindt, F. Agerer, K. Michaelis, A. Janka, C. Buchrieser et al., Analysis of Genome Plasticity in Pathogenic and Commensal Escherichia coli Isolates by Use of DNA Arrays, Journal of Bacteriology, vol.185, issue.6, pp.1831-1840, 2003.
DOI : 10.1128/JB.185.6.1831-1840.2003

U. Dobrindt, G. Blum-oehler, G. Nagy, G. Schneider, A. Johann et al., Genetic Structure and Distribution of Four Pathogenicity Islands (PAI I536 to PAI IV536) of Uropathogenic Escherichia coli Strain 536, Infection and Immunity, vol.70, issue.11, pp.6365-6372, 2002.
DOI : 10.1128/IAI.70.11.6365-6372.2002

R. F. Doolittle, D. F. Feng, S. Tsang, G. Cho, and E. Little, Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock, Science, vol.271, issue.5248, pp.470-477, 1996.
DOI : 10.1126/science.271.5248.470

C. W. Dorsey, M. C. Laarakker, A. D. Humphries, E. H. Weening, and A. J. Baumler, Salmonella enterica serotype Typhimurium MisL is an intestinal colonization factor that binds fibronectin, Molecular Microbiology, vol.107, issue.1, pp.196-211, 2005.
DOI : 10.1111/j.1365-2958.2005.04666.x

S. J. Drews, S. M. Poutanen, T. Mazzulli, A. J. Mcgeer, A. Sarabia et al., Decreased Prevalence of Virulence Factors among Ciprofloxacin-Resistant Uropathogenic Escherichia coli Isolates, Journal of Clinical Microbiology, vol.43, issue.8, pp.4218-4220, 2005.
DOI : 10.1128/JCM.43.8.4218-4220.2005

L. Durant, A. Metais, C. Soulama-mouze, J. M. Genevard, X. Nassif et al., Identification of Candidates for a Subunit Vaccine against Extraintestinal Pathogenic Escherichia coli, Infection and Immunity, vol.75, issue.4, pp.1916-1925, 2007.
DOI : 10.1128/IAI.01269-06

F. Dziva, I. Vlisidou, V. F. Crepin, T. S. Wallis, G. Frankel et al., Vaccination of calves with EspA, a key colonisation factor of Escherichia coli O157:H7, induces antigen-specific humoral responses but does not confer protection against intestinal colonisation, Veterinary Microbiology, vol.123, issue.1-3, pp.254-261, 2007.
DOI : 10.1016/j.vetmic.2007.02.016

K. Ehrbar and W. D. Hardt, Bacteriophage-encoded type III effectors in Salmonella enterica subspecies 1 serovar Typhimurium, Infection, Genetics and Evolution, vol.5, issue.1, pp.1-9, 2005.
DOI : 10.1016/S1567-1348(04)00071-1

K. Ehrbar, S. Mirold, A. Friebel, S. Stender, and W. D. Hardt, Characterization of effector proteins translocated via the SPI1 type III secretion system of Salmonella typhimurium, International Journal of Medical Microbiology, vol.291, issue.6-7, pp.479-485, 2002.
DOI : 10.1078/1438-4221-00156

P. Escobar-paramo, O. Clermont, A. B. Blanc-potard, H. Bui, L. Bouguenec et al., A Specific Genetic Background Is Required for Acquisition and Expression of Virulence Factors in Escherichia coli, Molecular Biology and Evolution, vol.21, issue.6, pp.1085-1094, 2004.
DOI : 10.1093/molbev/msh118

N. Figueroa-bossi and L. Bossi, Inducible prophages contribute to Salmonella virulence in mice, Molecular Microbiology, vol.118, issue.1, pp.167-176, 1999.
DOI : 10.1016/0378-1119(85)90120-9

N. Figueroa-bossi, S. Uzzau, D. Maloriol, and L. Bossi, Variable assortment of prophages provides a transferable repertoire of pathogenic determinants in Salmonella, Molecular Microbiology, vol.125, issue.2, pp.260-271, 2001.
DOI : 10.1046/j.1365-2958.2000.01902.x

B. Foultier, P. Troisfontaines, S. Muller, F. R. Opperdoes, and G. R. Cornelis, Characterization of the ysa Pathogenicity Locus in the Chromosome of Yersinia enterocolitica and Phylogeny Analysis of Type III Secretion Systems, Journal of Molecular Evolution, vol.55, issue.1, pp.37-51, 2002.
DOI : 10.1007/s00239-001-0089-7

O. Gal-mor and B. B. Finlay, Pathogenicity islands: a molecular toolbox for bacterial virulence, Cellular Microbiology, vol.66, issue.11, pp.1707-1719, 2006.
DOI : 10.1128/IAI.69.4.2107-2115.2001

J. Garmendia, A. D. Phillips, M. F. Carlier, Y. Chong, S. Schüller et al., TccP is an enterohaemorrhagic Escherichia coli O157:H7 type III effector protein that couples Tir to the actin-cytoskeleton+, Cellular Microbiology, vol.107, issue.12, pp.1167-1183, 2004.
DOI : 10.1093/emboj/cdf319

A. Gauthier, M. L. Robertson, M. Lowden, J. A. Ibarra, J. L. Puente et al., Transcriptional Inhibitor of Virulence Factors in Enteropathogenic Escherichia coli, Antimicrobial Agents and Chemotherapy, vol.49, issue.10, pp.4101-4109, 2005.
DOI : 10.1128/AAC.49.10.4101-4109.2005

R. G. Gerlach, D. Jackel, B. Stecher, C. Wagner, A. Lupas et al., Salmonella Pathogenicity Island 4 encodes a giant non-fimbrial adhesin and the cognate type 1 secretion system, Cellular Microbiology, vol.66, issue.7, pp.1834-1850, 2007.
DOI : 10.1126/science.1108472

S. Gruenheid, I. Sekirov, N. A. Thomas, W. Deng, P. O-'donnell et al., Identification and characterization of NleA, a non-LEE-encoded type III translocated virulence factor of enterohaemorrhagic Escherichia coli O157:H7, Molecular Microbiology, vol.69, issue.5, pp.1233-1249, 2004.
DOI : 10.1046/j.1365-2958.2003.03911.x

K. Gupta, T. M. Hooton, and W. E. Stamm, Increasing Antimicrobial Resistance and the Management of Uncomplicated Community-Acquired Urinary Tract Infections, Annals of Internal Medicine, vol.135, issue.1, pp.41-50, 2001.
DOI : 10.7326/0003-4819-135-1-200107030-00012

D. M. Guyer, I. R. Henderson, J. P. Nataro, and H. L. Mobley, Identification of Sat, an autotransporter toxin produced by uropathogenic Escherichia coli, Molecular Microbiology, vol.142, issue.1, pp.53-66, 2000.
DOI : 10.1038/325458a0

D. M. Guyer, J. S. Kao, and H. L. Mobley, Genomic analysis of a pathogenicity island in uropathogenic Escherichia coli CFT073: distribution of homologous sequences among isolates from patients with pyelonephritis, cystitis, and catheter-associated bacteriuria and from fecal samples, Infect. Immun, vol.66, pp.4411-4417, 1998.

D. M. Guyer, S. Radulovic, F. E. Jones, and H. L. Mobley, Sat, the Secreted Autotransporter Toxin of Uropathogenic Escherichia coli, Is a Vacuolating Cytotoxin for Bladder and Kidney Epithelial Cells, Infection and Immunity, vol.70, issue.8, pp.4539-4546, 2002.
DOI : 10.1128/IAI.70.8.4539-4546.2002

J. Hacker, L. Bender, M. Ott, J. Wingender, B. Lund et al., Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vitro and in vivo in various extra intestinal Escherichia coli isolates, Microbial Pathogenesis, vol.8, issue.3, pp.213-225, 1990.
DOI : 10.1016/0882-4010(90)90048-U

E. C. Hagan and H. L. Mobley, Uropathogenic Escherichia coli Outer Membrane Antigens Expressed during Urinary Tract Infection, Infection and Immunity, vol.75, issue.8, pp.3941-3949, 2007.
DOI : 10.1128/IAI.00337-07

S. Hapfelmeier, K. Ehrbar, B. Stecher, M. Barthel, M. Kremer et al., Role of the Salmonella Pathogenicity Island 1 Effector Proteins SipA, SopB, SopE, and SopE2 in Salmonella enterica Subspecies 1 Serovar Typhimurium Colitis in Streptomycin-Pretreated Mice, Infection and Immunity, vol.72, issue.2, pp.795-809, 2004.
DOI : 10.1128/IAI.72.2.795-809.2004

S. Hapfelmeier and W. D. Hardt, A mouse model for S. typhimurium-induced enterocolitis, Trends in Microbiology, vol.13, issue.10, pp.497-503, 2005.
DOI : 10.1016/j.tim.2005.08.008

S. Hapfelmeier, B. Stecher, M. Barthel, M. Kremer, A. J. Muller et al., The Salmonella Pathogenicity Island (SPI)-2 and SPI-1 Type III Secretion Systems Allow Salmonella Serovar typhimurium to Trigger Colitis via MyD88-Dependent and MyD88-Independent Mechanisms, The Journal of Immunology, vol.174, issue.3, pp.1675-1685, 2005.
DOI : 10.4049/jimmunol.174.3.1675

W. D. Hardt, H. Urlaub, and J. E. Galan, A substrate of the centisome 63 type III protein secretion system of Salmonella typhimurium is encoded by a cryptic bacteriophage, Proceedings of the National Academy of Sciences, vol.95, issue.5, pp.2574-2579, 1998.
DOI : 10.1073/pnas.95.5.2574

T. Hayashi, K. Makino, M. Ohnishi, K. Kurokawa, K. Ishii et al., Complete Genome Sequence of Enterohemorrhagic Eschelichia coli O157:H7 and Genomic Comparison with a Laboratory Strain K-12, DNA Research, vol.8, issue.1, pp.11-22, 2001.
DOI : 10.1093/dnares/8.1.11

P. J. Herzer, S. Inouye, M. Inouye, and T. S. Whittam, Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli., Journal of Bacteriology, vol.172, issue.11, pp.6175-6181, 1990.
DOI : 10.1128/jb.172.11.6175-6181.1990

D. L. Hudson, A. N. Layton, T. R. Field, A. J. Bowen, H. Wolf-watz et al., Inhibition of Type III Secretion in Salmonella enterica Serovar Typhimurium by Small-Molecule Inhibitors, Antimicrobial Agents and Chemotherapy, vol.51, issue.7, pp.2631-2635, 2007.
DOI : 10.1128/AAC.01492-06

I. R. Henderson, F. Navarro-garcia, M. Desvaux, R. C. Fernandez, and D. Ala-'aldeen, Type V Protein Secretion Pathway: the Autotransporter Story, Microbiology and Molecular Biology Reviews, vol.68, issue.4, pp.692-744, 2004.
DOI : 10.1128/MMBR.68.4.692-744.2004

M. Hensel, J. E. Shea, A. J. Baumler, C. Gleeson, F. Blattner et al., Analysis of the boundaries of Salmonella pathogenicity island 2 and the corresponding chromosomal region of Escherichia coli K-12., Journal of Bacteriology, vol.179, issue.4, pp.1105-1111, 1997.
DOI : 10.1128/jb.179.4.1105-1111.1997

K. L. Hopkins and E. J. Threlfall, Frequency and polymorphism of sopE in isolates of Salmonella enterica belonging to the ten most prevalent serotypes in England and Wales, Journal of Medical Microbiology, vol.53, issue.6, pp.539-543, 2004.
DOI : 10.1099/jmm.0.05510-0

J. P. Horcajada, S. Soto, A. Gajewski, A. Smithson, M. T. Jimenez-de-anta et al., Quinolone-Resistant Uropathogenic Escherichia coli Strains from Phylogenetic Group B2 Have Fewer Virulence Factors than Their Susceptible Counterparts, Journal of Clinical Microbiology, vol.43, issue.6, pp.2962-2964, 2005.
DOI : 10.1128/JCM.43.6.2962-2964.2005

J. R. Johnson and M. Kuskowski, Clonal Origin, Virulence Factors, and Virulence, Infection and Immunity, vol.68, issue.1, pp.424-425, 2000.
DOI : 10.1128/IAI.68.1.424-425.2000
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC97155

J. R. Johnson, M. A. Kuskowski, T. T. O-'bryan, R. Colodner, and R. Raz, Virulence Genotype and Phylogenetic Origin in Relation to Antibiotic Resistance Profile among Escherichia coli Urine Sample Isolates from Israeli Women with Acute Uncomplicated Cystitis, Antimicrobial Agents and Chemotherapy, vol.49, issue.1, pp.26-31, 2005.
DOI : 10.1128/AAC.49.1.26-31.2005

J. R. Johnson, M. A. Kuskowski, K. Owens, A. Gajewski, and P. L. Winokur, Isolates from Animals and Humans, The Journal of Infectious Diseases, vol.188, issue.5, pp.759-768, 2003.
DOI : 10.1086/377455

J. R. Johnson and T. A. Russo, Molecular epidemiology of extraintestinal pathogenic (uropathogenic) Escherichia coli, International Journal of Medical Microbiology, vol.295, issue.6-7, pp.383-404, 2005.
DOI : 10.1016/j.ijmm.2005.07.005

J. R. Johnson, C. Van-der-schee, M. A. Kuskowski, W. Goessens, and A. Van-belkum, Isolates from The Netherlands, The Journal of Infectious Diseases, vol.186, issue.12, pp.1852-1856, 2002.
DOI : 10.1086/345767

J. B. Kaper, Pathogenic Escherichia coli, International Journal of Medical Microbiology, vol.295, issue.6-7, pp.355-356, 2005.
DOI : 10.1016/j.ijmm.2005.06.008

J. B. Kaper, J. P. Nataro, and H. L. Mobley, Pathogenic Escherichia coli, Nature Reviews Microbiology, vol.63, issue.2, pp.123-140, 2004.
DOI : 10.1128/IAI.69.1.315-324.2001

H. Karch, P. I. Tarr, and M. Bielaszewska, Enterohaemorrhagic Escherichia coli in human medicine, International Journal of Medical Microbiology, vol.295, issue.6-7, pp.405-418, 2005.
DOI : 10.1016/j.ijmm.2005.06.009

L. A. Knodler, J. Celli, W. D. Hardt, B. A. Vallance, C. Yip et al., Salmonella effectors within a single pathogenicity island are differentially expressed and translocated by separate type III secretion systems, Molecular Microbiology, vol.39, issue.5, pp.1089-1103, 2002.
DOI : 10.1046/j.1365-2958.2002.02820.x

M. C. Lane and H. L. Mobley, Role of P-fimbrial-mediated adherence in pyelonephritis and persistence of uropathogenic Escherichia coli (UPEC) in the mammalian kidney, Kidney International, vol.72, issue.1, pp.19-25, 2007.
DOI : 10.1038/sj.ki.5002230

W. W. Lathem, T. E. Grys, S. E. Witowski, A. G. Torres, J. B. Kaper et al., StcE, a metalloprotease secreted by Escherichia coli O157:H7, specifically cleaves C1 esterase inhibitor, Molecular Microbiology, vol.61, issue.2, pp.277-288, 2002.
DOI : 10.1128/IAI.69.11.6660-6669.2001

J. P. Lavigne, A. B. Blanc-potard, G. Bourg, J. Moreau, C. Chanal et al., Virulence genotype and nematode-killing properties of extra-intestinal Escherichia coli producing CTX-M ??-lactamases, Clinical Microbiology and Infection, vol.12, issue.12, pp.1199-1206, 2006.
DOI : 10.1111/j.1469-0691.2006.01536.x
URL : https://hal.archives-ouvertes.fr/hal-00275629

L. Bouguénec, C. Servin, and A. L. , Diffusely adherent Escherichia coli strains expressing Afa/Dr adhesins (Afa/Dr DAEC): hitherto unrecognized pathogens, FEMS Microbiology Letters, vol.256, issue.2, pp.185-194, 2006.
DOI : 10.1111/j.1574-6968.2006.00144.x

Y. M. Lee, F. Almqvist, and S. J. Hultgren, Targeting virulence for antimicrobial chemotherapy, Current Opinion in Pharmacology, vol.3, issue.5, pp.513-519, 2003.
DOI : 10.1016/j.coph.2003.04.001

Y. Li, E. Frey, A. M. Mackenzie, and B. B. Finlay, Human Response to Escherichia coli O157:H7 Infection: Antibodies to Secreted Virulence Factors, Infection and Immunity, vol.68, issue.9, pp.5090-5095, 2000.
DOI : 10.1128/IAI.68.9.5090-5095.2000

M. Li, I. Rosenshine, H. B. Yu, C. Nadler, E. Mills et al., Identification and characterization of NleI, a new non-LEE-encoded effector of enteropathogenic Escherichia coli (EPEC) Microbes Infect, pp.2890-2898, 2006.

A. L. Lloyd, D. A. Rasko, and H. L. Mobley, Defining Genomic Islands and Uropathogen-Specific Genes in Uropathogenic Escherichia coli, Journal of Bacteriology, vol.189, issue.9, pp.3532-3546, 2007.
DOI : 10.1128/JB.01744-06

C. P. Lostroh and C. A. Lee, The Salmonella pathogenicity island-1 type III secretion system, Microbes and Infection, vol.3, issue.14-15, pp.1281-1291, 2001.
DOI : 10.1016/S1286-4579(01)01488-5

M. Mcclelland, K. E. Sanderson, J. Spieth, S. W. Clifton, P. Latreille et al., Complete genome sequence of Salmonella enterica serovar Typhimurium LT2, Nature, vol.413, issue.6858, pp.852-856, 2001.
DOI : 10.1038/35101614

P. Marcato, T. P. Griener, G. L. Mulvey, and G. D. Armstrong, Recombinant Shiga Toxin B-Subunit-Keyhole Limpet Hemocyanin Conjugate Vaccine Protects Mice from Shigatoxemia, Infection and Immunity, vol.73, issue.10, pp.6523-6529, 2005.
DOI : 10.1128/IAI.73.10.6523-6529.2005

O. Marches, T. N. Ledger, M. Boury, M. Ohara, X. Tu et al., Enteropathogenic and enterohaemorrhagic Escherichia coli deliver a novel effector called Cif, which blocks cell cycle G2/M transition, Molecular Microbiology, vol.66, issue.5, pp.1553-1567, 2003.
DOI : 10.1046/j.1365-2958.2003.03821.x

B. I. Marklund, J. M. Tennent, E. Garcia, A. Hamers, M. Båga et al., Horizontal gene transfer of the Escherichia coli pap and prs pili operons as a mechanism for the development of tissue-specific adhesive properties, Molecular Microbiology, vol.172, issue.16, pp.2225-2242, 1992.
DOI : 10.1016/0882-4010(87)90091-X

D. M. Mills, V. Bajaj, and C. A. Lee, A 40 kb chromosomal fragment encoding Salmonella typhimurium invasion genes is absent from the corresponding region of the Escherichia coli K-12 chromosome, Molecular Microbiology, vol.15, issue.4, pp.749-759, 1995.
DOI : 10.1111/j.1365-2958.1995.tb02382.x

S. Mirold, W. Rabsch, M. Rohde, S. Stender, H. Tschape et al., Isolation of a temperate bacteriophage encoding the type III effector protein SopE from an epidemic Salmonella typhimurium strain, Proceedings of the National Academy of Sciences, vol.96, issue.17, pp.9845-9850, 1999.
DOI : 10.1073/pnas.96.17.9845

E. Morgan, A. J. Bowen, S. C. Carnell, T. S. Wallis, and M. P. Stevens, SiiE Is Secreted by the Salmonella enterica Serovar Typhimurium Pathogenicity Island 4-Encoded Secretion System and Contributes to Intestinal Colonization in Cattle, Infection and Immunity, vol.75, issue.3, pp.1524-1533, 2007.
DOI : 10.1128/IAI.01438-06

S. Muller, M. F. Feldman, and G. R. Cornelis, The Type III secretion system of Gram-negative bacteria: a potential therapeutic target?, Expert Opinion on Therapeutic Targets, vol.29, issue.3, pp.327-339, 2001.
DOI : 10.1086/317489

R. Nordfelth, A. M. Kauppi, H. A. Norberg, H. Wolf-watz, and M. Elofsson, Small-Molecule Inhibitors Specifically Targeting Type III Secretion, Infection and Immunity, vol.73, issue.5, pp.3104-3114, 2005.
DOI : 10.1128/IAI.73.5.3104-3114.2005

H. Ochman, F. C. Soncini, F. Solomon, and E. A. Groisman, Identification of a pathogenicity island required for Salmonella survival in host cells., Proceedings of the National Academy of Sciences, vol.93, issue.15, pp.7800-7804, 1996.
DOI : 10.1073/pnas.93.15.7800

O. Hanley, P. Lalonde, G. Ji, and G. , Alpha-hemolysin contributes to the pathogenicity of piliated digalactoside-binding Escherichia coli in the kidney: efficacy of an alpha-hemolysin vaccine in preventing renal injury in the BALB/c mouse model of pyelonephritis, Infect. Immun, vol.59, pp.1153-1161, 1991.

M. Ohnishi, K. Kurokawa, and T. Hayashi, Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol, pp.481-485, 2001.

M. Ohnishi, J. Terajima, K. Kurokawa, K. Nakayama, T. Murata et al., Genomic diversity of enterohemorrhagic Escherichia coli O157 revealed by whole genome PCR scanning, Proceedings of the National Academy of Sciences, vol.99, issue.26, pp.17043-17048, 2002.
DOI : 10.1073/pnas.262441699

R. U. Palaniappan, Y. Zhang, D. Chiu, A. Torres, C. Debroy et al., Differentiation of Escherichia coli Pathotypes by Oligonucleotide Spotted Array, Journal of Clinical Microbiology, vol.44, issue.4, pp.1495-1501, 2006.
DOI : 10.1128/JCM.44.4.1495-1501.2006

N. J. Parham, U. Srinivasan, M. Desvaux, B. Foxman, C. F. Marrs et al., PicU, a second serine protease autotransporter of uropathogenic Escherichia coli, FEMS Microbiology Letters, vol.230, issue.1, pp.73-83, 2004.
DOI : 10.1016/S0378-1097(03)00862-0

C. Parsot, pathogenicity factors, FEMS Microbiology Letters, vol.252, issue.1, pp.11-18, 2005.
DOI : 10.1016/j.femsle.2005.08.046

N. T. Perna, G. Plunkett-3rd, V. Burland, B. Mau, J. D. Glasner et al., Genome sequence of enterohaemorrhagic Escherichia coli O157:H7, Genome sequence of enterohaemorrhagic Escherichia coli O157:H7, pp.529-533, 2001.
DOI : 10.1038/35054089

A. D. Phillips and G. Frankel, Interaction with Human Intestinal Organ Cultures, The Journal of Infectious Diseases, vol.181, issue.4, pp.1496-1500, 2000.
DOI : 10.1086/315404

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

S. Porwollik and M. Mcclelland, Lateral gene transfer in Salmonella, Microbes and Infection, vol.5, issue.11, pp.977-989, 2003.
DOI : 10.1016/S1286-4579(03)00186-2

A. A. Potter, S. Klashinsky, Y. Li, E. Frey, H. Townsend et al., Decreased shedding of Escherichia coli O157:H7 by cattle following vaccination with type III secreted proteins, Vaccine, vol.22, issue.3-4, pp.362-369, 2004.
DOI : 10.1016/j.vaccine.2003.08.007

J. A. Roberts, M. B. Kaack, G. Baskin, M. R. Chapman, D. A. Hunstad et al., ANTIBODY RESPONSES AND PROTECTION FROM PYELONEPHRITIS FOLLOWING VACCINATION WITH PURIFIED ESCHERICHIA COLI PAPDG PROTEIN, The Journal of Urology, vol.171, issue.4, pp.1682-1685, 2004.
DOI : 10.1097/01.ju.0000116123.05160.43

R. Rotger and J. Casadesus, The virulence plasmids of Salmonella, Int. Microbiol, vol.2, pp.177-184, 1999.

T. A. Russo, C. D. Mcfadden, U. B. Carlino-macdonald, J. M. Beanan, R. Olson et al., The Siderophore Receptor IroN of Extraintestinal Pathogenic Escherichia coli Is a Potential Vaccine Candidate, Infection and Immunity, vol.71, issue.12, pp.7164-7169, 2003.
DOI : 10.1128/IAI.71.12.7164-7169.2003

J. Sánchez and J. Holmgren, Virulence factors, pathogenesis and vaccine protection in cholera and ETEC diarrhea, Current Opinion in Immunology, vol.17, issue.4, pp.388-398, 2005.
DOI : 10.1016/j.coi.2005.06.007

R. L. Santos, S. Zhang, R. M. Tsolis, R. A. Kingsley, L. G. Adams et al., Animal models of Salmonella infections: enteritis versus typhoid fever, Microbes and Infection, vol.3, issue.14-15, pp.1335-1344, 2001.
DOI : 10.1016/S1286-4579(01)01495-2

J. Schlundt, H. Toyofuku, J. Jansen, and S. A. Herbst, Emerging food-borne zoonoses, Revue Scientifique et Technique de l'OIE, vol.23, issue.2, pp.513-533, 2004.
DOI : 10.20506/rst.23.2.1506

H. Schmidt and M. Hensel, Pathogenicity Islands in Bacterial Pathogenesis, Clinical Microbiology Reviews, vol.17, issue.1, pp.14-56, 2004.
DOI : 10.1128/CMR.17.1.14-56.2004

H. Schmidt, B. Henkel, and H. Karch, A gene cluster closely related to type II secretion pathway operons of Gram-negative bacteria is located on the large plasmid of enterohemorrhagic Escherichia coli O157 strains, FEMS Microbiology Letters, vol.148, issue.2, pp.265-272, 1997.
DOI : 10.1111/j.1574-6968.1997.tb10299.x

H. Schmidt, C. Kernbach, and H. Karch, Analysis of the EHEC hly operon and its location in the physical map of the large plasmid of enterohaemorrhagic Escherichia coli O157:H7, Microbiology, vol.142, issue.4, pp.907-914, 1996.
DOI : 10.1099/00221287-142-4-907

J. E. Shea, M. Hensel, C. Gleeson, and D. W. Holden, Identification of a virulence locus encoding a second type III secretion system in Salmonella typhimurium., Proceedings of the National Academy of Sciences, vol.93, issue.6, pp.2593-2597, 1996.
DOI : 10.1073/pnas.93.6.2593

D. R. Shelton, J. S. Karns, J. A. Higgins, J. A. Van-kessel, M. L. Perdue et al., in surface waters, FEMS Microbiology Letters, vol.261, issue.1, pp.95-101, 2006.
DOI : 10.1111/j.1574-6968.2006.00334.x

S. M. Soto, I. Rodríguez, M. R. Rodicio, J. Vila, and M. C. Mendoza, Detection of virulence determinants in clinical strains of Salmonella enterica serovar Enteritidis and mapping on macrorestriction profiles, Journal of Medical Microbiology, vol.55, issue.4, pp.365-373, 2006.
DOI : 10.1099/jmm.0.46257-0

K. J. Spears, A. J. Roe, and D. L. Gally, pathogenesis, FEMS Microbiology Letters, vol.255, issue.2, pp.187-202, 2006.
DOI : 10.1111/j.1574-6968.2006.00119.x

M. Strömberg, B. I. Marklund, B. Lund, D. Ilver, A. Hamers et al., Host-specificity of uropathogenic Escherichia coli depends on differences in binding specificity to Gala 1- 4Gal-containing isoreceptors, EMBO J, vol.9, 1990.

I. Tatsuno, M. Horie, H. Abe, T. Miki, K. Makino et al., toxB Gene on pO157 of Enterohemorrhagic Escherichiacoli O157:H7 Is Required for Full Epithelial Cell Adherence Phenotype, Infection and Immunity, vol.69, issue.11, pp.6660-6669, 2001.
DOI : 10.1128/IAI.69.11.6660-6669.2001

T. Tobe, S. A. Beatson, H. Taniguchi, H. Abe, C. M. Bailey et al., An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination, Proc. Natl. Acad. Sci. U.S.A. 103, pp.14941-14946, 2006.
DOI : 10.1073/pnas.0604891103

J. Van-donkersgoed, D. Hancock, D. Rogan, and A. A. Potter, Escherichia coli O157:H7 vaccine field trial in 9 feedlots in Alberta and Saskatchewan, Can. Vet. J, vol.46, pp.724-728, 2005.

J. Vila, K. Simon, J. Ruiz, J. P. Horcajada, M. Velasco et al., Less Virulent?, The Journal of Infectious Diseases, vol.186, issue.7, pp.1039-1042, 2002.
DOI : 10.1086/342955

I. Vlisidou, O. Marches, F. Dziva, R. Mundy, G. Frankel et al., O157:H7, FEMS Microbiology Letters, vol.263, issue.1, pp.32-40, 2006.
DOI : 10.1111/j.1574-6968.2006.00410.x
URL : https://hal.archives-ouvertes.fr/hal-00532212

S. R. Waterman and D. W. Holden, Functions and effectors of the Salmonella pathogenicity island 2 type III secretion system, Cellular Microbiology, vol.67, issue.8, pp.501-511, 2003.
DOI : 10.1046/j.1365-2958.2003.03373.x

A. Weintraub, Enteroaggregative Escherichia coli: epidemiology, virulence and detection, Journal of Medical Microbiology, vol.56, issue.1, pp.4-8, 2007.
DOI : 10.1099/jmm.0.46930-0

R. A. Welch, V. Burland, I. Plunkett, G. Redford, P. Roesch et al., Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli, Proc. Natl. Acad. Sci. U.S.A. 99, pp.17020-17024, 2002.
DOI : 10.1073/pnas.252529799

T. J. Wells, J. J. Tree, G. C. Ulett, and M. A. Schembri, Autotransporter proteins: novel targets at the bacterial cell surface, FEMS Microbiology Letters, vol.274, issue.2, pp.163-172, 2007.
DOI : 10.1111/j.1574-6968.2007.00833.x

B. Wullt, G. Bergsten, H. Connell, P. Rollano, N. Gebretsadik et al., P fimbriae enhance the early establishment of Escherichia coli in the human urinary tract, Molecular Microbiology, vol.56, issue.3, pp.456-464, 2000.
DOI : 10.1016/S0022-5347(01)63246-4

K. K. Wong, M. Mcclelland, L. C. Stillwell, E. C. Sisk, S. J. Thurston et al., Identification and sequence analysis of a 27-kilobase chromosomal fragment containing a Salmonella pathogenicity island located at 92 minutes on the chromosome map of Salmonella enterica serovar typhimurium LT2, Infect. Immun, vol.66, pp.3365-3371, 1998.

M. W. Wood, M. A. Jones, P. R. Watson, S. Hedges, T. S. Wallis et al., Identification of a pathogenicity island required for Salmonella enteropathogenicity, Molecular Microbiology, vol.29, issue.3, pp.883-891, 1998.
DOI : 10.1073/pnas.93.6.2593

S. Yamamoto, Molecular epidemiology of uropathogenic Escherichia coli, Journal of Infection and Chemotherapy, vol.13, issue.2, pp.68-73, 2007.
DOI : 10.1007/s10156-007-0506-Y

W. L. Zhang, B. Kohler, E. Oswald, L. Beutin, H. Karch et al., Genetic Diversity of Intimin Genes of Attaching and Effacing Escherichia coli Strains, Journal of Clinical Microbiology, vol.40, issue.12, pp.4486-4492, 2002.
DOI : 10.1128/JCM.40.12.4486-4492.2002

S. Zhang, R. L. Santos, R. M. Tsolis, S. Mirold, W. D. Hardt et al., serotype Typhimurium for calves, FEMS Microbiology Letters, vol.217, issue.2, pp.243-247, 2002.
DOI : 10.1111/j.1574-6968.2002.tb11482.x

S. Zhang, R. L. Santos, R. M. Tsolis, S. Stender, W. D. Hardt et al., The Salmonella enterica Serotype Typhimurium Effector Proteins SipA, SopA, SopB, SopD, and SopE2 Act in Concert To Induce Diarrhea in Calves, Infection and Immunity, vol.70, issue.7, pp.3843-3855, 2002.
DOI : 10.1128/IAI.70.7.3843-3855.2002