S. C. Andrews, A. K. Robinson, and F. Rodriguez-quinones, Bacterial iron homeostasis, FEMS Microbiol. Rev, vol.27, pp.215-237, 2003.

T. Baba, T. Ara, M. Hasegawa, Y. Takai, Y. Okumura et al., Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Mol. Syst. Biol, vol.2, p.8, 2006.

S. W. Bearden and R. D. Perry, The Yfe system of Yersinia pestis transports iron and manganese and is required for full virulence of plague, Mol. Microbiol, vol.32, pp.403-414, 1999.

E. Boyer, I. Bergevin, D. Malo, P. Gros, and M. F. Cellier, Acquisition of Mn(II) in addition to Fe(II) is required for full virulence of Salmonella enterica serovar Typhimurium, Infect. Immun, vol.70, pp.6032-6042, 2002.

V. Braun, Bacterial iron transport related to virulence, Contrib. Microbiol, vol.12, pp.210-233, 2005.

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. USA, vol.103, pp.12879-12884, 2006.

A. Carlioz and D. Touati, Isolation of superoxide dismutase mutants in Escherichia coli: is superoxide dismutase necessary for aerobic life?, EMBO J, vol.5, pp.623-630, 1986.

S. Casjens, Prophages and bacterial genomics: what have we learned so far?, Mol. Microbiol, vol.49, pp.277-300, 2003.

A. C. Chang and S. N. Cohen, Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid, J. Bacteriol, vol.134, pp.1141-1156, 1978.

R. R. Chaudhuri, A. M. Khan, and M. J. Pallen, coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics, Nucleic Acids Res, vol.32, pp.296-299, 2004.

S. L. Chen, C. S. Hung, J. Xu, C. S. Reigstad, V. Magrini et al.,

J. Latreille, T. M. Spieth, E. R. Hooton, S. J. Mardis, J. I. Hultgren et al., Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach, Proc. Natl. Acad. Sci. USA, vol.103, pp.5977-5982, 2006.

J. P. Claverys, A new family of high-affinity ABC manganese and zinc permeases, Res. Microbiol, vol.152, pp.231-243, 2001.

O. Clermont, S. Bonacorsi, and E. Bingen, Rapid and simple determination of the Escherichia coli phylogenetic group, Appl. Environ. Microbiol, vol.66, pp.4555-4558, 2000.

K. A. Datsenko and B. L. Wanner, One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products, Proc. Natl. Acad. Sci. USA, vol.97, pp.6640-6645, 2000.

C. M. Dozois, F. Daigle, R. Curtiss, and I. , Identification of pathogenspecific and conserved genes expressed in vivo by an avian pathogenic Escherichia coli strain, Proc. Natl. Acad. Sci. USA, vol.100, pp.247-252, 2003.

C. M. Dozois, M. Dho-moulin, A. Brée, J. M. Fairbrother, C. Desautels et al., Relationship between the Tsh autotransporter and pathogenicity of avian Escherichia coli and localization and analysis of the Tsh genetic region, Infect. Immun, vol.68, pp.4145-4154, 2000.
URL : https://hal.archives-ouvertes.fr/hal-02697225

C. Ewers, G. Li, H. Wilking, S. Kiessling, K. Alt et al., Avian pathogenic, uropathogenic, and newborn meningitis-causing Escherichia coli: how closely related are they?, Int. J. Med. Microbiol, vol.297, pp.163-176, 2007.

C. A. Ginns, M. L. Benham, L. M. Adams, K. G. Whithear, K. A. Bettelheim et al., Colonization of the respiratory tract by a virulent strain of avian Escherichia coli requires carriage of a conjugative plasmid, Infect. Immun, vol.68, pp.1535-1541, 2000.

D. Hanahan, J. Jessee, and F. R. Bloom, Techniques for transformation of E. coli, DNA cloning I: core techniques, pp.1-35, 1995.

K. Hantke, Is the bacterial ferrous iron transporter FeoB a living fossil?, Trends Microbiol, vol.11, pp.192-195, 2003.

H. M. Hassan and I. Fridovich, Intracellular production of superoxide radical and of hydrogen peroxide by redox active compounds, Arch. Biochem. Biophys, vol.196, pp.385-395, 1979.

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, J. Bacteriol, vol.172, pp.6175-6181, 1990.

M. J. Horsburgh, S. J. Wharton, M. Karavolos, and S. J. Foster, Manganese: elemental defence for a life with oxygen, Trends Microbiol, vol.10, pp.496-501, 2002.

K. Ike, K. Kawahara, H. Danbara, and K. Kume, Serum resistance and aerobactin iron uptake in avian Escherichia coli mediated by conjugative 100-megadalton plasmid, J. Vet. Med. Sci, vol.54, pp.1091-1098, 1992.

A. Janakiraman and J. M. Slauch, The putative iron transport system SitABCD encoded on SPI1 is required for full virulence of Salmonella typhimurium, Mol. Microbiol, vol.35, pp.1146-1155, 2000.

Q. Jin, Z. Yuan, J. Xu, Y. Wang, Y. Shen et al., Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157, Nucleic Acids Res, vol.30, pp.4432-4441, 2002.

T. J. Johnson, S. J. Johnson, and L. K. Nolan, Complete DNA sequence of a ColBM plasmid from avian pathogenic Escherichia coli suggests that it evolved from closely related ColV virulence plasmids, J. Bacteriol, vol.188, pp.5975-5983, 2006.

T. J. Johnson, S. Kariyawasam, Y. Wannemuehler, P. Mangiamele, S. J. Johnson et al., The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes, J. Bacteriol, vol.189, pp.3228-3236, 2007.

T. J. Johnson, K. E. Siek, S. J. Johnson, and L. K. Nolan, DNA sequence of a ColV plasmid and prevalence of selected plasmid-encoded virulence genes among avian Escherichia coli strains, J. Bacteriol, vol.188, pp.745-758, 2006.

T. H. Jukes and C. R. Cantor, Evolution of protein molecules, Mammalian protein metabolism, pp.21-132, 1969.

M. Kammler, C. Schon, and K. Hantke, Characterization of the ferrous iron uptake system of Escherichia coli, J. Bacteriol, vol.175, pp.6212-6219, 1993.

D. G. Kehres, A. Janakiraman, J. M. Slauch, and M. E. Maguire, SitABCD is the alkaline Mn 2? transporter of Salmonella enterica serovar Typhimurium, J. Bacteriol, vol.184, pp.3159-3166, 2002.

D. G. Kehres and M. E. Maguire, Emerging themes in manganese transport, biochemistry and pathogenesis in bacteria, FEMS Microbiol. Rev, vol.27, pp.263-290, 2003.

K. Keyer, A. S. Gort, and J. A. Imlay, Superoxide and the production of oxidative DNA damage, J. Bacteriol, vol.177, pp.6782-6790, 1995.

S. Kumar, K. Tamura, and M. Nei, MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment, Brief. Bioinform, vol.5, pp.150-163, 2004.

M. G. Lamarche, C. M. Dozois, F. Daigle, M. Caza, R. Curtiss et al., Inactivation of the pst system reduces the virulence of an avian pathogenic Escherichia coli O78 strain, Infect. Immun, vol.73, pp.4138-4145, 2005.
URL : https://hal.archives-ouvertes.fr/pasteur-00720810

G. Li, C. Laturnus, C. Ewers, and L. H. Wieler, Identification of genes required for avian Escherichia coli septicemia by signature-tagged mutagenesis, Infect. Immun, vol.73, pp.2818-2827, 2005.

M. Liu, H. Liu, L. Sun, J. Dong, Y. Xue et al., Construction, detection and microarray analysis on the Shigella flexneri 2a sitC mutant, Sci. China C, vol.48, pp.228-240, 2005.

S. Lucchini, H. Liu, Q. Jin, J. C. Hinton, and J. Yu, Transcriptional adaptation of Shigella flexneri during infection of macrophages and epithelial cells: insights into the strategies of a cytosolic bacterial pathogen, Infect. Immun, vol.73, pp.88-102, 2005.

M. H. Lymberopoulos, S. Houle, F. Daigle, S. Léveillé, A. Brée et al., Characterization of Stg fimbriae from an avian pathogenic Escherichia coli O78:K80 strain and assessment of their contribution to colonization of the chicken respiratory tract, J. Bacteriol, vol.188, pp.6449-6459, 2006.
URL : https://hal.archives-ouvertes.fr/pasteur-00720804

H. Makui, E. Roig, S. T. Cole, J. D. Helmann, P. Gros et al., , p.610

, Identification of the Escherichia coli K-12 Nramp orthologue (MntH) as a selective divalent metal ion transporter, Mol. Microbiol, vol.35, pp.1065-1078

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, pp.852-856, 2001.

P. Mehta, S. Casjens, and S. Krishnaswamy, Analysis of the lambdoid prophage element e14 in the E. coli K-12 genome, BMC Microbiol, vol.4, p.4, 2004.

M. Mellata, M. Dho-moulin, C. M. Dozois, R. Curtiss, I. et al., Role of avian pathogenic Escherichia coli virulence factors in bacterial interaction with chicken heterophils and macrophages, Infect. Immun, vol.71, pp.494-503, 2003.
URL : https://hal.archives-ouvertes.fr/hal-02676834

V. L. Miller, R. K. Taylor, and J. J. Mekalanos, Cholera toxin transcriptional activator toxR is a transmembrane DNA binding protein, Cell, vol.48, pp.271-279, 1987.

M. Ohnishi, K. Kurokawa, and T. Hayashi, Diversification of Escherichia coli genomes: are bacteriophages the major contributors?, Trends Microbiol, vol.9, pp.481-485, 2001.

D. L. Provence, R. Curtiss, and I. , Role of crl in avian pathogenic Escherichia coli: a knockout mutation of crl does not affect hemagglutination activity, fibronectin binding, or Curli production, Infect. Immun, vol.60, pp.4460-4467, 1992.

C. Restieri, G. Garriss, M. C. Locas, and C. M. Dozois, Autotransporter-encoding sequences are phylogenetically distributed among Escherichia coli clinical isolates and reference strains, Appl. Environ. Microbiol, vol.73, pp.1553-1562, 2007.
URL : https://hal.archives-ouvertes.fr/pasteur-00720799

E. Richer, P. Courville, I. Bergevin, and M. F. Cellier, Horizontal gene transfer of "prototype" Nramp in bacteria, J. Mol. Evol, vol.57, pp.363-376, 2003.

K. E. Rodriguez-siek, C. W. Giddings, C. Doetkott, T. J. Johnson, M. K. Fakhr et al., Comparison of Escherichia coli isolates implicated in human urinary tract infection and avian colibacillosis, Microbiology, vol.151, pp.2097-2110, 2005.

K. E. Rodriguez-siek, C. W. Giddings, C. Doetkott, T. J. Johnson, and L. K. Nolan, Characterizing the APEC pathotype, Vet. Res, vol.36, pp.241-256, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00902960

V. Roos, G. C. Ulett, M. A. Schembri, and P. Klemm, The asymptomatic bacteriuria Escherichia coli strain 83972 outcompetes uropathogenic E. coli strains in human urine, Infect. Immun, vol.74, pp.615-624, 2006.

L. Runyen-janecky, E. Dazenski, S. Hawkins, and L. Warner, Role and regulation of the Shigella flexneri Sit and MntH systems, Infect. Immun, vol.74, pp.4666-4672, 2006.

L. J. Runyen-janecky and S. M. Payne, Identification of chromosomal Shigella flexneri genes induced by the eukaryotic intracellular environment, Infect. Immun, vol.70, pp.4379-4388, 2002.

L. J. Runyen-janecky, S. A. Reeves, E. G. Gonzales, and S. M. Payne, Contribution of the Shigella flexneri Sit, Iuc, and Feo iron acquisition systems to iron acquisition in vitro and in cultured cells, Infect. Immun, vol.71, pp.1919-1928, 2003.

M. Sabri, S. Léveillé, and C. M. Dozois, A SitABCD homologue from an avian pathogenic Escherichia coli strain mediates transport of iron and manganese and resistance to hydrogen peroxide, Microbiology, vol.152, pp.745-758, 2006.
URL : https://hal.archives-ouvertes.fr/pasteur-00720808

N. Saitou and M. Nei, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol, vol.4, pp.406-425, 1987.

J. Sambrook and D. W. Russell, Molecular cloning: a laboratory manual, 2001.

C. Schouler, F. Koffmann, C. Amory, S. Leroy-setrin, and M. Moulin-schouleur, Genomic subtraction for the identification of putative new virulence factors of an avian pathogenic Escherichia coli strain of O2 serogroup, Microbiology, vol.150, pp.2973-2984, 2004.
URL : https://hal.archives-ouvertes.fr/hal-02683268

C. E. Schwartz, J. Krall, L. Norton, K. Mckay, D. Kay et al., Catalase and superoxide dismutase in Escherichia coli, J. Biol. Chem, vol.258, pp.6277-6281, 1983.

J. A. Skyberg, T. J. Johnson, J. R. Johnson, C. Clabots, C. M. Logue et al., Acquisition of avian pathogenic Escherichia coli plasmids by a commensal E. coli isolate enhances its abilities to kill chicken embryos, grow in human urine, and colonize the murine kidney, Infect. Immun, vol.74, pp.6287-6292, 2006.

H. W. Smith, A search for transmissible pathogenic characters in invasive strains of Escherichia coli: the discovery of a plasmid-controlled toxin and a plasmid-controlled lethal character closely associated, or identical, with colicine V, J. Gen. Microbiol, vol.83, pp.95-111, 1974.

J. A. Snyder, B. J. Haugen, E. L. Buckles, C. V. Lockatell, D. E. Johnson et al., Transcriptome of uropathogenic Escherichia coli during urinary tract infection, Infect. Immun, vol.72, pp.6373-6381, 2004.

K. A. Tivendale, J. L. Allen, C. A. Ginns, B. S. Crabb, and G. F. Browning, Association of iss and iucA, but not tsh, with plasmid-mediated virulence of avian pathogenic Escherichia coli, Infect. Immun, vol.72, pp.6554-6560, 2004.

A. G. Torres, P. Redford, R. A. Welch, and S. M. Payne, TonBdependent systems of uropathogenic Escherichia coli: aerobactin and heme transport and TonB are required for virulence in the mouse, Infect. Immun, vol.69, pp.6179-6185, 2001.

J. Wei, M. B. Goldberg, V. Burland, M. M. Venkatesan, W. Deng et al., Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T, Infect. Immun, vol.71, pp.2775-2786, 2003.

R. A. Welch, V. Burland, G. Plunkett, I. , P. Redford et al., Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli, Proc. Natl. Acad. Sci. USA, vol.99, pp.17020-17024, 2002.

D. Zhou, W. D. Hardt, and J. E. Galan, Salmonella typhimurium encodes a putative iron transport system within the centisome 63 pathogenicity island, Infect. Immun, vol.67, pp.1974-1981, 1999.

C. Sitabcd, . To-apec-o78, and . Virulence, , p.611