B. Bachmann, Derivations and genotypes of some mutant derivatives of Escherichia coli K-12 In Escherichia coli and Salmonella typhimurium: cellular and molecular biology, 2004.

J. Hobman, C. Penn, and M. Pallen, Laboratory strains of Escherichia coli: model citizens or deceitful delinquents growing old disgracefully?, Molecular Microbiology, vol.103, issue.4, pp.881-885, 2007.
DOI : 10.1073/pnas.252529799

M. Savageau, Escherichia coli Habitats, Cell Types, and Molecular Mechanisms of Gene Control, The American Naturalist, vol.122, issue.6, pp.732-744, 1983.
DOI : 10.1086/284168

M. Donnenberg, Escherichia coli Virulence mechanisms of a versatile pathogen, 2002.

K. Rolland, N. Lambert-zeschovsky, B. Picard, and E. Denamur, Shigella and enteroinvasive Escherichia coli strains are derived from distinct ancestral strains of E. coli, Microbiology, vol.144, issue.9, pp.2667-2672, 1998.
DOI : 10.1099/00221287-144-9-2667

G. Pupo, R. Lan, and P. Reeves, Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics, Proceedings of the National Academy of Sciences, vol.97, issue.19, pp.10567-10572, 2000.
DOI : 10.1073/pnas.180094797

P. Escobar-páramo, C. Giudicelli, C. Parsot, and E. Denamur, The Evolutionary History of Shigella and Enteroinvasive Escherichia coli Revised, Journal of Molecular Evolution, vol.57, issue.2, pp.140-148, 2003.
DOI : 10.1007/s00239-003-2460-3

K. Kotloff, J. Winickoff, B. Ivanoff, J. Clemens, and D. Swerdlow, Global burden of Shigella infections: implications for vaccine development and implementation of control strategies, Bull World Health Organ, vol.77, pp.651-66, 1999.

M. Kosek, C. Bern, and R. Guerrant, The global burden of diarrhoeal disease, as estimated from studies published between 1992 and, Bull World Health Organ, vol.81, pp.197-204, 2000.

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

H. Ochman and R. Selander, Standard reference strains of Escherichia coli from natural populations, J Bacteriol, vol.157, pp.690-693, 1984.

R. Selander, D. Caugant, and T. Whittam, Genetic structure and variation in natural populations of Escherichia coli, Escherichia coli and Salmonella typhimurium: cellular and molecular biology, pp.1625-1648, 1987.

P. Herzer, S. Inouye, M. Inouye, and T. 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

P. Desjardins, B. Picard, B. Kaltenbock, 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

O. Clermont, S. Bonacorsi, and E. Bingen, Rapid and Simple Determination of the Escherichia coli Phylogenetic Group, Applied and Environmental Microbiology, vol.66, issue.10, pp.4555-4558, 2000.
DOI : 10.1128/AEM.66.10.4555-4558.2000

P. Escobar-páramo, A. Sabbagh, P. Darlu, O. Pradillon, and C. Vaury, Decreasing the effects of horizontal gene transfer on bacterial phylogeny: the Escherichia coli case study, Molecular Phylogenetics and Evolution, vol.30, issue.1, pp.243-250, 2004.
DOI : 10.1016/S1055-7903(03)00181-7

T. Wirth, D. Falush, R. Lan, F. Colles, and P. Mensa, Sex and virulence in Escherichia coli: an evolutionary perspective, Molecular Microbiology, vol.179, issue.5, pp.1136-1151, 2006.
DOI : 10.1111/j.1365-2958.2005.04985.x

URL : https://hal.archives-ouvertes.fr/hal-00174910

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

D. Gordon, The influence of ecological factors on the distribution and genetic structure of Escherichia coli In Escherichia coli and Salmonella typhimurium: cellular and molecular biology, 2004.

E. Boyd and D. Hartl, Chromosomal regions specific to pathogenic isolates of Escherichia coli have a phylogenetically clustered distribution, J Bacteriol, vol.180, pp.1159-1165, 1998.

P. Escobar-páramo, O. Clermont, A. 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

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

S. Walk, E. Alm, L. Calhoun, J. Mladonicky, and T. Whittam, Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches, Environmental Microbiology, vol.61, issue.6, pp.2274-2288, 2007.
DOI : 10.1111/j.1365-2958.2006.05172.x

L. Zhang, B. Foxman, and C. Marrs, Both Urinary and Rectal Escherichia coli Isolates Are Dominated by Strains of Phylogenetic Group B2, Journal of Clinical Microbiology, vol.40, issue.11, pp.3951-3955, 2002.
DOI : 10.1128/JCM.40.11.3951-3955.2002

P. Escobar-páramo, K. Grenet, L. Menac-'h, A. Rode, L. Salgado et al., Large-Scale Population Structure of Human Commensal Escherichia coli Isolates, Applied and Environmental Microbiology, vol.70, issue.9, pp.5698-5700, 2004.
DOI : 10.1128/AEM.70.9.5698-5700.2004

D. Guttman and D. Dykhuizen, Clonal divergence in Escherichia coli as a result of recombination, not mutation, Science, vol.266, issue.5189, pp.1380-1383, 1994.
DOI : 10.1126/science.7973728

C. Médigue, T. Rouxel, P. Vigier, A. Henaut, and A. Danchin, Evidence for horizontal gene transfer in Escherichia coli speciation, Journal of Molecular Biology, vol.222, issue.4, pp.851-856, 1991.
DOI : 10.1016/0022-2836(91)90575-Q

J. Lawrence and H. Ochman, Molecular archaeology of the Escherichia coli genome, Proceedings of the National Academy of Sciences, vol.95, issue.16, pp.9413-9417, 1998.
DOI : 10.1073/pnas.95.16.9413

R. Welch, V. Burland, G. Plunkett, R. P. Roesch, and P. , Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli, Proceedings of the National Academy of Sciences, vol.99, issue.26, pp.17020-17024, 2002.
DOI : 10.1073/pnas.252529799

J. Lawrence, H. Ochman, and D. Hartl, Molecular and evolutionary relationships among enteric bacteria, Journal of General Microbiology, vol.137, issue.8, pp.1911-1921, 1991.
DOI : 10.1099/00221287-137-8-1911

J. Johnson, O. Clermont, M. Menard, M. Kuskowski, and B. Picard, Isolates, in Relation to Accessory Traits, Phylogenetic Group, and Ecological Source, The Journal of Infectious Diseases, vol.194, issue.8, pp.1141-1150, 2006.
DOI : 10.1086/507305

N. Thomson, S. Baker, D. Pickard, M. Fookes, and M. Anjum, The Role of Prophage-like Elements in the Diversity of Salmonella enterica Serovars, Journal of Molecular Biology, vol.339, issue.2, pp.279-300, 2004.
DOI : 10.1016/j.jmb.2004.03.058

H. Willenbrock, P. Hallin, T. Wassenaar, and D. Ussery, Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray, Genome Biology, vol.8, issue.12, p.267, 2007.
DOI : 10.1186/gb-2007-8-12-r267

T. Baba, A. T. Hasegawa, M. Takai, Y. Okumura, and Y. , Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Molecular Systems Biology, vol.170, p.8, 2006.
DOI : 10.1038/msb4100050

E. Lerat and H. Ochman, Recognizing the pseudogenes in bacterial genomes, Nucleic Acids Research, vol.33, issue.10, pp.3125-3132, 2005.
DOI : 10.1093/nar/gki631

URL : https://hal.archives-ouvertes.fr/hal-00427776

G. Fang, E. Rocha, and A. Danchin, How Essential Are Nonessential Genes?, Molecular Biology and Evolution, vol.22, issue.11, pp.2147-2156, 2005.
DOI : 10.1093/molbev/msi211

G. Mcvean, P. Awadalla, and P. Fearnhead, A coalescent-based method for detecting and estimating recombination from gene sequences, Genetics, vol.160, pp.1231-1241, 2002.

B. Padhukasahasram, J. Wall, P. Marjoram, and M. Nordborg, Estimating Recombination Rates From Single-Nucleotide Polymorphisms Using Summary Statistics, Genetics, vol.174, issue.3, pp.1517-1528, 2006.
DOI : 10.1534/genetics.106.060723

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1667054

M. Beaumont, W. Zhang, and D. Balding, Approximate Bayesian computation in population genetics, Genetics, vol.162, pp.2025-2035, 2002.

L. Excoffier, A. Estoup, and J. Cornuet, Bayesian Analysis of an Admixture Model With Mutations and Arbitrarily Linked Markers, Genetics, vol.169, issue.3, pp.1727-1738, 2005.
DOI : 10.1534/genetics.104.036236

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.2373-2384, 2007.
DOI : 10.1093/molbev/msm172

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

M. Mckane and R. Milkman, Transduction, restriction and recombination patterns in Escherichia coli, Genetics, vol.139, pp.35-43, 1995.

M. Vulic, F. Dionisio, F. Taddei, and M. Radman, Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria, Proceedings of the National Academy of Sciences, vol.94, issue.18, pp.9763-9767, 1997.
DOI : 10.1073/pnas.94.18.9763

D. Robinson and L. Foulds, Comparison of phylogenetic trees, Mathematical Biosciences, vol.53, issue.1-2, pp.131-147, 1981.
DOI : 10.1016/0025-5564(81)90043-2

J. Johnson, K. Owens, C. Clabots, S. Weissman, and S. Cannon, Phylogenetic relationships among clonal groups of extraintestinal pathogenic Escherichia coli as assessed by multi-locus sequence analysis, Microbes and Infection, vol.8, issue.7, pp.1702-1713, 2006.
DOI : 10.1016/j.micinf.2006.02.007

G. Lecointre, L. Rachdi, P. Darlu, and E. Denamur, Escherichia coli molecular phylogeny using the incongruence length difference test, Molecular Biology and Evolution, vol.15, issue.12, pp.1685-1695, 1998.
DOI : 10.1093/oxfordjournals.molbev.a025895

S. Reid, C. Herbelin, A. Bumbaugh, R. Selander, and T. Whittam, Parallel evolution of virulence in pathogenic Escherichia coli, Nature, vol.406, pp.64-67, 2000.

R. Hershberg, H. Tang, and D. Petrov, Reduced selection leads to accelerated gene loss in Shigella, Genome Biology, vol.8, issue.8, p.164, 2007.
DOI : 10.1186/gb-2007-8-8-r164

B. Snel, P. Bork, and M. Huynen, Genome phylogeny based on gene content, Nature Genetics, vol.21, issue.1, pp.108-110, 1999.
DOI : 10.1038/5052

U. Dobrindt, B. Hochhut, U. Hentschel, and J. Hacker, Genomic islands in pathogenic and environmental microorganisms, Nature Reviews Microbiology, vol.31, issue.5, pp.414-424, 2004.
DOI : 10.1006/plas.1997.1280

A. Maurelli, R. Fernandez, C. Bloch, C. Rode, and A. Fasano, "Black holes" and bacterial pathogenicity: A large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli, Proceedings of the National Academy of Sciences, vol.95, issue.7, pp.3943-3948, 1998.
DOI : 10.1073/pnas.95.7.3943

M. Lane and H. 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

H. Jiang, C. Yang, H. Qu, Z. Liu, and Q. Fu, Cloning of a Novel Aldo-Keto Reductase Gene from Klebsiella sp. Strain F51-1-2 and Its Functional Expression in Escherichia coli, Applied and Environmental Microbiology, vol.73, issue.15, pp.4959-4965, 2007.
DOI : 10.1128/AEM.02993-06

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

C. Buchrieser, P. Glaser, C. Rusniok, H. Nedjari, D. Hauteville et al., The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri, Molecular Microbiology, vol.11, issue.4, pp.760-771, 2000.
DOI : 10.1038/358167a0

V. Cooper and R. Lenski, The population genetics of ecological specialization in evolving Escherichia coli populations, Nature, vol.407, issue.6805, pp.736-745, 2000.
DOI : 10.1038/35037572

I. Fernandez, M. Silva, R. Schuch, W. Walker, and A. Siber, from the Phagolysosome: A Connection between Bacterial Dissemination and Neutrophil Transepithelial Signaling, The Journal of Infectious Diseases, vol.184, issue.6, pp.743-745, 2001.
DOI : 10.1086/323035

E. Rocha, The Organization of the Bacterial Genome, Annual Review of Genetics, vol.42, issue.1, pp.211-233, 2008.
DOI : 10.1146/annurev.genet.42.110807.091653

H. Ochman and I. Jones, Evolutionary dynamics of full genome content in Escherichia coli, The EMBO Journal, vol.19, issue.24, pp.6637-6643, 2000.
DOI : 10.1093/emboj/19.24.6637

U. Bergthorsson and H. Ochman, Distribution of chromosome length variation in natural isolates of Escherichia coli, Molecular Biology and Evolution, vol.15, issue.1, pp.6-16, 1998.
DOI : 10.1093/oxfordjournals.molbev.a025847

E. Groisman and H. Ochman, Pathogenicity Islands: Bacterial Evolution in Quantum Leaps, Cell, vol.87, issue.5, pp.791-794, 1996.
DOI : 10.1016/S0092-8674(00)81985-6

J. Hacker and J. Kaper, Pathogenicity Islands and the Evolution of Microbes, Annual Review of Microbiology, vol.54, issue.1, pp.641-679, 2000.
DOI : 10.1146/annurev.micro.54.1.641

L. Frost, R. Leplae, A. Summers, and A. Toussaint, Mobile genetic elements: the agents of open source evolution, Nature Reviews Microbiology, vol.11, issue.9, pp.722-732, 2005.
DOI : 10.1093/nar/gkh059

N. Garcia-russell, T. Harmon, T. Le, N. Amaladas, and R. Mathewson, Unequal access of chromosomal regions to each other in Salmonella: probing chromosome structure with phage ?? integrase-mediated long-range rearrangements, Molecular Microbiology, vol.257, issue.2, pp.329-344, 2004.
DOI : 10.1111/j.1365-2958.2004.03976.x

E. Sokurenko, V. Chesnokova, D. Dykhuizen, I. Ofek, and X. Wu, Pathogenic adaptation of Escherichia coli by natural variation of the FimH adhesin, Proceedings of the National Academy of Sciences, vol.95, issue.15, pp.8922-8926, 1998.
DOI : 10.1073/pnas.95.15.8922

R. Milkman, E. Jaeger, and R. Mcbride, Molecular evolution of the Escherichia coli chromosome. VI. Two regions of high effective recombination, Genetics, vol.163, pp.475-483, 2003.

S. Weissman, S. Chattopadhyay, P. Aprikian, M. Obata-yasuoka, and Y. Yarova-yarovaya, Clonal analysis reveals high rate of structural mutations in fimbrial adhesins of extraintestinal pathogenic Escherichia coli, Molecular Microbiology, vol.165, issue.3, pp.975-988, 2006.
DOI : 10.1073/pnas.252529799

S. Schubert, P. Darlu, O. Clermont, A. Wieser, and G. Magistro, Role of Intraspecies Recombination in the Spread of Pathogenicity Islands within the Escherichia coli Species, PLoS Pathogens, vol.172, issue.1, 2008.
DOI : 10.1371/journal.ppat.1000257.s007

E. Denamur, G. Lecointre, P. Darlu, O. Tenaillon, and C. Acquaviva, Evolutionary Implications of the Frequent Horizontal Transfer of Mismatch Repair Genes, Cell, vol.103, issue.5, pp.711-721, 2000.
DOI : 10.1016/S0092-8674(00)00175-6

R. Barrangou, C. Fremaux, H. Deveau, M. Richards, and P. Boyaval, CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes, Science, vol.315, issue.5819, pp.1709-1712, 2007.
DOI : 10.1126/science.1138140

N. Kaplan, T. Darden, and R. Hudson, The coalescent process in models with selection, Genetics, vol.120, pp.819-829, 1988.

V. Daubin and G. Perriere, G+C3 Structuring Along the Genome: A Common Feature in Prokaryotes, Molecular Biology and Evolution, vol.20, issue.4, pp.471-483, 2003.
DOI : 10.1093/molbev/msg022

URL : https://hal.archives-ouvertes.fr/hal-00427485

P. Sharp, D. Shields, K. Wolfe, and W. Li, Chromosomal location and evolutionary rate variation in enterobacterial genes, Science, vol.246, issue.4931, pp.808-810, 1989.
DOI : 10.1126/science.2683084

R. Hudson, U. Bergthorsson, J. Roth, and H. Ochman, Effect of Chromosome Location on Bacterial Mutation Rates, Molecular Biology and Evolution, vol.19, issue.1, pp.85-92, 2002.
DOI : 10.1093/oxfordjournals.molbev.a003986

B. Charlesworth, M. Morgan, and D. Charlesworth, The effect of deleterious mutations on neutral molecular variation, Genetics, vol.134, pp.1289-1303, 1993.

K. Balbi, E. Rocha, and E. Feil, The Temporal Dynamics of Slightly Deleterious Mutations in Escherichia coli and Shigella spp., Molecular Biology and Evolution, vol.26, issue.2, 2008.
DOI : 10.1093/molbev/msn252

N. Galtier, G. Piganeau, D. Mouchiroud, and L. Duret, GC-content evolution in mammalian genomes: the biased gene conversion hypothesis, Genetics, vol.159, pp.907-911, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00427173

E. Rocha, M. Touchon, and E. Feil, Similar compositional biases are caused by very different mutational effects, Genome Research, vol.16, issue.12, pp.1537-1547, 2006.
DOI : 10.1101/gr.5525106

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665637

E. Couturier and E. Rocha, Replication-associated gene dosage effects shape the genomes of fast-growing bacteria but only for transcription and translation genes, Molecular Microbiology, vol.52, issue.5, pp.1506-1518, 2006.
DOI : 10.1111/j.1365-2958.2006.05046.x

T. Treangen, O. Ambur, T. Tonjum, and E. Rocha, The impact of the neisserial DNA uptake sequences on genome evolution and stability, Genome Biology, vol.9, issue.3, p.60, 2008.
DOI : 10.1186/gb-2008-9-3-r60

URL : https://hal.archives-ouvertes.fr/pasteur-00336122

M. Valens, S. Penaud, M. Rossignol, F. Cornet, and F. Boccard, Macrodomain organization of the Escherichia coli chromosome, The EMBO Journal, vol.241, issue.21, pp.4330-4341, 2004.
DOI : 10.1038/sj.emboj.7600028

H. Tettelin, V. Masignani, M. Cieslewicz, C. Donati, and D. Medini, Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome", Proceedings of the National Academy of Sciences, vol.102, issue.39, pp.13950-13955, 2005.
DOI : 10.1073/pnas.0506758102

W. Hao and G. Golding, The fate of laterally transferred genes: Life in the fast lane to adaptation or death, Genome Research, vol.16, issue.5, pp.636-643, 2006.
DOI : 10.1101/gr.4746406

G. Vernikos, N. Thomson, and J. Parkhill, Genetic flux over time in the Salmonella lineage, Genome Biology, vol.8, issue.6, p.100, 2007.
DOI : 10.1186/gb-2007-8-6-r100

C. Mossoro, P. Glaziou, S. Yassibanda, N. Lan, and C. Bekondi, Chronic Diarrhea, Hemorrhagic Colitis, and Hemolytic-Uremic Syndrome Associated with HEp-2 Adherent Escherichia coli in Adults Infected with Human Immunodeficiency Virus in Bangui, Central African Republic, Journal of Clinical Microbiology, vol.40, issue.8, pp.3086-3088, 2002.
DOI : 10.1128/JCM.40.8.3086-3088.2002

C. Bernier, P. Gounon, L. Bouguénec, and C. , Identification of an Aggregative Adhesion Fimbria (AAF) Type III-Encoding Operon in Enteroaggregative Escherichia coli as a Sensitive Probe for Detecting the AAF-Encoding Operon Family, Infection and Immunity, vol.70, issue.8, pp.4302-4313, 2002.
DOI : 10.1128/IAI.70.8.4302-4311.2002

A. Manges, J. Johnson, B. Foxman, O. Bryan, T. Fullerton et al., Clonal Group, New England Journal of Medicine, vol.345, issue.14, pp.1007-1013, 2001.
DOI : 10.1056/NEJMoa011265

S. Bonacorsi, O. Clermont, V. Houdouin, C. Cordevant, and N. Brahimi, Neonatal Meningitis Isolates: Identification of a New Virulent Clone, The Journal of Infectious Diseases, vol.187, issue.12, pp.1895-1906, 2003.
DOI : 10.1086/375347

J. Farmer, G. Fanning, B. Davis, O. Hara, C. Riddle et al., Escherichia fergusonii and Enterobacter taylorae, two new species of Enterobacteriaceae isolated from clinical specimens, J Clin Microbiol, vol.21, pp.77-81, 1985.

A. Chaudhury, G. Nath, A. Tikoo, and S. Sanyal, Enteropathogenicity and antimicrobial susceptibility of new Escherichia spp, J Diarrhoeal Dis Res, vol.17, pp.85-87, 1999.

A. Mahapatra, S. Mahapatra, and A. Mahapatra, Escherichia fergusonii: An emerging pathogen in South Orissa, Indian Journal of Medical Microbiology, vol.23, issue.3, p.204, 2005.
DOI : 10.4103/0255-0857.16598

D. Vallenet, P. Nordmann, V. Barbe, L. Poirel, and S. Mangenot, Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles, PLoS ONE, vol.20, issue.3, p.1805, 2008.
DOI : 10.1371/journal.pone.0001805.s003

S. Bocs, S. Cruveiller, D. Vallenet, G. Nuel, and C. Medigue, AMIGene: Annotation of MIcrobial Genes, Nucleic Acids Research, vol.31, issue.13, pp.3723-3726, 2003.
DOI : 10.1093/nar/gkg590

URL : https://hal.archives-ouvertes.fr/hal-00271511

D. Vallenet, L. Labarre, Z. Rouy, V. Barbe, and S. Bocs, MaGe: a microbial genome annotation system supported by synteny results, Nucleic Acids Research, vol.34, issue.1, pp.53-65, 2006.
DOI : 10.1093/nar/gkj406

M. Riley, T. Abe, M. Arnaud, M. Berlyn, and F. Blattner, Escherichia coli K-12: a cooperatively developed annotation snapshot--2005, Nucleic Acids Research, vol.34, issue.1, pp.1-9, 2005.
DOI : 10.1093/nar/gkj405

S. Cruveiller, L. Saux, J. Vallenet, D. Lajus, A. Bocs et al., MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes, Nucleic Acids Research, vol.33, issue.Web Server, pp.471-479, 2005.
DOI : 10.1093/nar/gki498

A. Darling, B. Mau, F. Blattner, and N. Perna, Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements, Genome Research, vol.14, issue.7, pp.1394-1403, 2004.
DOI : 10.1101/gr.2289704

H. Chiapello, A. Gendrault, C. Caron, J. Blum, and M. Petit, MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level, BMC Bioinformatics, vol.9, issue.1, p.948, 2008.
DOI : 10.1186/1471-2105-9-498

URL : https://hal.archives-ouvertes.fr/hal-00489678

K. Katoh, K. Kuma, H. Toh, and T. Miyata, MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Research, vol.33, issue.2, pp.511-518, 2005.
DOI : 10.1093/nar/gki198

H. Schmidt, K. Strimmer, M. Vingron, and A. Von-haeseler, TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing, Bioinformatics, vol.18, issue.3, pp.502-504, 2002.
DOI : 10.1093/bioinformatics/18.3.502

O. Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Molecular Biology and Evolution, vol.14, issue.7, pp.685-695, 1997.
DOI : 10.1093/oxfordjournals.molbev.a025808

URL : https://hal.archives-ouvertes.fr/lirmm-00730410

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

Z. Yang, PAML: a program package for phylogenetic analysis by maximum likelihood, Bioinformatics, vol.13, issue.5, pp.555-556, 1997.
DOI : 10.1093/bioinformatics/13.5.555

H. Shimodaira and M. Hasegawa, Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference, Molecular Biology and Evolution, vol.16, issue.8, pp.1114-1116, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026201

H. Kishino and M. Hasegawa, Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea, Journal of Molecular Evolution, vol.46, issue.2, pp.170-179, 1989.
DOI : 10.1007/BF02100115

N. Goldman, J. Anderson, and A. Rodrigo, Likelihood-Based Tests of Topologies in Phylogenetics, Systematic Biology, vol.49, issue.4, pp.652-670, 2000.
DOI : 10.1080/106351500750049752

K. Strimmer and A. Rambaut, Inferring confidence sets of possibly misspecified gene trees, Proceedings of the Royal Society B: Biological Sciences, vol.269, issue.1487, pp.137-142, 2002.
DOI : 10.1098/rspb.2001.1862

J. Felsenstein, Evolutionary trees from DNA sequences: A maximum likelihood approach, Journal of Molecular Evolution, vol.24, issue.6, pp.368-376, 1981.
DOI : 10.1007/BF01734359

R. Hudson, Generating samples under a Wright-Fisher neutral model of genetic variation, Bioinformatics, vol.18, issue.2, pp.337-338, 2002.
DOI : 10.1093/bioinformatics/18.2.337

A. Rambaut and N. Grassly, Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees, Bioinformatics, vol.13, issue.3, pp.235-238, 1997.
DOI : 10.1093/bioinformatics/13.3.235

E. Paradis, C. J. Strimmer, and K. , APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-290, 2004.
DOI : 10.1093/bioinformatics/btg412

J. Felsenstein, Phylogenies and the Comparative Method, The American Naturalist, vol.125, issue.1, pp.1-15, 1985.
DOI : 10.1086/284325

M. Pagel, Detecting Correlated Evolution on Phylogenies: A General Method for the Comparative Analysis of Discrete Characters, Proceedings of the Royal Society B: Biological Sciences, vol.255, issue.1342, pp.37-45, 1994.
DOI : 10.1098/rspb.1994.0006

F. Blattner, G. Iii, C. Bloch, N. Perna, and V. Burland, The Complete Genome Sequence of Escherichia coli K-12, Science, vol.277, issue.5331, pp.1453-1461, 1997.
DOI : 10.1126/science.277.5331.1453

F. Yang, Y. J. Zhang, X. Chen, L. Jiang, and Y. , Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery, Nucleic Acids Research, vol.33, issue.19, pp.6445-6458, 2005.
DOI : 10.1093/nar/gki954

Q. Jin, Z. Yuan, J. Xu, Y. Wang, and Y. Shen, Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157, Nucleic Acids Research, vol.30, issue.20, pp.4432-4441, 2002.
DOI : 10.1093/nar/gkf566

J. Wei, M. Goldberg, V. Burland, M. Venkatesan, and W. Deng, Complete Genome Sequence and Comparative Genomics of Shigella flexneri Serotype 2a Strain 2457T, Infection and Immunity, vol.71, issue.5, pp.2775-2786, 2003.
DOI : 10.1128/IAI.71.5.2775-2786.2003

H. Nie, F. Yang, X. Zhang, Y. J. Chen, and L. , Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a, BMC Genomics, vol.7, issue.1, p.173, 2006.
DOI : 10.1186/1471-2164-7-173

N. Perna, G. Plunkett, V. Burland, B. Mau, and J. Glasner, Genome sequence of enterohaemorrhagic Escherichia coli O157:H7, Nature, vol.409, issue.6819, pp.529-533, 2001.
DOI : 10.1038/35054089

T. Hayashi, K. Makino, M. Ohnishi, K. Kurokawa, and K. Ishii, 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

S. Chen, C. Hung, J. Xu, C. Reigstad, and V. Magrini, 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

T. Johnson, S. Kariyawasam, Y. Wannemuehler, P. Mangiamele, and S. Johnson, The Genome Sequence of Avian Pathogenic Escherichia coli Strain O1:K1:H7 Shares Strong Similarities with Human Extraintestinal Pathogenic E. coli Genomes, Journal of Bacteriology, vol.189, issue.8, pp.3228-3236, 2007.
DOI : 10.1128/JB.01726-06

E. Brzuszkiewicz, H. Bruggemann, H. Liesegang, M. Emmerth, and T. Olschlager, How to become a uropathogen: Comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains, Proceedings of the National Academy of Sciences, vol.103, issue.34, pp.12879-12884, 2006.
DOI : 10.1073/pnas.0603038103

M. Serres, S. Goswami, and M. Riley, GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins, Nucleic Acids Research, vol.32, issue.90001, pp.300-302, 2004.
DOI : 10.1093/nar/gkh087

F. Tajima, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, vol.123, pp.585-595, 1989.

R. Gil, F. Silva, J. Pereto, and A. Moya, Determination of the Core of a Minimal Bacterial Gene Set, Microbiology and Molecular Biology Reviews, vol.68, issue.3, pp.518-537, 2004.
DOI : 10.1128/MMBR.68.3.518-537.2004