A. Kostic, R. Xavier, and D. Gevers, The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead, Gastroenterology, vol.146, issue.6, pp.1489-99, 2014.
DOI : 10.1053/j.gastro.2014.02.009

L. Jostins, S. Ripke, and R. Weersma, Host???microbe interactions have shaped the genetic architecture of inflammatory bowel disease, Nature, vol.286, issue.7422, pp.119-143, 2012.
DOI : 10.1074/jbc.M111.291492

J. Van-sommeren, S. Huang, and H. , Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations, Nat Genet, vol.47, pp.979-86, 2015.

D. Gevers, S. Kugathasan, and L. Denson, The Treatment-Naive Microbiome in New-Onset Crohn???s Disease, Cell Host & Microbe, vol.15, issue.3, pp.382-92, 2014.
DOI : 10.1016/j.chom.2014.02.005

S. Kang, S. Denman, and M. Morrison, Dysbiosis of fecal microbiota in Crohn??s disease patients as revealed by a custom phylogenetic microarray, Inflammatory Bowel Diseases, vol.16, issue.12, pp.2034-2076, 2010.
DOI : 10.1002/ibd.21319

X. Morgan, T. Tickle, and H. Sokol, Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment, Genome Biology, vol.13, issue.9, p.79, 2012.
DOI : 10.1186/gb-2011-12-6-r60

URL : https://hal.archives-ouvertes.fr/hal-00736429

C. Brien, P. Pavli, and D. Gordon, Detection of bacterial DNA in lymph nodes of Crohn's disease patients using high throughput sequencing, Gut, vol.326, issue.(Pt 8), pp.1596-606, 2014.
DOI : 10.1126/science.1177486

D. , S. Amand, A. Feldman, and R. , Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases, Proc Natl Acad Sci, vol.104, pp.13780-13785, 2007.

A. Darfeuille-michaud, J. Boudeau, and P. Bulois, High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn???s disease, Gastroenterology, vol.127, issue.2, pp.412-433, 2004.
DOI : 10.1053/j.gastro.2004.04.061

R. Kotlowski, C. Bernstein, and S. Sepehri, High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease, Gut, vol.56, issue.5, pp.669-75, 2007.
DOI : 10.1136/gut.2006.099796

H. Martin, B. Campbell, and C. Hart, Enhanced Escherichia coli adherence and invasion in Crohn???s disease and colon cancer 1 1The authors thank Professor T. K. Korhonen (Division of General Microbiology, University of Helsinki, Finland), who kindly donated Escherichia coli IH11165; Professor J.-F. Colombel (Laboratoire de Recherche sur les Maladies Inflammatoire de l???Intestine, Centre Hospitalier Universitaire, Lille, France) and Professor A. Darfeuille-Michaud (Faculte de Pharmacie, Clermont-Ferrand, France), who kindly donated the Crohn???s disease ileal isolates LF10 and LF82; and Dr. Keith Leiper (Gastroenterology Unit, Royal Liverpool & Broadgreen University Hospitals Trust, Liverpool, UK) for his cooperation in obtaining colorectal tissue specimens.As a consequence of the work described herein, a patent application has been filed by the University of Liverpool regarding the use of soluble plantain fiber in Crohn???s disease., Gastroenterology, vol.127, issue.1, pp.80-93, 2004.
DOI : 10.1053/j.gastro.2004.03.054

M. Martinez-medina, X. Aldeguer, and M. Lopez-siles, Molecular diversity of Escherichia coli in the human gut: New ecological evidence supporting the role of adherent-invasive E. coli (AIEC) in Crohn??s disease, Inflammatory Bowel Diseases, vol.15, issue.6, pp.872-82, 2009.
DOI : 10.1002/ibd.20860

M. Mylonaki, N. Rayment, and D. Rampton, Molecular Characterization of Rectal Mucosa-Associated Bacterial Flora in Inflammatory Bowel Disease, Inflammatory Bowel Diseases, vol.11, issue.5, pp.481-488, 2005.
DOI : 10.1097/01.MIB.0000159663.62651.4f

M. Sasaki, S. Sitaraman, and B. Babbin, Invasive Escherichia coli are a feature of Crohn's disease, Laboratory Investigation, vol.115, issue.10, pp.1042-54, 2007.
DOI : 10.1016/S0002-9440(10)63051-9

J. Boudeau, A. Glasser, and E. Masseret, Invasive ability of an Escherichia coli strain isolated from the ileal mucosa of a patient with Crohn's disease, Infect Immun, vol.67, pp.4499-509, 1999.

K. Simpson, B. Dogan, and M. Rishniw, Adherent and Invasive Escherichia coli Is Associated with Granulomatous Colitis in Boxer Dogs, Infection and Immunity, vol.74, issue.8, pp.4778-92, 2006.
DOI : 10.1128/IAI.00067-06

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539603

M. Conte, C. Longhi, and M. Marazzato, Adherent-invasive Escherichia coli (AIEC) in pediatric Crohn???s disease patients: phenotypic and genetic pathogenic features, BMC Research Notes, vol.7, issue.1, p.748, 2014.
DOI : 10.1136/gutjnl-2012-304119

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4210564

O. Clermont, J. Christenson, and E. Denamur, phylo-typing method revisited: improvement of specificity and detection of new phylo-groups, Environmental Microbiology Reports, vol.1, issue.1, pp.58-65, 2013.
DOI : 10.1128/AEM.01262-09

D. Gordon, O. Brien, C. Pavli, and P. , diversity in the lower intestinal tract of humans, Environmental Microbiology Reports, vol.60, issue.4, pp.642-650, 2015.
DOI : 10.1099/jmm.0.027037-0

O. Tenaillon, D. Skurnik, and B. Picard, The population genetics of commensal Escherichia coli, Nature Reviews Microbiology, vol.75, issue.3, pp.207-224, 2010.
DOI : 10.1016/j.tig.2007.12.007

F. Jaureguy, L. Landraud, and V. Passet, Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains, BMC Genomics, vol.9, issue.1, p.560, 2008.
DOI : 10.1186/1471-2164-9-560

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639426

S. Reid, C. Herbelin, and A. Bumbaugh, Parallel evolution of virulence in pathogenic Escherichia coli, Nature, vol.406, pp.64-71, 2000.

T. Wirth, D. Falush, and R. Lan, Sex and virulence in Escherichia coli: an evolutionary perspective, Molecular Microbiology, vol.179, issue.5, pp.1136-51, 2006.
DOI : 10.1111/j.1365-2958.2005.04985.x

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

O. Clermont, J. Christenson, and A. Daubié, Development of an allele-specific PCR for Escherichia coli B2 sub-typing, a rapid and easy to perform substitute of multilocus sequence typing, Journal of Microbiological Methods, vol.101, pp.24-31, 2014.
DOI : 10.1016/j.mimet.2014.03.008

M. Martinez-medina, A. Mora, and M. Blanco, Similarity and Divergence among Adherent-Invasive Escherichia coli and Extraintestinal Pathogenic E. coli Strains, Journal of Clinical Microbiology, vol.47, issue.12, pp.3968-79, 2009.
DOI : 10.1128/JCM.01484-09

URL : http://jcm.asm.org/content/47/12/3968.full.pdf

N. Barnich, F. Carvalho, and A. Glasser, CEACAM6 acts as a receptor for adherent-invasive E. coli, supporting ileal mucosa colonization in Crohn disease, Journal of Clinical Investigation, vol.117, issue.6, pp.1566-74, 2007.
DOI : 10.1172/JCI30504

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868786

F. Carvalho, N. Barnich, and A. Sivignon, colonize and induce strong gut inflammation in transgenic mice expressing human CEACAM, The Journal of Experimental Medicine, vol.56, issue.10, pp.2179-89, 2009.
DOI : 10.1371/journal.pone.0002040

URL : http://jem.rupress.org/content/jem/206/10/2179.full.pdf

N. Dreux, J. Denizot, and M. Martinez-medina, Point Mutations in FimH Adhesin of Crohn's Disease-Associated Adherent-Invasive Escherichia coli Enhance Intestinal Inflammatory Response, PLoS Pathogens, vol.8, issue.9, p.1003141, 2013.
DOI : 10.1371/journal.ppat.1003141.s003

B. Dogan, H. Suzuki, and D. Herlekar, Inflammation-associated Adherent-invasive Escherichia coli Are Enriched in Pathways for Use of Propanediol and Iron and M-cell Translocation, Inflammatory Bowel Diseases, vol.20, issue.11, pp.1919-1951, 2014.
DOI : 10.1097/MIB.0000000000000183

URL : https://hal.archives-ouvertes.fr/hal-01332099

M. Desilets, X. Deng, and C. Rao, Genome-based Definition of an Inflammatory Bowel Disease-associated Adherent-Invasive Escherichia coli Pathovar, Inflammatory Bowel Diseases, vol.22, issue.1, pp.1-12, 2016.
DOI : 10.1097/MIB.0000000000000574

N. Deshpande, M. Wilkins, and H. Mitchell, Novel genetic markers define a subgroup of pathogenic Escherichia coli strains belonging to the B2 phylogenetic group, FEMS Microbiol Lett, vol.362, 2015.

S. Miquel, E. Peyretaillade, and L. Claret, Complete Genome Sequence of Crohn's Disease-Associated Adherent-Invasive E. coli Strain LF82, PLoS ONE, vol.277, issue.9, 2010.
DOI : 10.1371/journal.pone.0012714.s005

URL : http://doi.org/10.1371/journal.pone.0012714

M. Touchon, C. Hoede, and O. Tenaillon, 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

D. Gordon, O. Brien, C. Pavli, and P. , diversity in the lower intestinal tract of humans, Environmental Microbiology Reports, vol.60, issue.4, pp.642-650, 2015.
DOI : 10.1099/jmm.0.027037-0

D. Gordon, S. Stern, and P. Collignon, Influence of the age and sex of human hosts on the distribution of Escherichia coli ECOR groups and virulence traits, Microbiology, vol.151, issue.1, pp.15-23, 2005.
DOI : 10.1099/mic.0.27425-0

K. Joensen, A. Tetzschner, and A. Iguchi, Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data, Journal of Clinical Microbiology, vol.53, issue.8, pp.2410-2436, 2015.
DOI : 10.1128/JCM.00008-15

A. Darling, B. Mau, and F. Blattner, Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements, Genome Research, vol.14, issue.7, pp.1394-403, 2004.
DOI : 10.1101/gr.2289704

D. Vallenet, E. Belda, and A. Calteau, MicroScope???an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data, Nucleic Acids Research, vol.41, issue.D1, pp.636-683, 2013.
DOI : 10.1093/nar/gks1194

B. Chassaing, E. Garénaux, and J. Carriere, ABSTRACT, Journal of Bacteriology, vol.197, issue.8, pp.1451-65, 2015.
DOI : 10.1128/JB.02499-14

M. Bringer, N. Barnich, and A. Glasser, HtrA Stress Protein Is Involved in Intramacrophagic Replication of Adherent and Invasive Escherichia coli Strain LF82 Isolated from a Patient with Crohn's Disease, Infection and Immunity, vol.73, issue.2, pp.712-733, 2005.
DOI : 10.1128/IAI.73.2.712-721.2005

M. Bringer, N. Rolhion, and A. Glasser, The Oxidoreductase DsbA Plays a Key Role in the Ability of the Crohn's Disease-Associated Adherent-Invasive Escherichia coli Strain LF82 To Resist Macrophage Killing, Journal of Bacteriology, vol.189, issue.13, pp.4860-71, 2007.
DOI : 10.1128/JB.00233-07

K. Simonsen, G. Nielsen, and J. Bjerrum, A Role for the RNA Chaperone Hfq in Controlling Adherent-Invasive Escherichia coli Colonization and Virulence, PLoS ONE, vol.294, issue.1, p.16387, 2011.
DOI : 10.1371/journal.pone.0016387.s001

E. Vazeille, B. Chassaing, and A. Buisson, GipA Factor Supports Colonization of Peyer??s Patches by Crohn??s Disease-associated Escherichia Coli, Inflammatory Bowel Diseases, vol.22, issue.1, pp.68-81, 2016.
DOI : 10.1097/MIB.0000000000000609

B. Chassaing and A. Darfeuille-michaud, et plaques de Peyer dans la maladie de Crohn, m??decine/sciences, vol.27, issue.6-7, pp.572-575, 2011.
DOI : 10.1051/medsci/2011276003

M. Prorok-hamon, M. Friswell, and A. Alswied, are increased in inflammatory bowel disease and colon cancer, Gut, vol.317, issue.5, pp.761-70, 2014.
DOI : 10.1126/science.1140488

J. Arthur, E. Perez-chanona, and M. Mühlbauer, Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota, Science, vol.57, issue.12, pp.120-123, 2012.
DOI : 10.1073/pnas.120163297

K. Tamura, G. Stecher, and D. Peterson, MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0, Molecular Biology and Evolution, vol.30, issue.12, pp.2725-2734, 2013.
DOI : 10.1093/molbev/mst197

URL : https://academic.oup.com/mbe/article-pdf/30/12/2725/19498310/mst197.pdf

T. Treangen, B. Ondov, and S. Koren, The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes, Genome Biology, vol.15, issue.11, p.524, 2014.
DOI : 10.1038/msb4100049

J. Nuñez, A. Lee, and A. Engelman, Integrase-mediated spacer acquisition during CRISPR???Cas adaptive immunity, Nature, vol.14, issue.7542, pp.193-201, 2015.
DOI : 10.1101/gr.849004

I. Grissa, G. Vergnaud, and C. Pourcel, CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats, Nucleic Acids Research, vol.35, issue.Web Server, pp.52-59, 2007.
DOI : 10.1093/nar/gkm360

URL : https://hal.archives-ouvertes.fr/hal-00194414

J. Raisch, N. Rolhion, and A. Dubois, Intracellular colon cancer-associated Escherichia coli promote protumoral activities of human macrophages by inducing sustained COX-2 expression, Laboratory Investigation, vol.191, issue.3, pp.296-307, 2015.
DOI : 10.1124/mol.104.005199

URL : https://hal.archives-ouvertes.fr/hal-01222408

J. Masters, TIMELINEHeLa cells 50 years on: the good, the bad and the ugly, Nature Reviews Cancer, vol.2, issue.4, pp.315-334, 2002.
DOI : 10.1038/nrc775

K. Nishiyama, Y. Seto, and K. Yoshioka, Lactobacillus gasseri SBT2055 reduces infection by and colonization of Campylobacter jejuni Crohn disease--associated adherent-invasive E. coli bacteria target mouse and human Peyer's patches via long polar fimbriae, PloS ONE J Clin Invest, vol.9121, pp.966-75, 2011.

J. Denizot, A. Sivignon, and F. Barreau, Adherent-Invasive Escherichia coli Induce Claudin-2 Expression and Barrier Defect in CEABAC10 Mice and Crohn??s Disease Patients??, Inflammatory Bowel Diseases, vol.18, issue.2, pp.294-304, 2012.
DOI : 10.1002/ibd.21787

N. Bokil, M. Totsika, and A. Carey, Intramacrophage survival of uropathogenic Escherichia coli: Differences between diverse clinical isolates and between mouse and human macrophages, Immunobiology, vol.216, issue.11, pp.1164-71, 2011.
DOI : 10.1016/j.imbio.2011.05.011

S. Subramanian, C. Roberts, and C. Hart, Replication of Colonic Crohn's Disease Mucosal Escherichia coli Isolates within Macrophages and Their Susceptibility to Antibiotics, Antimicrobial Agents and Chemotherapy, vol.52, issue.2, pp.427-461, 2008.
DOI : 10.1128/AAC.00375-07

T. Elliott, B. Hudspith, and N. Rayment, in Crohn's disease, Journal of Gastroenterology and Hepatology, vol.61, issue.8, pp.1265-74, 2015.
DOI : 10.1136/gutjnl-2012-302514a.140

H. Nguyen, P. Lapaquette, and M. Bringer, Autophagy and Crohn's Disease, Journal of Innate Immunity, vol.5, issue.5, pp.434-477, 2013.
DOI : 10.1159/000345129