M. A. Karmali, V. Gannon, and J. M. Sargeant, Verocytotoxinproducing Escherichia coli (VTEC), Vet Microbiol, vol.140, pp.360-370, 2010.

D. Bibbal, E. Loukiadis, M. Kérourédan, F. Ferré, F. Dilasser et al., Prevalence of carriage of Shiga toxin-producing Escherichia coli serotypes O157:H7, O26:H11, O103:H2, O111:H8, and O145:H28 among slaughtered adult cattle in France, vol.81, pp.3315-3329, 2015.

F. Auvray, C. Lecureuil, F. Dilasser, J. Taché, and S. Derzelle, Development of a real-time PCR assay with an internal amplification control for the screening of Shiga toxin-producing Escherichia coli in foods, Lett Appl Microbiol, vol.48, pp.554-559, 2009.

J. Madic, C. Peytavin-de-garam, N. Vingadassalon, E. Oswald, P. Fach et al., Simplex and multiplex real-time PCR assays for the detection of flagellar (H-antigen) fliC alleles and intimin (eae) variants associated with enterohaemorrhagic Escherichia coli (EHEC) serotypes O26:H11, O103:H2, O111:H8, O145:H28 and O157:H7, J Appl Microbiol, vol.109, pp.1696-1705, 2010.

J. Mariette, F. Escudié, N. Allias, G. Salin, C. Noirot et al., Evaluation of the anti-terminator Q933 gene as a marker for Escherichia coli O157:H7 with high Shiga toxin production, Curr. Microbiol, vol.53, pp.324-328, 2006.

N. Amigo, E. Mercado, A. Bentancor, P. Singh, D. Vilte et al., Clade 8 and Clade 6 strains of Escherichia coli O157:H7 from cattle in Argentina have hypervirulent-like phenotypes, PLoS ONE, vol.10, p.127710, 2015.

M. S. Aschtgen, C. S. Bernard, S. De-bentzmann, R. Lloubès, C. et al., SciN is an outer membrane lipoprotein required for type VI secretion in enteroaggregative Escherichia coli, J. Bacteriol, vol.190, pp.7523-7531, 2008.

P. Auffret, A. Segura, Y. Bertin, C. Klopp, O. Bouchez et al., Draft genome sequence of enterohemorrhagic Escherichia coli O157:H7 strain MC2 isolated from cattle in France, Genome Announc, vol.5, pp.1097-1114, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01658407

F. Auvray, C. Lecureuil, F. Dilasser, É. Tach, J. et al., Development of a real-time PCR assay with an internal amplification control for the screening of Shiga toxin-producing Escherichia coli in foods, Lett. Appl. Microbiol, vol.48, pp.554-559, 2009.

D. Baines, B. Lee, and T. Mcallister, Heterogeneity in enterohemorrhagic Escherichia coli O157:H7 fecal shedding in cattle is related to Escherichia coli O157:H7 colonization of the small and large intestine, Can. J. Microbiol, vol.54, pp.984-995, 2008.

Y. Bertin, F. Chaucheyras-durand, C. Robbe-masselot, A. Durand, A. De-la-foye et al., Carbohydrate utilization by enterohaemorrhagic Escherichia coli O157:H7 in bovine intestinal content, Environ. Microbiol, vol.15, pp.610-622, 2013.

Y. Bertin, J. P. Girardeau, F. Chaucheyras-durand, B. Lyan, E. Pujosguillot et al., Enterohaemorrhagic Escherichia coli gains a competitive advantage by using ethanolamine as a nitrogen source in the bovine intestinal content, Environ. Microbiol, vol.13, pp.365-377, 2011.

T. E. Besser, N. Shaikh, N. J. Holt, P. I. Tarr, M. E. Konkel et al., Greater diversity of Shiga toxin-encoding bacteriophage insertion sites among Escherichia coli O157:H7 isolates from cattle than in those from humans, Appl. Environ. Microbiol, vol.73, pp.671-679, 2007.

D. Bibbal, E. Loukiadis, M. Kérourédan, É. Ferr, F. Dilasser et al., Prevalence of carriage of Shiga toxin-producing Escherichia coli serotypes O157:H7, O26:H11, O103:H2, O111:H8, and O145:H28 among slaughtered adult cattle in France, vol.81, pp.1397-1405, 2015.

R. E. Bishop, B. K. Leskiw, R. S. Hodges, C. M. Kay, and J. H. Weiner, The entericidin locus of Escherichia coli and its implications for programmed bacterial cell death, J. Mol. Biol, vol.280, pp.583-596, 1998.

V. Braun, Iron uptake by Escherichia coli, Front. Biosci, vol.8, 2003.

C. Chassard, K. P. Scott, P. Marquet, J. C. Martin, C. Del'homme et al., Fates of acid-resistant and non-acid-resistant Shiga toxinproducing Escherichia coli strains in ruminant digestive contents in the absence and presence of probiotics, Appl. Environ. Microbiol, vol.66, pp.640-647, 2008.

F. Chaucheyras-durand, J. Madic, F. Doudin, M. , and C. , Biotic and abiotic factors influencing in vitro growth of Escherichia coli O157:H7 in ruminant digestive contents, Appl. Environ. Microbiol, vol.72, pp.4136-4142, 2006.

L. Chen, J. Yang, J. Yu, Z. Yao, L. Sun et al., VFDB: a reference database for bacterial virulence factors, Nucleic Acids Res, vol.1, 2005.

H. Y. Cheng, V. W. Soo, S. Islam, M. J. Mcanulty, M. J. Benedik et al., Toxin GhoT of the GhoT/GhoS toxin/antitoxin system damages the cell membrane to reduce adenosine triphosphate and to reduce growth under stress, Environ. Microbiol, vol.16, pp.1741-1754, 2014.

K. R. Clarke and N. J. Owens, A simple and versatile microcomputer program for the determination of most probable number, J. Microbial Methods, vol.1, pp.133-137, 1983.

O. Clermont, J. K. Christenson, E. Denamur, G. , and D. M. , The clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups, Environ. Microbiol. Rep, vol.5, pp.58-65, 2013.

G. Conedera, P. A. Chapman, S. Marangon, E. Tisato, P. Dalvit et al., A field survey of Escherichia coli O157 ecology on a cattle farm in Italy, Int. J. Food Microbiol, vol.66, pp.85-93, 2001.

F. Dziva, A. Mahajan, P. Cameron, C. Currie, I. J. Mckendrick et al., EspP, a Type V-secreted serine protease of enterohaemorrhagic Escherichia coli O157:H7, influences intestinal colonization of calves and adherence to bovine primary intestinal epithelial cells, FEMS Microbiol. Lett, vol.271, pp.258-264, 2007.

F. Dziva, P. M. Van-diemen, M. P. Stevens, A. J. Smith, W. et al., Identification of Escherichia coli O157:H7 genes influencing colonization of the bovine gastrointestinal tract using signature-tagged mutagenesis, Microbiology, vol.150, pp.3631-3645, 2004.

D. M. Easton, L. P. Allsopp, M. D. Phan, D. G. Moriel, G. K. Goh et al., The intimin-like protein FdeC Is regulated by H-NS and temperature in enterohemorrhagic Escherichia coli, Appl. Environ. Microbiol, vol.80, pp.7337-7347, 2014.

M. Eppinger, M. K. Mammel, J. E. Leclerc, J. Ravel, and T. A. Cebula, , 2011.

, Genome signatures of Escherichia coli O157:H7 isolates from the bovine host reservoir, Appl. Environ. Microbiol, vol.77, pp.2916-2925

E. Franz, A. H. Van-hoek, E. Bouw, A. , and H. J. , Variability of Escherichia coli O157 strain survival in manure-amended soil in relation to strain origin, virulence profile, and carbon nutrition profile, Appl. Environ. Microbiol, vol.77, pp.8088-8096, 2011.

B. Fremaux, S. Raynaud, L. Beutin, R. , and C. V. , Dissemination and persistence of Shiga toxin-producing Escherichia coli (STEC) strains on French dairy farms, Vet. Microbiol, vol.117, pp.180-191, 2006.

M. Gouy, S. Guindon, and O. Gascuel, SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511794

, Mol. Biol. Evol, vol.27, pp.221-224

E. C. Hagan and H. L. Mobley, Haem acquisition is facilitated by a novel receptor Hma and required by uropathogenic Escherichia coli for kidney infection, Mol. Microbiol, vol.71, pp.79-91, 2009.

G. Halliwell and M. P. Bryant, The cellulolytic activity of pure strains of bacteria from the rumen of cattle, J. Gen. Microbiol, vol.32, pp.441-448, 1963.

C. L. Hews, S. L. Tran, U. Wegmann, B. Brett, A. D. Walsham et al., The StcE metalloprotease of enterohaemorrhagic Escherichia coli reduces the inner mucus layer and promotes adherence to human colonic epithelium ex vivo, Cell Microbiol, vol.19, p.12717, 2017.

T. Ivancic, P. Jamnik, and D. Stopar, Cold shock CspA and CspB protein production during periodic temperature cycling in Escherichia coli, BMC Res. Notes, vol.6, p.248, 2013.

K. C. Jeong, O. Hiki, M. Y. Kang, D. Park, K. et al., Prevalent and persistent Escherichia coli O157:H7 strains on farms are selected by bovine passage, Vet. Microbiol, vol.162, pp.912-920, 2013.

K. G. Joensen, A. M. Tetzschner, A. Iguchi, F. M. Aarestrup, and F. Scheutz, Rapid and easy in silico serotyping of Escherichia coli using whole genome sequencing (WGS) data, J. Clin. Microbiol, vol.53, pp.2410-2426, 2015.

M. G. Jørgensen, D. P. Pandey, M. Jaskolska, G. , and K. , HicA of Escherichia coli defines a novel family of translation-independent mRNA interferases in bacteria and archaea, J. Bacteriol, vol.191, pp.1191-1199, 2009.

R. S. Kaas, P. Leekitcharoenphon, F. M. Aarestrup, and O. Lund, Solving the problem of comparing whole bacterial genomes across different sequencing platforms, PLoS ONE, vol.9, 2014.

N. Kapitein and A. Mogk, Deadly syringes: type VI secretion system activities in pathogenicity and interbacterial competition, Curr. Opin. Microbiol, vol.16, pp.52-58, 2013.

M. A. Karmali, Infection by verocytotoxin-producing Escherichia coli, Clin. Microbiol. Rev, vol.2, pp.15-38, 1989.

J. A. Leedle and R. B. Hespell, Differential carbohydrate media and anaerobic replica plating techniques in delineating carbohydrate-utilizing subgroups in rumen bacterial populations, Appl. Environ. Microbiol, vol.39, pp.709-719, 1980.

E. Liebana, R. P. Smith, M. Batchelor, I. Mclaren, C. Cassar et al., Persistence of Escherichia coli O157 isolates on bovine farms in England and Wales, J. Clin. Microbiol, vol.43, pp.898-902, 2005.

A. Mahajan, C. G. Currie, S. Mackie, J. Tree, S. Mcateer et al., An investigation of the expression and adhesin function of H7 flagella in the interaction of Escherichia coli O157:H7 with bovine intestinal epithelium, Cell Microbiol, vol.11, pp.121-137, 2009.

B. D. Mcwilliams and A. G. Torres, Enterohemorrhagic Escherichia coli Adhesins. Microbiol. Spectr, vol.2, pp.1-19, 2014.

G. E. Mellor, E. M. Sim, R. S. Barlow, B. A. Astek, L. Galli et al., Phylogenetically related Argentinean and Australian Escherichia coli O157 isolates are distinguished by virulence clades and alternative Shiga toxin 1 and 2 prophages, Appl. Environ. Microbiol, vol.78, pp.4724-4731, 2012.

A. Mukherjee, M. K. Mammel, J. E. Leclerc, and T. A. Cebula, Altered utilization of N-acetyl-D-galactosamine by Escherichia coli O157:H7 from the 2006 spinach outbreak, J. Bacteriol, vol.190, pp.1710-1717, 2008.

K. D. Munns, R. Zaheer, Y. Xu, K. Stanford, C. R. Laing et al., Comparative genomic analysis of Escherichia coli O157:H7 isolated from super-shedder and low-shedder cattle, PLoS ONE, vol.11, 2016.

J. P. Nataro and J. B. Kaper, Diarrheagenic Escherichia coli, Clin. Microbiol. Rev, vol.11, pp.142-201, 1998.

Y. Ogura, S. I. Mondal, M. R. Islam, T. Mako, K. Arisawa et al., The Shiga toxin 2 production level in enterohemorrhagic Escherichia coli O157:H7 is correlated with the subtypes of toxin-encoding phage, Sci. Rep, vol.5, p.16663, 2015.

Y. Otsuka, Prokaryotic toxin-antitoxin systems: novel regulations of the toxins, Curr. Genet, vol.62, 2016.

R. Page, P. , and W. , Toxin-antitoxin systems in bacterial growth arrest and persistence, Nat. Chem. Biol, vol.12, pp.208-214, 2016.

J. S. Pearson and E. L. Hartland, The inflammatory response during enterohemorrhagic Escherichia coli infection, Microbiol. Spectr, vol.2, 2014.

A. K. Persad and J. T. Lejeune, Animal reservoirs of shiga toxin-producing Escherichia coli, Microbiol. Spectr, vol.2, 2014.

S. Puttamreddy, N. A. Cornick, and F. C. Minion, , 2010.

, Genome-wide transposon mutagenesis reveals a role for pO157 genes in biofilm development in Escherichia coli O157:H7 EDL933. Infect Immun, vol.78, pp.2377-2384

M. A. Rendón, Z. Saldaña, A. L. Erdem, V. Monteiro-neto, A. Vázquez et al., Commensal and pathogenic Escherichia coli use a common pilus adherence factor for epithelial cell colonization, Proc. Natl. Acad. Sci. U.S.A, vol.104, pp.10637-10642, 2007.

L. W. Riley, R. S. Remis, S. D. Helgerson, H. B. Mcgee, J. G. Wells et al., Hemorrhagic colitis associated with a rare Escherichia-Coli serotype, New Engl. J. Med, vol.308, pp.681-685, 1983.

J. T. Riordan, S. B. Viswanath, S. D. Manning, and T. S. Whittam, Genetic differentiation of Escherichia coli O157:H7 clades associated with human disease by real-time PCR, J. Clin. Microbiol, vol.46, pp.2070-2073, 2008.

A. Segura, P. Auffret, C. Klopp, Y. Bertin, and E. Forano, Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastro-intestinal tract, Stand. Genomic Sci, vol.12, p.61, 2017.

N. Shaikh and P. I. Tarr, Escherichia coli O157:H7 Shiga toxin-encoding bacteriophages: integrations, excisions, truncations, and evolutionary implications, J. Bacteriol, vol.185, pp.3596-3605, 2003.

V. K. Sharma and B. L. Bearson, Hha controls Escherichia coli O157:H7 biofilm formation by differential regulation of global transcriptional regulators FlhDC and CsgD, Appl. Environ. Microbiol, vol.79, pp.2384-2396, 2013.

J. A. Shere, K. J. Bartlett, K. , and C. W. , Longitudinal study of Escherichia coli O157:H7 dissemination on four dairy farms in Wisconsin, Appl. Environ. Microbiol, vol.64, pp.1390-1399, 1998.

S. Shringi, C. Schmidt, K. Katherine, K. A. Brayton, D. D. Hancock et al., Carriage of stx2a differentiates clinical and bovine-biased strains of Escherichia coli O157, PLoS ONE, vol.7, 2012.

P. Simon-assmann, C. Spenle, O. Lefebvre, and M. Kedinger, The role of the basement membrane as a modulator of intestinal epithelialmesenchymal interactions, Prog. Mol. Biol. Transl. Sci, vol.96, pp.175-206, 2010.

J. Skorko-glonek, A. Sobiecka-szkatula, J. Narkiewicz, and B. Lipinska, The proteolytic activity of the HtrA (DegP) protein from Escherichia coli at low temperatures, Microbiology, vol.154, pp.3649-2658, 2008.

R. Söderlund, C. Jernberg, S. Ivarsson, I. Hedenström, E. Eriksson et al., Molecular typing of Escherichia coli O157:H7 isolates from Swedish cattle and human cases: population dynamics and virulence, J. Clin. Microbiol, vol.52, pp.3906-3912, 2014.

J. M. Soon, S. A. Chadd, and R. N. Baines, Escherichia coli O157:H7 in beef cattle: on farm contamination and pre-slaughter control methods, Anim. Health Res. Rev, vol.12, pp.197-211, 2011.

C. Spiess, A. Beil, and M. Ehrmann, A temperature-dependent switch from chaperone to protease in a widely conserved heat shock protein, Cell, vol.97, pp.80743-80749, 1999.

P. I. Tarr, S. S. Bilge, J. C. Vary, S. Jelacic, R. L. Habeeb et al., Iha: a novel Escherichia coli O157:H7 adherence-conferring molecule encoded on a recently acquired chromosomal island of conserved structure, Infect Immun, vol.68, pp.1400-1407, 2000.

O. Tenaillon, D. Skurnik, B. Picard, and E. Denamur, The population genetics of commensal Escherichia coli, Nat. Rev. Microbiol, vol.8, pp.207-217, 2010.

C. H. Teng, Y. T. Tseng, R. Maruvada, D. Pearce, Y. Xie et al., NlpI contributes to Escherichia coli K1 strain RS218 interaction with human brain microvascular endothelial cells, Infect Immun, vol.78, pp.3090-3096, 2010.

A. G. Torres and S. M. Payne, Haem iron-transport system in enterohaemorrhagic Escherichia coli O157:H7, Mol. Microbiol, vol.23, pp.825-833, 1997.

A. G. Torres, N. T. Perna, V. Burland, A. Ruknudin, F. R. Blattner et al., Characterization of Cah, a calcium-binding and heat-extractable autotransporter protein of enterohaemorrhagic Escherichia coli, Mol. Microbiol, vol.45, pp.951-966, 2002.

M. Totsika, T. J. Wells, C. Beloin, J. Valle, L. P. Allsopp et al., Molecular characterization of the EhaG and UpaG trimeric autotransporter proteins from pathogenic Escherichia coli, Appl. Environ. Microbiol, vol.78, pp.2179-2189, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01385600

K. J. Turnbull, G. , and K. , HicA toxin of Escherichia coli derepresses hicAB transcription to selectively produce HicB antitoxin, Mol. Microbiol, vol.104, pp.781-792, 2017.

S. K. Vanaja, A. C. Springman, T. E. Besser, T. S. Whittam, and S. D. Manning, Differential expression of virulence and stress fitness genes between Escherichia coli O157:H7 strains with clinical or bovine-biased genotypes, Appl. Environ. Microbiol, vol.76, pp.60-68, 2010.

P. Vogeleer, Y. D. Tremblay, G. Jubelin, M. Jacques, and J. Harel, , 2015.

, Biofilm-forming abilities of Shiga toxin-producing Escherichia coli isolates associated with human infections, Appl. Environ. Microbiol, vol.82, pp.1448-1458

B. Wan, Q. Zhang, J. Ni, S. Li, D. Wen et al., Type VI secretion system contributes to Enterohemorrhagic Escherichia coli virulence by secreting catalase against host reactive oxygen species (ROS), PLoS Pathog, vol.13, p.1006246, 2017.

X. Wang, D. M. Lord, S. H. Hong, W. Peti, M. J. Benedik et al., , 2013.

/. Ghot and . Ghos, Environ. Microbiol, vol.15, pp.1734-1744

T. J. Wells, T. N. Mcneilly, M. Totsika, A. Mahajan, D. L. Gally et al., The Escherichia coli O157:H7 EhaB autotransporter protein binds to laminin and collagen I and induces a serum IgA Frontiers in Microbiology | www, vol.9, p.375, 2009.

N. Amigo, E. Mercado, A. Bentancor, P. Singh, D. Vilte et al., Clade 8 and Clade 6 strains of Escherichia coli O157:H7 from cattle in Argentina have hypervirulent-like phenotypes, PLoS One, vol.10, issue.6, p.127710, 2015.

R. Cote, R. Katani, M. R. Moreau, I. T. Kudva, T. M. Arthur et al., Comparative analysis of super-shedder strains of Escherichia coli O157:H7 reveals distinctive genomic features and a strongly aggregative adherent phenotype on bovine rectoanal junction squamous epithelial cells, PLoS One, vol.10, issue.2, p.116743, 2015.

S. E. Dowd, T. L. Crippen, Y. Sun, V. Gontcharova, E. Youn et al., Microarray analysis and draft genomes of two Escherichia coli O157:H7 lineage II cattle isolates FRIK966 and FRIK2000 investigating lack of Shiga toxin expression, Foodborne Pathog Dis, vol.7, pp.763-73, 2010.

M. Eppinger, M. K. Mammel, J. E. Leclerc, J. Ravel, and T. A. Cebula, Genome signatures of Escherichia coli O157:H7 isolates from the bovine host reservoir, Appl Environ Microbiol, vol.77, pp.2916-2925, 2011.

T. Hayashi, K. Makino, M. Ohnishi, K. Kurokawa, K. Ishii et al., Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12, DNA Res, vol.8, pp.11-22, 2001.

R. Katani, R. Cote, I. T. Kudva, C. Debroy, T. M. Arthur et al., Comparative genomics of two super-shedder isolates of Escherichia coli O157:H7, PLoS One, vol.12, issue.8, p.182940, 2017.

K. D. Munns, R. Zaheer, Y. Xu, K. Stanford, C. R. Laing et al., Comparative genomic analysis of Escherichia coli O157:H7 isolated from Super-Shedder and Low-Shedder cattle, PLoS One, vol.11, issue.3, p.151673, 2016.

R. Söderlund, C. Jernberg, S. Ivarsson, I. Hedenström, E. Eriksson et al., Molecular typing of Escherichia coli O157:H7 isolates from Swedish cattle and human cases: population dynamics and virulence, J ClinMicrobiol, vol.52, pp.3906-3912, 2014.

N. J. Strachan, O. Rotariu, B. Lopes, M. Macrae, S. Fairley et al., Whole genome sequencing demonstrates that geographic variation of Escherichia coli O157 genotypes dominates host association, Sci Rep, vol.5, p.14145, 2015.

L. Teng, A. Ginn, S. Jeon, M. Kang, J. et al., Complete genome sequence of an Escherichia coli O157:H7 strain isolated from a Super-Shedder steer, The Prokaryotes, vol.4, pp.60-71, 2006.

Z. D. Blount, The unexhausted potential of E. coli. elife, vol.4, p.5826, 2015.

S. A. Jones, T. Gibson, R. C. Maltby, F. Z. Chowdhury, V. Stewart et al., Anaerobic respiration of Escherichia coli in the mouse intestine, Infect Immun, vol.79, pp.4218-4244, 2011.

T. Conway and P. S. Cohen, Commensal and pathogenic Escherichia coli metabolism in the gut, Microbiol Spectr, 2015.

J. B. Kaper, J. P. Nataro, and H. L. Mobley, Pathogenic Escherichia coli, Nat Rev Microbiol, vol.2, pp.123-163, 2004.

M. A. Karmali, V. Gannon, and J. M. Sargeant, Verocytotoxin-producing Escherichia coli (VTEC), Vet Microbiol, vol.140, pp.360-70, 2010.

K. Oshima, H. Toh, Y. Ogura, H. Sasamoto, H. Morita et al., Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult, DNA Res, vol.15, pp.375-86, 2008.

D. A. Rasko, M. J. Rosovitz, G. S. Myers, E. F. Mongodin, W. F. Fricke et al., The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates, J Bacteriol, vol.190, pp.6881-93, 2008.

H. Toh, K. Oshima, A. Toyoda, Y. Ogura, T. Ooka et al., Complete genome sequence of the wild-type commensal Escherichia coli strain SE15, belonging to phylogenetic group B2, J Bacteriol, vol.192, pp.1165-1171, 2010.

Y. Bertin, F. Chaucheyras-durand, C. Robbe-masselot, A. Durand, A. De-la-foye et al., Carbohydrate utilization by enterohaemorrhagic Escherichia coli O157:H7 in bovine intestinal content, Environ Microbiol, vol.15, pp.610-632, 2013.

Y. Bertin, J. P. Girardeau, F. Chaucheyras-durand, B. Lyan, E. Pujos-guillot et al., Enterohaemorrhagic Escherichia coli gains a competitive advantage by using ethanolamine as a nitrogen source in the bovine intestinal content, Environ Microbiol, vol.13, pp.365-77, 2011.

K. G. Joensen, A. M. Tetzschner, A. Iguchi, F. M. Aarestrup, and F. Scheutz, Rapid and easy in silico serotyping of Escherichia coli isolates by use of whole-genome sequencing data, J Clin Microbiol, vol.53, pp.2410-2436, 2015.

E. Zankari, H. Hasman, S. Cosentino, M. Vestergaard, S. Rasmussen et al., Identification of acquired antimicrobial resistance genes, J Antimicrob Chemother, vol.67, pp.2640-2644, 2012.

O. Clermont, J. K. Christenson, E. Denamur, and D. M. Gordon, The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups, Environ Microbiol Rep, vol.5, pp.58-65, 2013.

P. Rice, I. Longden, and A. Bleasby, EMBOSS: the European Molecular Biology Open Software Suite, Trends Genet, vol.16, pp.276-283, 2000.

A. Badouei, M. Jajarmi, M. Mirsalehian, and A. , Virulence profiling and genetic relatedness of Shiga toxin-producing Escherichia coli isolated from humans and ruminants, Comp Immunol Microbiol Infect Dis, vol.38, pp.15-20, 2015.

E. Bok, J. Mazurek, M. Stosik, M. Wojciech, and K. Baldy-chudzik, Prevalence of virulence determinants and antimicrobial resistance among commensal Escherichia coli derived from dairy and beef cattle, Int J Environ Res Public Health, vol.12, pp.970-85, 2015.

R. S. Kaas, P. Leekitcharoenphon, F. M. Aarestrup, and O. Lund, Solving the problem of comparing whole bacterial genomes across different sequencing platforms, PLoS One, vol.9, p.104984, 2014.

J. Mariette, F. Escudie, N. Allias, G. Salin, C. Noirot et al., NG6: Integrated next generation sequencing storage and processing environment, BMC Genomics, vol.13, p.462, 2012.
URL : https://hal.archives-ouvertes.fr/inserm-00733481

S. Andrews, FastQC: a quality control tool for high throughput sequence data, 2010.

A. Bankevich, S. Nurk, D. Antipov, A. A. Gurevich, M. Dvorkin et al., SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J Comput Biol, vol.19, pp.455-77, 2012.

T. Seemann, Prokka: rapid prokaryotic genome annotation, Bioinformatics, vol.30, pp.2068-2077, 2014.

L. Y. Geer, A. Marchler-bauer, R. C. Geer, L. Han, J. He et al., The NCBI BioSystems database, Nucleic Acids Res, vol.38, pp.492-498, 2010.

A. Krogh, B. Larsson, G. Von-heijne, and E. L. Sonnhammer, Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes, J Mol Biol, vol.305, pp.567-80, 2001.

T. N. Petersen, S. Brunak, G. Von-heijne, and H. Nielsen, SignalP 4.0: discriminating signal peptides from transmembrane regions, Nat Methods, vol.8, pp.785-791, 2011.

I. Grissa, G. Vergnaud, and C. Pourcel, CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats, Nucleic Acids Res, vol.35, pp.52-59, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00194414

A. M. Varani, P. Siguier, E. Gourbeyre, V. Charneau, and M. Chandler, ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes
URL : https://hal.archives-ouvertes.fr/hal-00667053

, Genome Biol, vol.12, p.30, 2011.

D. Arndt, J. R. Grant, A. Marcu, T. Sajed, A. Pon et al., PHASTER: a better, faster version of the PHAST phage search tool, Nucleic Acids Res, vol.44, pp.16-21, 2016.

A. Carattoli, E. Zankari, A. Garcia-fernandez, V. Larsen, M. Lund et al., In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing, Antimicrob Agents Chemother, vol.58, pp.3895-903, 2014.

T. Hayashi, K. Makino, M. Ohnishi, K. Kurokawa, K. Ishii et al., Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12, DNA Res, vol.8, pp.11-22, 2001.

R. Lodinova-zadnikova and U. Sonnenborn, Effect of preventive administration of a nonpathogenic Escherichia coli strain on the colonization of the intestine with microbial pathogens in newborn infants, Biol Neonate, vol.71, pp.224-256, 1997.

L. Grozdanov, C. Raasch, J. Schulze, U. Sonnenborn, G. Gottschalk et al., Analysis of the genome structure of the nonpathogenic probiotic Escherichia coli strain Nissle 1917, J Bacteriol, vol.186, pp.5432-5473, 2004.

J. Sun, F. Gunzer, A. M. Westendorf, J. Buer, M. Scharfe et al., Genomic peculiarity of coding sequences and metabolic potential of probiotic Escherichia coli strain Nissle 1917 inferred from raw genome data, J Biotechnol, vol.117, pp.147-61, 2005.

L. Chen, J. Yang, J. Yu, Z. Yao, L. Sun et al., VFDB: a reference database for bacterial virulence factors, Nucleic Acids Res, vol.33, pp.325-333, 2005.

E. M. Antao, L. H. Wieler, and C. Ewers, Adhesive threads of extraintestinal pathogenic Escherichia coli, Gut Pathog, vol.1, p.22, 2009.

M. A. Croxen, R. J. Law, R. Scholz, K. M. Keeney, M. Wlodarska et al., Recent advances in understanding enteric pathogenic Escherichia coli, Clin Microbiol Rev, vol.26, pp.822-80, 2013.

B. D. Mcwilliams and A. G. Torres, Enterohemorrhagic Escherichia coli adhesins, Microbiol Spectrum, 2014.

D. M. Easton, L. P. Allsopp, M. D. Phan, D. G. Moriel, G. K. Goh et al., The intimin-like protein FdeC is regulated by H-NS and temperature in enterohemorrhagic Escherichia coli, Appl Environ Microbiol, vol.80, pp.7337-7384, 2014.

J. Xicohtencatl-cortes, V. Monteiro-neto, M. A. Ledesma, D. M. Jordan, O. Francetic et al., Intestinal adherence associated with type IV pili of enterohemorrhagic Escherichia coli O157:H7, J Clin Invest, vol.117, pp.3519-3548, 2007.

F. Dziva, P. M. Van-diemen, M. P. Stevens, A. J. Smith, and T. S. Wallis, Identification of Escherichia coli O157 : H7 genes influencing colonization of the bovine gastrointestinal tract using signature-tagged mutagenesis, Microbiology, vol.150, pp.3631-3676, 2004.

M. H. Lymberopoulos, S. Houle, F. Daigle, S. Leveille, A. Bree 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.6449-59, 2006.
URL : https://hal.archives-ouvertes.fr/pasteur-00720804

D. J. Wurpel, M. Totsika, L. P. Allsopp, L. E. Hartley-tassell, C. J. Day et al., F9 fimbriae of uropathogenic Escherichia coli are expressed at low temperature and recognise Galbeta13GlcNAc-containing glycans, PLoS One, vol.9, p.93177, 2014.

R. C. Team, R: A language and environment for statistical computing, The R Project for Statistical Computing, 2016.

M. Arthur, C. Campanelli, R. D. Arbeit, C. Kim, S. Steinbach et al., Structure and copy number of gene clusters related to the pap Padhesin operon of uropathogenic Escherichia coli, Infect Immun, vol.57, pp.314-335, 1989.

P. Simon-assmann, C. Spenle, O. Lefebvre, and M. Kedinger, The role of the basement membrane as a modulator of intestinal epithelial-mesenchymal interactions, Prog Mol Biol Transl Sci, vol.96, pp.175-206, 2010.

M. P. Leatham-jensen, J. Frimodt-moller, J. Adediran, M. E. Mokszycki, M. E. Banner et al., The streptomycin-treated mouse intestine selects Escherichia coli envZ missense mutants that interact with dense and diverse intestinal microbiota, Infect Immun, vol.80, pp.1716-1743, 2012.

B. Nagy and P. Z. Fekete, Enterotoxigenic Escherichia coli in veterinary medicine, Int J Med Microbiol, vol.295, pp.443-54, 2005.

C. Valat, K. Forest, F. Auvray, V. Metayer, T. Meheut et al., Assessment of adhesins as an indicator of pathovarassociated virulence factors in bovine Escherichia coli, Appl Environ Microbiol, vol.80, pp.7230-7234, 2014.

M. Zhou, Y. Yang, P. Chen, H. Hu, P. R. Hardwidge et al., More than a locomotive organelle: flagella in Escherichia coli, Appl Microbiol Biotechnol, vol.99, pp.8883-90, 2015.

S. C. Sampaio, W. B. Luiz, M. A. Vieira, R. C. Ferreira, B. G. Garcia et al., Flagellar cap protein FliD mediates adherence of atypical enteropathogenic Escherichia coli to enterocyte microvilli, Infect Immun, vol.84, pp.1112-1134, 2016.

G. M. Baranzoni, P. M. Fratamico, J. Gangiredla, I. Patel, L. K. Bagi et al., Characterization of shiga toxin subtypes and virulence genes in porcine shiga toxin-producing Escherichia coli, Front Microbiol, vol.7, p.574, 2016.

C. P. Pigatto, R. P. Schocken-iturrino, E. M. Souza, F. O. Pedrosa, L. Comarella et al., Fadel-Picheth CM. Virulence properties and antimicrobial susceptibility of Shiga toxin-producing Escherichia coli strains isolated from healthy cattle from Parana State, Brazil Can J Microbiol, vol.54, pp.588-93, 2008.

L. J. Searle, G. Meric, I. Porcelli, S. K. Sheppard, and S. Lucchini, Variation in siderophore biosynthetic gene distribution and production across environmental and faecal populations of Escherichia coli, PLoS One, vol.10, p.117906, 2015.

H. Pi, S. A. Jones, L. E. Mercer, J. P. Meador, J. E. Caughron et al., Role of catecholate siderophores in gram-negative bacterial colonization of the mouse gut, PLoS One, vol.7, p.50020, 2012.

D. A. Garsin, Ethanolamine utilization in bacterial pathogens: roles and regulation, Nat Rev Microbiol, vol.8, pp.290-295, 2010.

M. Gouy, S. Guindon, and O. Gascuel, SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building, Mol Biol Evol, vol.27, pp.221-225, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511794

L. A. Kelley, S. Mezulis, C. M. Yates, M. N. Wass, and M. J. Sternberg, The Phyre2 web portal for protein modeling, prediction and analysis, Nat Protoc, vol.10, pp.845-58, 2015.

D. Field, G. Garrity, T. Gray, N. Morrison, J. Selengut et al., The minimum information about a genome sequence (MIGS) specification, Nat Biotechnol, vol.26, pp.541-548, 2008.

C. R. Woese, O. Kandler, and M. L. Wheelis, Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya, Proc Natl Acad Sci U S A, vol.87, pp.4576-4585, 1990.

G. M. Garrity, J. A. Bell, T. Lilburn, X. Phylum, G. M. Garrity et al., Bergey's Manual of Systematic Bacteriology, Part B, vol.2, p.1, 2005.

G. M. Garrity, J. A. Bell, T. Lilburn, G. M. Garrity, D. J. Brenner et al., Bergey's Manual of Systematic Bacteriology, Part B, vol.2, p.1, 2005.

J. Euzeby, Validation list no. 106. Validation of publication of new names and new combinations previously effectively published outside the IJSEM, Int J Syst Evol Microbiol, vol.55, pp.2235-2243, 2005.

G. M. Garrity and J. G. Holt, Taxonomic outline of the archaea and bacteria, vol.1, pp.155-66, 2001.

L. R. Hill, V. Skerman, and P. Sneath, Corrigenda to the approved lists of bacterial names: edited for the international committee on systematic bacteriology, Int J Syst Bacteriol, vol.34, pp.508-519, 1984.

O. Rahn, Zentralblatt für Backteriologie, Parasitenkunde, Infektionskrankheiten und Hygiene, vol.96, pp.273-86, 1937.

V. Skerman, V. Mcgowan, and P. Sneath, Approved lists of bacterial names, Int J Syst Bacteriol, pp.225-420, 1980.

A. Castellani and A. J. Chalmers, Genus Escherichia Castellani and Chalmers, 1918. Wood W. And Co. Manual of Tropical Medicine

W. Wood and . Company, , pp.941-944, 1919.

M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler et al., Gene ontology: tool for the unification of biology. The Gene Ontology Consortium, Nat Genet, vol.25, pp.25-34, 2000.

S. F. Stoddard, B. J. Smith, R. Hein, B. R. Roller, and T. M. Schmidt, rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development, Nucleic Acids Res, vol.43, pp.593-601, 2015.

, AUTRES PARTICIPATIONS Publication publiée dans Plos One

Y. Bertin, C. Habouzit, L. Dunière, M. Laurier, A. Durand et al., Lactobacillus reuteri suppresses E. coli O157:H7 in bovine ruminal fluid: Toward a pre-slaughter strategy to improve food safety, p.2017

. Communications-orale,

Y. Bertin, C. Habouzit, M. Laurier, A. Durand, D. Duchez et al., Lactobacillus reuteri suppresses enterohaemorrhagic Escherichia coli O157:H7 in bovine ruminal fluid, The 10 th international INRA-Rowett Symposium of Gut Microbiology: 20 years & counting, 2016.

, References 1. Law D. Virulence factors of Escherichia coli O157 and other Shiga toxin-producing E. coli, Journal of Applied Microbiology, vol.88, p.10792533, 2000.

A. Caprioli, S. Morabito, H. Brugere, and E. Oswald, Enterohaemorrhagic Escherichia coli: emerging issues on virulence and modes of transmission, Veterinary Research, vol.36, p.15845227, 2005.
DOI : 10.1051/vetres:2005002

URL : https://hal.archives-ouvertes.fr/hal-00902971

F. Gagg?à, P. Mattarelli, and B. Biavati, Probiotics and prebiotics in animal feeding for safe food production, International Journal of Food Microbiology, vol.141, issue.1, pp.15-28, 2010.

V. Pandey, V. Berwal, N. Solanki, and N. S. Malik, Probiotics: Healthy bugs and nourishing elements of diet, Journal of International Society of Preventive & Community Dentistry, vol.5, pp.81-87, 2015.
DOI : 10.4103/2231-0762.155726

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4415334/pdf

L. A. B¡hle, D. A. Brede, D. B. Diep, H. Holo, and I. F. Nes, Specific degradation of the mucus adhesion-promoting protein (MapA) of Lactobacillus reuteri to an antimicrobial peptide. Applied and Environmental Microbiology, vol.76, p.20833791, 2010.

T. L. Talarico and W. J. Dobrogosz, Chemical characterization of an antimicrobial substance produced by Lactobacillus reuteri, Antimicrobial Agents and Chemotherapy, vol.33, p.2751282, 1989.
DOI : 10.1128/aac.33.5.674

URL : https://aac.asm.org/content/33/5/674.full.pdf

S. Vollenweider, S. Evers, K. Zurbriggen, and C. Lacroix, Unraveling the hydroxypropionaldehyde (HPA) system: an active antimicrobial agent against human pathogens, Journal of Agricultural and Food Chemistry, vol.58, p.20845960, 2010.
DOI : 10.1021/jf1010897

, L. reuteri suppresses EHEC in bovine rumen fluid PLOS ONE, 201718-11-01.

L. Schaefer, T. A. Auchtung, K. E. Hermans, D. Whitehead, B. Borhan et al., The antimicrobial compound reuterin (3-hydroxypropionaldehyde) induces oxidative stress via interaction with thiol groups. Microbiology, vol.156, p.20150236, 2010.
DOI : 10.1099/mic.0.035642-0

URL : http://mic.microbiologyresearch.org/deliver/fulltext/micro/156/6/1589.pdf?itemId=/content/journal/micro/10.1099/mic.0.035642-0&mimeType=pdf&isFastTrackArticle=

Q. Lüthi-peng, S. Schärer, and Z. Puhan, Production and stability of 3-hydroxypropionaldehyde in Lactobacillus reuteri, Applied Microbiology and Biotechnology, vol.60, pp.73-80, 2002.

S. Vollenweider, G. Grassi, I. König, and Z. Puhan, Purification and structural characterization of 3-hydroxypropionaldehyde and its derivatives, Journal of Agricultural and Food Chemistry, vol.51, p.12744656, 2003.
DOI : 10.1021/jf021086d

K. A. Eaton, A. Honkala, T. A. Auchtung, and R. A. Britton, Probiotic Lactobacillus reuteri ameliorates disease due to enterohemorrhagic Escherichia coli in germfree mice, Infection and Immunity, vol.79, p.20974822, 2011.
DOI : 10.1016/s0016-5085(10)60235-1

S. W. Naylor, J. C. Low, T. E. Besser, A. Mahajan, G. J. Gunn et al., Lymphoid follicle-dense mucosa at the terminal rectum is the principal site of colonization of enterohemorrhagic Escherichia coli O157:H7 in the bovine host, Infection and Immunity, vol.71, p.12595469, 2003.

C. Brown, B. G. Harmon, T. Zhao, and M. P. Doyle, Experimental Escherichia coli O157:H7 carriage in calves, Applied and Environmental Microbiology, vol.63, p.8979335, 1997.

J. E. Keen, W. W. Laegreid, C. G. Chitko-mckown, L. M. Durso, and J. L. Bono, Distribution of Shiga-toxigenic Escherichia coli O157 in the gastrointestinal tract of naturally O157-shedding cattle at necropsy, Applied and Environmental Microbiology, vol.76, p.20543036, 2010.

C. Walker, X. Shi, M. Sanderson, J. Sargeant, and T. G. Nagaraja, Prevalence of Escherichia coli O157:H7 in gut contents of beef cattle at slaughter. Foodborne Pathogens and Disease, vol.7, pp.249-255, 2010.

V. Sperandio, SdiA sensing of acyl-homoserine lactones by enterohemorrhagic E. coli (EHEC) serotype O157:H7 in the bovine rumen, Gut Microbes, vol.1, p.21468228, 2010.

F. Baruzzi, P. Poltronieri, G. M. Quero, M. Morea, and L. Morelli, An in vitro protocol for direct isolation of potential probiotic lactobacilli from raw bovine milk and traditional fermented milks, Applied Microbiology and Biotechnology, vol.90, p.21318359, 2011.

F. Chaucheyras-durand, J. Madic, F. Doudin, and C. Martin, Biotic and abiotic factors influencing in vitro growth of Escherichia coli O157:H7 in ruminant digestive contents. Applied and Environmental Microbiology, vol.72, p.16751525, 2006.

Y. Bertin, F. Chaucheyras-durand, C. Robbe-masselot, A. Durand, A. De-la-foye et al., Carbohydrate utilization by enterohaemorrhagic Escherichia coli O157:H7 in bovine intestinal content. Environmental Microbiology, vol.15, p.23126484, 2013.

J. K. Spinler, M. Taweechotipatr, C. L. Rognerud, C. N. Ou, S. Tumwasorn et al., Human-derived probiotic Lactobacillus reuteri demonstrate antimicrobial activities targeting diverse enteric bacterial pathogens, Anaerobe, vol.14, p.18396068, 2008.
DOI : 10.1016/j.anaerobe.2008.02.001

URL : http://europepmc.org/articles/pmc2494590?pdf=render

M. D. Stern, A. Bach, and S. Calsamiglia, Alternative techniques for measuring digestion in ruminants, Journal of Animal Science, vol.75, p.9263075, 1997.

A. T. Adesogan, Effect of bag type on the apparent digestibility of feeds in ANKOM Daisy II incubators, Animal Feed Science and Technology, vol.119, pp.333-334, 2005.

D. Damiran, D. Curto, T. Bohnert, D. W. Findhol, and S. L. , Comparison of techniques and grinding size to estimate digestibility of forage based ruminant diets, Animal Feed Science and Technology, vol.141, pp.15-35, 2008.

H. K. Goering, V. Soest, and P. J. , Forage Fiber Analyses (Apparatus, Reagents, Procedures, and Some Applications). Agri Handbook No. 379, ARSUSDA, 1970.

Y. Bertin, C. Deval, A. De-la-foye, L. Masson, V. Gannon et al., The gluconeogenesis pathway is involved in maintenance of enterohaemorrhagic Escherichia coli O157:H7 in bovine intestinal content, PLoS One, vol.9, p.24887187, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01190039

M. Ogawa, K. Shimizu, K. Nomoto, R. Tanaka, T. Hamabata et al., Inhibition of in vitro growth of Shiga toxin-producing Escherichia coli O157:H7 by probiotic Lactobacillus strains due to production of lactic acid, International Journal of Food Microbiology, vol.68, p.11545213, 2001.

P. Mosoni, F. Chaucheyras-durand, C. Béra-maillet, and E. Forano, Quantification by real-time PCR of cellulolytic bacteria in the rumen of sheep after supplementation of a forage diet with readily fermentable carbohydrates: effect of a yeast additive, Journal of Applied Microbiology, vol.103, p.18045448, 2007.

, L. reuteri suppresses EHEC in bovine rumen fluid PLOS ONE, 201719-11-01.

H. G. Heilig, E. G. Zoetendal, E. E. Vaughan, P. Marteau, A. D. Akkermans et al., Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA, Appl Environ Microbiol, vol.68, p.11772617, 2002.

L. Rivas, B. Coffey, O. Mcauliffe, M. J. Mcdonnell, C. M. Burgess et al., In vivo and ex vivo evaluations of bacteriophages e11/2 and e4/1c for use in the control of Escherichia coli O157:H7. Applied and Environmental Microbiology, vol.76, p.20851992, 2010.

L. V. Wisener, J. M. Sargeant, O. Connor, A. M. Faires, M. C. Glass-kaastra et al., The use of direct-fed microbials to reduce shedding of Escherichia coli O157 in beef cattle: a systematic review and meta-analysis, Zoonoses and Public Health, vol.62, p.24751204, 2015.

M. M. Brashears and B. D. Chaves, The diversity of beef safety: A global reason to strengthen our current systems, Meat Sci, issue.17, pp.30213-30219, 2017.

D. Luongo, J. Miyamoto, P. Bergamo, F. Nazzaro, F. Baruzzi et al., Differential modulation of innate immunity in vitro by probiotic strains of Lactobacillus gasseri, BMC Microbiology, vol.13, p.24365457, 2013.

S. Mcsweeney and R. I. Mackie, Micro-organisms and ruminant digestion: state of knowledge, trends and future prospects. FAO Background study paper N?61N?61, 2012.

H. Vaidyanathan, V. Kandasamy, G. G. Ramakrishnan, K. B. Ramachandran, G. Jayaraman et al., Glycerol conversion to 1, 3-Propanediol is enhanced by the expression of a heterologous alcohol dehydrogenase gene in Lactobacillus reuteri, pp.1-37

B. A. White, R. Lamed, E. A. Bayer, and H. J. Flint, Biomass utilization by gut microbiomes, Annual Review of Microbiology, vol.68, p.25002092, 2014.
DOI : 10.1146/annurev-micro-092412-155618

H. Biebl, K. Menzel, A. P. Zeng, and W. D. Deckwer, Microbial production of 1,3-propanediol, Applied Microbiology and Biotechnology, vol.52, p.10531640, 1999.
DOI : 10.1007/s002530051523

E. Jami and I. Mizrahi, Composition and similarity of bovine rumen microbiota across individual animals, PLoS One, vol.7, p.22432013, 2012.
DOI : 10.1371/journal.pone.0033306

URL : https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0033306&type=printable

G. A. Garton, A. K. Lough, and E. Vioque, Glyceride hydrolysis and glycerol fermentation by sheep rumen contents, Journal of General Microbiology, vol.25, p.13703779, 1961.

R. Danielsson, A. Werner-omazic, M. Ramin, A. Schnürer, M. Griinari et al., Effects on enteric methane production and bacterial and archaeal communities by the addition of cashew nut shell extract or glycerol-an in vitro evaluation, Journal of Dairy Science, vol.97, p.24996274, 2014.

P. N. Hobson and S. O. Mann, The isolation of glycerol-fermenting and lipolytic bacteria from the rumen of the sheep, Journal of General Microbiology, vol.25, p.13714763, 1961.

W. H. Hoover and T. K. Miller, Rumen digestive physiology and microbial ecology, Veterinary Clinics of North America: Food Animal Practice, vol.7, pp.311-325, 1991.
DOI : 10.1016/s0749-0720(15)30801-x

S. L. Gruber, J. D. Tatum, T. E. Engle, P. L. Chapman, K. E. Belk et al., Relationships of behavioral and physiological symptoms of preslaughter stress to beef longissimus muscle tenderness, Journal of Animal Science, vol.88, pp.1148-1159, 2010.

M. G. Elramady, S. S. Aly, P. V. Rossitto, J. A. Crook, and J. S. Cullor, Synergistic effects of lactic acid and sodium dodecyl sulfate to decontaminate Escherichia coli O157:H7 on cattle hide sections. Foodborne Pathogens and Disease, vol.10, p.23594235, 2013.

C. C. Chancey, J. C. Brooks, J. N. Martin, A. Echeverry, S. P. Jackson et al., Survivability of Escherichia coli O157:H7 in mechanically tenderized beef steaks subjected to lactic acid application and cooking under simulated industry conditions, Journal of Food Protection, vol.76, p.24112580, 2013.

F. Chaucheyras-durand and H. Durand, Probiotics in animal nutrition and health, Beneficial Microbes, vol.1, p.21840795, 2010.
DOI : 10.3920/bm2008.1002

S. S. Donkin, S. L. Koser, M. White, H. Doane, and M. J. Cecava, Feeding value of glycerol as a replacement for corn grain in rations fed to lactating dairy cows, Journal of Dairy Science, vol.92, p.19762829, 2009.

H. Lomander, J. Frössling, K. L. Ingvartsen, H. Gustafsson, and C. Svensson, Supplemental feeding with glycerol or propylene glycol of dairy cows in early lactation-effects on metabolic status, body condition, and milk yield, Journal of Dairy Science, vol.95, p.22541468, 2012.

D. Rémond, J. P. Chaise, E. Delval, and C. Poncet, Net flux of metabolites across the ruminal wall of sheep fed twice a day with orchardgrass hay, Journal of Animal Sciences, vol.71, pp.2529-2538, 1993.

, L. reuteri suppresses EHEC in bovine rumen fluid PLOS ONE, 201720-11-01.

P. Adhikari, S. A. Berish, A. J. Nowalk, K. L. Veraldi, S. A. Morse et al., The fbpABC locus of Neisseria gonorrhoeae functions in the periplasm-to-cytosol transport of iron, J Bacteriol, vol.178, issue.7, pp.2145-2149, 1996.

A. , Bilan des connaissances relatives aux Escherichia coli producteurs de shiga-toxines (STEC), 2003.

A. , Avis relatif aux souches d'Escherichia coli productrices de shiga-toxines considérées comme pathogènes pour l'homme, 2008.

D. R. Baker, R. A. Moxley, and D. H. Francis, Variation in virulence in the gnotobiotic pig model of O157:H7 Escherichia coli strains of bovine and human origin, Adv Exp Med Biol, vol.412, pp.53-58, 1997.

T. Bansal, D. Englert, J. Lee, M. Hegde, T. K. Wood et al., Differential effects of epinephrine, norepinephrine, and indole on Escherichia coli O157:H7 chemotaxis, colonization, and gene expression, Infect Immun, vol.75, issue.9, pp.4597-4607, 2007.

G. A. Barkocy-gallagher, T. M. Arthur, G. R. Siragusa, J. E. Keen, R. O. Elder et al., Genotypic analyses of Escherichia coli O157:H7 and O157 nonmotile isolates recovered from beef cattle and carcasses at processing plants in the Midwestern states of the United States, Appl Environ Microbiol, vol.67, issue.9, pp.3810-3818, 2001.

B. Foster, D. Abul-milh, M. Huesca, M. Lingwood, and C. A. , Enterohemorrhagic Escherichia coli induces apoptosis which augments bacterial binding and phosphatidylethanolamine exposure on the plasma membrane outer leaflet, Infect Immun, vol.68, issue.6, pp.3108-3115, 2000.

I. Batisson, M. P. Guimond, F. Girard, H. An, C. Zhu et al.,

J. Harel, Characterization of the novel factor paa involved in the early steps of the adhesion mechanism of attaching and effacing Escherichia coli, Infect Immun, vol.71, issue.8, pp.4516-4525, 2003.
URL : https://hal.archives-ouvertes.fr/hal-00529349

A. Battesti, N. Majdalani, and S. Gottesman, The RpoS-mediated general stress response in Escherichia coli, Annu Rev Microbiol, vol.65, pp.189-213, 2011.

A. Bauwens, J. Betz, I. Meisen, B. Kemper, H. Karch et al., Facing glycosphingolipidShiga toxin interaction: dire straits for endothelial cells of the human vasculature, Cell Mol Life Sci, vol.70, issue.3, pp.425-457, 2013.

C. Beloin, A. Roux, and J. M. Ghigo, Escherichia coli biofilms, Curr Top Microbiol Immunol, vol.322, pp.249-289, 2008.
URL : https://hal.archives-ouvertes.fr/pasteur-00473297

L. V. Bentancor, M. Bilen, R. J. Brando, M. V. Ramos, L. C. Ferreira et al., A DNA vaccine encoding the enterohemorragic Escherichia coli Shiga-like toxin 2 A2 and B subunits confers protective immunity to Shiga toxin challenge in the murine model, Clin Vaccine Immunol, vol.16, issue.5, pp.712-718, 2009.

C. N. Berger, V. F. Crepin, K. Baruch, A. Mousnier, I. Rosenshine et al., EspZ of enteropathogenic and enterohemorrhagic Escherichia coli regulates type III secretion system protein translocation, MBio, issue.5, p.3, 2012.

E. D. Berry and J. E. Wells, Escherichia coli O157:H7: recent advances in research on occurrence, transmission, and control in cattle and the production environment, Adv Food Nutr Res, vol.60, pp.67-117, 2010.

Y. Bertin, F. Chaucheyras-durand, C. Robbe-masselot, A. Durand, A. De-la-foye et al.,

C. Martin, Carbohydrate utilization by enterohaemorrhagic Escherichia coli O157:H7 in bovine intestinal content, Environ Microbiol, vol.15, issue.2, pp.610-622, 2013.

Y. Bertin, C. Deval, A. De-la-foye, L. Masson, V. Gannon et al., The gluconeogenesis pathway is involved in maintenance of enterohaemorrhagic Escherichia coli O157:H7 in bovine intestinal content, PLoS One, vol.9, issue.6, p.98367, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01190039

Y. Bertin and E. Forano, Sécurité microbiologique de la viande de boeuf. Viandes & Produits Carnés, 2013.

Y. Bertin, J. P. Girardeau, F. Chaucheyras-durand, B. Lyan, E. Pujos-guillot et al., Enterohaemorrhagic Escherichia coli gains a competitive advantage by using ethanolamine as a nitrogen source in the bovine intestinal content, Environ Microbiol, vol.13, issue.2, pp.365-377, 2011.

Y. Bertin, C. Habouzit, L. Dunière, M. Laurier, A. Durand et al., Lactobacillus reuteri suppresses E. coli O157:H7 in bovine ruminal fluid: Toward a preslaughter strategy to improve food safety?, PLoS One, vol.12, issue.11, 2017.

T. E. Besser, D. D. Hancock, L. C. Pritchett, E. M. Mcrae, D. H. Rice et al., Duration of detection of fecal excretion of Escherichia coli O157:H7 in cattle, J Infect Dis, vol.175, issue.3, pp.726-729, 1997.

T. E. Besser, B. L. Richards, D. H. Rice, and D. D. Hancock, Escherichia coli O157:H7 infection of calves: infectious dose and direct contact transmission, Epidemiol Infect, vol.127, issue.3, pp.555-560, 2001.

D. Bibbal, E. Loukiadis, M. Kerouredan, F. Ferre, F. Dilasser et al.,

H. Brugere, Prevalence of carriage of shiga toxin-producing Escherichia coli serotypes O157:H7, O26:H11, O103:H2, O111:H8, and O145:H28 among slaughtered adult cattle in France, vol.81, pp.1397-1405, 2015.

M. Bielaszewska, T. Aldick, A. Bauwens, and H. Karch, Hemolysin of enterohemorrhagic Escherichia coli: structure, transport, biological activity and putative role in virulence, Int J Med Microbiol, vol.304, issue.5-6, pp.521-529, 2014.

M. Bielaszewska, E. A. Idelevich, W. Zhang, A. Bauwens, F. Schaumburg et al., Effects of antibiotics on Shiga toxin 2 production and bacteriophage induction by epidemic Escherichia coli O104:H4 strain, Antimicrob Agents Chemother, vol.56, issue.6, pp.3277-3282, 2012.
DOI : 10.1128/aac.06315-11

URL : https://aac.asm.org/content/56/6/3277.full.pdf

M. Bielaszewska, A. Mellmann, W. Zhang, R. Kock, A. Fruth et al., Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study, Lancet Infect Dis, vol.11, issue.9, pp.671-676, 2011.

J. Bien, O. Sokolova, and P. Bozko, Role of uropathogenic Escherichia coli virulence factors in development of urinary tract infection and kidney damage, Int J Nephrol, p.681473, 2012.

R. E. Bishop, B. K. Leskiw, R. S. Hodges, C. M. Kay, and J. H. Weiner, The entericidin locus of Escherichia coli and its implications for programmed bacterial cell death, J Mol Biol, vol.280, issue.4, pp.583-596, 1998.

D. J. Bolton, C. M. Byrne, J. J. Sheridan, D. A. Mcdowell, and I. S. Blair, The survival characteristics of a non-toxigenic strain of Escherichia coli O157:H7, J Appl Microbiol, vol.86, issue.3, pp.407-411, 1999.

S. L. Booher, N. A. Cornick, and H. W. Moon, Persistence of Escherichia coli O157:H7 in experimentally infected swine, Vet Microbiol, vol.89, issue.1, pp.69-81, 2002.

O. Borirak, M. D. Rolfe, L. J. De-koning, H. C. Hoefsloot, M. Bekker et al.,

K. J. Hellingwerf, Time-series analysis of the transcriptome and proteome of Escherichia coli upon glucose repression, Biochim Biophys Acta, issue.10 Pt A, pp.1269-1279, 2015.

L. T. Brandal, C. Sekse, B. A. Lindstedt, M. Sunde, I. Lobersli et al., Norwegian sheep are an important reservoir for human-pathogenic Escherichia coli O26, p.11, 2012.
DOI : 10.1128/aem.00186-12

URL : https://aem.asm.org/content/78/12/4083.full.pdf

, Appl Environ Microbiol, vol.78, issue.12, pp.4083-4091

M. M. Brashears, M. L. Galyean, G. H. Loneragan, J. E. Mann, and K. Killinger-mann, Prevalence of Escherichia coli O157:H7 and performance by beef feedlot cattle given Lactobacillus direct-fed microbials, J Food Prot, vol.66, issue.5, pp.748-754, 2003.

J. T. Brooks, E. G. Sowers, J. G. Wells, K. D. Greene, P. M. Griffin et al., Non-O157 shiga toxin-producing Escherichia coli infections in the United States, J Infect Dis, vol.192, issue.8, pp.1422-1429, 1983.

C. A. Brown, B. G. Harmon, T. Zhao, and M. P. Doyle, Experimental Escherichia coli O157:H7 carriage in calves, Appl Environ Microbiol, vol.63, issue.1, pp.27-32, 1997.

M. Bruyand, P. Mariani-kurkdijan, S. Le-hello, S. Lefevre, S. Bonacorsi et al., Surveillance du syndrome hémolytique et urémique post-diarrhéique chez l'enfant de moins de 15 ans, le réseau des néphrologues pédiatres, 2016.

M. Bruyand, P. Mariani-kurkdjian, S. Bonacorsi, M. Gouali, S. Le-hello et al., Surveillance du syndrome hémolytique et urémique post-diarrhéique chez les enfants de moins de 15 ans en France en, le réseau des néphrologues pédiatres, 2015.

A. Bryan, I. Youngster, and A. J. Mcadam, Shiga toxin producing Escherichia coli, Clin Lab Med, vol.35, issue.2, pp.247-272, 2015.

E. Brzuszkiewicz, A. Thurmer, J. Schuldes, A. Leimbach, H. Liesegang et al.,

R. Daniel, Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC), Arch Microbiol, vol.193, issue.12, pp.883-891, 2011.

E. Bueno, S. Mesa, E. J. Bedmar, D. J. Richardson, and M. J. Delgado, Bacterial adaptation of respiration from oxic to microoxic and anoxic conditions: redox control, Antioxid Redox Signal, vol.16, issue.8, pp.819-852, 2012.
DOI : 10.1089/ars.2011.4051

URL : http://europepmc.org/articles/pmc3283443?pdf=render

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 Res, vol.26, issue.18, pp.4196-4204, 1998.

U. Busch, S. Hormansdorfer, S. Schranner, I. Huber, K. H. Bogner et al., , 2007.

, Enterohemorrhagic Escherichia coli excretion by child and her cat, Emerg Infect Dis, vol.13, issue.2, pp.348-349

G. Buvens, P. Bogaerts, Y. Glupczynski, S. Lauwers, and D. Pierard, Antimicrobial resistance testing of verocytotoxin-producing Escherichia coli and first description of TEM-52 extendedspectrum beta-lactamase in serogroup O26, Antimicrob Agents Chemother, vol.54, issue.11, pp.4907-4909, 2010.

M. E. Caceres, A. I. Etcheverria, D. Fernandez, E. M. Rodriguez, and N. L. Padola, Variation in the distribution of putative virulence and colonization factors in shiga toxin-producing Escherichia coli isolated from different categories of cattle, Front Cell Infect Microbiol, vol.7, p.147, 2017.

T. R. Callaway, M. A. Carr, T. S. Edrington, R. C. Anderson, and D. J. Nisbet, Diet, Escherichia coli O157:H7, and cattle: a review after 10 years, vol.11, pp.67-79, 2009.

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, Dev Cell, vol.7, issue.2, pp.217-228, 2004.
DOI : 10.1016/j.devcel.2004.07.004

URL : https://doi.org/10.1016/j.devcel.2004.07.004

A. Caprioli, S. Morabito, H. Brugere, and E. Oswald, Enterohaemorrhagic Escherichia coli: emerging issues on virulence and modes of transmission, Vet Res, vol.36, issue.3, pp.289-311, 2005.
DOI : 10.1051/vetres:2005002

URL : https://hal.archives-ouvertes.fr/hal-00902971

M. Q. Carter, C. T. Parker, J. W. Louie, S. Huynh, C. K. Fagerquist et al., RcsB contributes to the distinct stress fitness among Escherichia coli O157:H7 curli variants of the 1993 hamburger-associated outbreak strains, Appl Environ Microbiol, vol.78, issue.21, pp.7706-7719, 2012.

C. , Foodborne Diseases Active Surveillance Network (FoodNet), Foodborne Diseases Active Surveillance Network (FoodNet, 2016.

R. M. Chalmers, R. L. Salmon, G. A. Willshaw, T. Cheasty, N. Looker et al., Vero-cytotoxin-producing Escherichia coli O157 in a farmer handling horses, Lancet, vol.349, issue.9068, p.1816, 1997.

D. E. Chang, D. J. Smalley, D. L. Tucker, M. P. Leatham, W. E. Norris et al.,

T. Conway, Carbon nutrition of Escherichia coli in the mouse intestine, Proc Natl Acad Sci U S A, vol.101, issue.19, pp.7427-7432, 2004.

M. Chase-topping, D. Gally, C. Low, L. Matthews, and M. Woolhouse, Super-shedding and the link between human infection and livestock carriage of Escherichia coli O157, Nat Rev Microbiol, vol.6, issue.12, pp.904-912, 2008.

F. Chaucheyras-durand and H. Durand, Probiotics in animal nutrition and health, Benef Microbes, vol.1, issue.1, pp.3-9, 2010.
DOI : 10.3920/bm2008.1002

F. Chaucheyras-durand, F. Faqir, A. Ameilbonne, C. Rozand, and C. Martin, Fates of acidresistant and non-acid-resistant shiga toxin-producing Escherichia coli strains in ruminant digestive contents in the absence and presence of probiotics, Appl Environ Microbiol, vol.76, issue.3, pp.640-647, 2010.

F. Chaucheyras-durand, J. Madic, F. Doudin, and C. Martin, Biotic and abiotic factors influencing in vitro growth of Escherichia coli O157:H7 in ruminant digestive contents, Appl Environ Microbiol, vol.72, issue.6, pp.4136-4142, 2006.

S. M. Chekabab, J. Paquin-veillette, C. M. Dozois, and J. Harel, The ecological habitat and transmission of Escherichia coli O157:H7, FEMS Microbiol Lett, vol.341, issue.1, pp.1-12, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01130833

H. Y. Cheng, V. W. Soo, S. Islam, M. J. Mcanulty, M. J. Benedik et al., Toxin GhoT of the GhoT/GhoS toxin/antitoxin system damages the cell membrane to reduce adenosine triphosphate and to reduce growth under stress, Environ Microbiol, vol.16, issue.6, pp.1741-1754, 2014.

N. Chin, J. Frey, C. F. Chang, and Y. F. Chang, Identification of a locus involved in the utilization of iron by Actinobacillus pleuropneumoniae, FEMS Microbiol Lett, vol.143, issue.1, pp.1-6, 1996.

W. Choi, Y. Yamaguchi, J. W. Lee, K. M. Jang, M. Inouye et al., Translation-dependent mRNA cleavage by YhaV in Escherichia coli, FEBS Lett, vol.591, issue.13, pp.1853-1861, 2017.
DOI : 10.1002/1873-3468.12705

URL : https://febs.onlinelibrary.wiley.com/doi/pdf/10.1002/1873-3468.12705

Y. Chong, R. Fitzhenry, R. Heuschkel, F. Torrente, G. Frankel et al., Human intestinal tissue tropism in Escherichia coli O157:H7-initial colonization of terminal ileum and Peyer's patches and minimal colonic adhesion ex vivo, Microbiology, vol.153, pp.794-802, 2007.

O. Clermont, S. Bonacorsi, and E. Bingen, Rapid and simple determination of the Escherichia coli phylogenetic group, Appl Environ Microbiol, vol.66, issue.10, pp.4555-4558, 2000.

R. Cobbold and P. Desmarchelier, Horizontal transmission of shiga toxin-producing Escherichia coli within groups of dairy calves, Appl Environ Microbiol, vol.68, issue.8, pp.4148-4152, 2002.

R. N. Cobbold, D. D. Hancock, D. H. Rice, J. Berg, R. Stilborn et al., Rectoanal junction colonization of feedlot cattle by Escherichia coli O157:H7 and its association with supershedders and excretion dynamics, Appl Environ Microbiol, vol.73, issue.5, pp.1563-1568, 2007.

J. R. Cole, Q. Wang, E. Cardenas, J. Fish, B. Chai et al., The ribosomal database project: improved alignments and new tools for rRNA analysis, Nucleic Acids Res, vol.37, pp.141-145, 2009.
DOI : 10.1093/nar/gkn879

URL : https://academic.oup.com/nar/article-pdf/37/suppl_1/D141/3337084/gkn879.pdf

T. Conway and P. S. Cohen, Commensal and pathogenic Escherichia coli metabolism in the gut, Microbiol Spectr, issue.3, p.3, 2015.
DOI : 10.1128/microbiolspec.mbp-0006-2014

URL : http://europepmc.org/articles/pmc4510460?pdf=render

T. Conway, K. A. Krogfelt, and P. S. Cohen, The life of commensal Escherichia coli in the mammalian intestine, EcoSal Plus, issue.1, p.1, 2004.

B. K. Coombes, M. E. Wickham, M. Mascarenhas, S. Gruenheid, B. B. Finlay et al., Molecular analysis as an aid to assess the public health risk of non-O157 shiga toxin producing Escherichia coli strains, Appl Environ Microbiol, vol.74, issue.7, pp.2153-2160, 2008.

C. Cordonnier, L. Etienne-mesmin, J. Thevenot, A. Rougeron, S. Renier et al.,

V. Livrelli, Enterohemorrhagic Escherichia coli pathogenesis: role of Long polar fimbriae in Peyer's patches interactions, Sci Rep, vol.7, p.44655, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02064681

C. Cordonnier, G. Le-bihan, J. G. Emond-rheault, A. Garrivier, J. Harel et al., Vitamin B12 uptake by the gut commensal bacteria Bacteroides thetaiotaomicron limits the production of shiga toxin by enterohemorrhagic Escherichia coli, Toxins (Basel), vol.8, issue.1, 2016.

C. Cordonnier, J. Thevenot, L. Etienne-mesmin, M. Alric, V. Livrelli et al., Probiotic and enterohemorrhagic Escherichia coli: An effective strategy against a deadly enemy, Crit Rev Microbiol, vol.43, issue.1, pp.116-132, 2017.
DOI : 10.1080/1040841x.2016.1185602

URL : https://hal.archives-ouvertes.fr/hal-01603948

N. A. Cornick, S. L. Booher, and H. W. Moon, Intimin facilitates colonization by Escherichia coli O157:H7 in adult ruminants, Infect Immun, vol.70, issue.5, pp.2704-2707, 2002.
DOI : 10.1128/iai.70.5.2704-2707.2002

URL : https://iai.asm.org/content/70/5/2704.full.pdf

N. A. Cornick, I. Matise, J. E. Samuel, B. T. Bosworth, and H. W. Moon, Edema disease as a model for systemic disease induced by Shiga toxin-producing E. coli, Adv Exp Med Biol, vol.473, pp.155-161, 1999.
DOI : 10.1007/978-1-4615-4143-1_14

J. M. Cowden and P. Christie, Scottish outbreak of Escherichia coli O157, Health Bull (Edinb), vol.55, issue.1, pp.9-10, 1997.

W. C. Cray, . Jr, and H. W. Moon, Experimental infection of calves and adult cattle with Escherichia coli O157:H7, Appl Environ Microbiol, vol.61, issue.4, pp.1586-1590, 1995.

M. A. Croxen and B. B. Finlay, Molecular mechanisms of Escherichia coli pathogenicity, Nat Rev Microbiol, vol.8, issue.1, pp.26-38, 2010.

M. Eppinger, M. K. Mammel, J. E. Leclerc, J. Ravel, and T. A. Cebula, Genome signatures of Escherichia coli O157:H7 isolates from the bovine host reservoir, Appl Environ Microbiol, vol.77, issue.9, pp.2916-2925, 2011.

A. L. Erdem, F. Avelino, J. Xicohtencatl-cortes, and J. A. Giron, Host protein binding and adhesive properties of H6 and H7 flagella of attaching and effacing Escherichia coli, J Bacteriol, vol.189, issue.20, pp.7426-7435, 2007.

M. G. Espey, Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota, Free Radic Biol Med, vol.55, pp.130-140, 2013.

E. Espié, F. Grimont, P. Mariani-kurkdjian, and V. Vaillant, Surveillance du syndrome hémolytique et urémique chez les enfants de moins de 15 ans en France en, & le réseau des néphrologues pédiatres, 2005.

A. I. Etcheverria and N. L. Padola, Shiga toxin-producing Escherichia coli: factors involved in virulence and cattle colonization, Virulence, vol.4, issue.5, pp.366-372, 2013.

L. Etienne-mesmin, B. Chassaing, P. Sauvanet, J. Denizot, S. Blanquet-diot et al., Interactions with M cells and macrophages as key steps in the pathogenesis of enterohemorrhagic Escherichia coli infections, PLoS One, vol.6, issue.8, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00748909

W. H. Ewing, Edwards and Ewing's identification of Enterobacteriaceae, 1986.

A. J. Fabich, S. A. Jones, F. Z. Chowdhury, A. Cernosek, A. Anderson et al.,

T. Conway, Comparison of carbon nutrition for pathogenic and commensal Escherichia coli strains in the mouse intestine, Infect Immun, vol.76, issue.3, pp.1143-1152, 2008.

J. M. Fairbrother and E. Nadeau, Escherichia coli: on-farm contamination of animals, Rev Sci Tech, vol.25, issue.2, pp.555-569, 2006.

N. G. Faith, J. A. Shere, R. Brosch, K. W. Arnold, S. E. Ansay et al.,

C. W. Kaspar, Prevalence and clonal nature of Escherichia coli O157:H7 on dairy farms in Wisconsin, Appl Environ Microbiol, vol.62, issue.5, pp.1519-1525, 1996.

M. J. Farfan, L. Cantero, R. Vidal, D. J. Botkin, and A. G. Torres, Long polar fimbriae of enterohemorrhagic Escherichia coli O157:H7 bind to extracellular matrix proteins, Infect Immun, vol.79, issue.9, pp.3744-3750, 2011.

C. Farrokh, K. Jordan, F. Auvray, K. Glass, H. Oppegaard et al., Review of Shiga-toxin-producing Escherichia coli (STEC) and their significance in dairy production, Int J Food Microbiol, vol.162, issue.2, pp.190-212, 2013.

W. A. Ferens and C. J. Hovde, Escherichia coli O157:H7: animal reservoir and sources of human infection, Foodborne Pathog Dis, vol.8, issue.4, pp.465-487, 2011.

R. Fitzhenry, S. Dahan, A. G. Torres, Y. Chong, R. Heuschkel et al., Long polar fimbriae and tissue tropism in Escherichia coli O157:H7. Microbes Infect, vol.8, pp.1741-1749, 2006.
DOI : 10.1016/j.micinf.2006.02.012

R. J. Fitzhenry, D. J. Pickard, E. L. Hartland, S. Reece, G. Dougan et al., Intimin type influences the site of human intestinal mucosal colonisation by enterohaemorrhagic Escherichia coli O157:H7, Gut, vol.50, issue.2, pp.180-185, 2002.

G. Fonty, P. Gouet, J. P. Jouany, and J. Senaud, Establishment of the microflora and anaerobic Fungi in the rumen of lamnbs, Journal of General Microbiology, vol.133, pp.1835-1843, 1987.

G. Fonty, P. Gouet, and J. M. Nebout, Development of the cellulolytic microflora in the rumen of lambs transferred into sterile isolators a few days after birth, Can J Microbiol, vol.35, issue.3, pp.416-422, 1989.

G. Fonty, J. Senaud, J. P. Jouany, and P. Gouet, Establishment of ciliate protozoa in the rumen of conventional and conventionalized lambs: influence of diet and management conditions, Can J Microbiol, vol.34, issue.3, pp.235-241, 1988.

C. Hill, Virulence or niche factors: what's in a name?, J Bacteriol, vol.194, issue.21, pp.5725-5727, 2012.

D. E. Hoey, C. Currie, R. W. Else, A. Nutikka, C. A. Lingwood et al., Expression of receptors for verotoxin 1 from Escherichia coli O157 on bovine intestinal epithelium, J Med Microbiol, vol.51, issue.2, pp.143-149, 2002.

R. A. Hogg, J. P. Holmes, S. Ghebrehewet, K. Elders, J. Hart et al.,

G. C. Pritchard, Probable zoonotic transmission of verocytotoxigenic Escherichia coli O157 by dogs, Vet Rec, vol.164, issue.10, pp.304-305, 2009.

D. T. Hughes, D. A. Terekhova, L. Liou, C. J. Hovde, J. W. Sahl et al., Chemical sensing in mammalian host-bacterial commensal associations, Proc Natl Acad Sci, vol.107, issue.21, pp.9831-9836, 2010.

J. Ihssen and T. Egli, Global physiological analysis of carbon-and energy-limited growing Escherichia coli confirms a high degree of catabolic flexibility and preparedness for mixed substrate utilization, Environ Microbiol, vol.7, issue.10, pp.1568-1581, 2005.

K. Iida, Y. Mizunoe, S. N. Wai, and S. Yoshida, Type 1 fimbriation and its phase switching in diarrheagenic Escherichia coli strains, Clin Diagn Lab Immunol, vol.8, issue.3, pp.489-495, 2001.

L. Imamovic, J. Jofre, H. Schmidt, R. Serra-moreno, and M. Muniesa, Phage-mediated shiga toxin 2 gene transfer in food and water, Appl Environ Microbiol, vol.75, issue.6, pp.1764-1768, 2009.

M. A. Islam, A. S. Mondol, E. De-boer, R. R. Beumer, M. H. Zwietering et al., Prevalence and genetic characterization of shiga toxin-producing Escherichia coli isolates from slaughtered animals in Bangladesh, Appl Environ Microbiol, vol.74, issue.17, pp.5414-5421, 2008.

M. Z. Islam, A. Musekiwa, K. Islam, S. Ahmed, S. Chowdhury et al., Regional variation in the prevalence of E. coli O157 in cattle: a meta-analysis and metaregression, PLoS One, vol.9, issue.4, p.93299, 2014.

R. Iyer, C. Williams, and C. Miller, Arginine-agmatine antiporter in extreme acid resistance in Escherichia coli, J Bacteriol, vol.185, issue.22, pp.6556-6561, 2003.

M. E. Jacob, T. R. Callaway, and T. G. Nagaraja, Dietary interactions and interventions affecting Escherichia coli O157 colonization and shedding in cattle, Foodborne Pathog Dis, vol.6, issue.7, pp.785-792, 2009.

E. Jami, A. Israel, A. Kotser, and I. Mizrahi, Exploring the bovine rumen bacterial community from birth to adulthood, ISME J, vol.7, issue.6, pp.1069-1079, 2013.

E. Jami and I. Mizrahi, Composition and similarity of bovine rumen microbiota across individual animals, PLoS One, vol.7, issue.3, p.33306, 2012.

I. G. Janausch, E. Zientz, Q. H. Tran, A. Kroger, and G. Unden, C4-dicarboxylate carriers and sensors in bacteria, Biochim Biophys Acta, vol.1553, issue.1-2, pp.39-56, 2002.

P. H. Janssen and M. Kirs, Structure of the archaeal community of the rumen, Appl Environ Microbiol, vol.74, issue.12, pp.3619-3625, 2008.

I. Jelcic, E. Hufner, H. Schmidt, and C. Hertel, Repression of the locus of the enterocyte effacement-encoded regulator of gene transcription of Escherichia coli O157:H7 by Lactobacillus reuteri culture supernatants is LuxS and strain dependent, Appl Environ Microbiol, vol.74, issue.10, pp.3310-3314, 2008.

S. J. Jeon, M. Elzo, N. Dilorenzo, G. C. Lamb, and K. C. Jeong, Evaluation of animal genetic and physiological factors that affect the prevalence of Escherichia coli O157 in cattle, PLoS One, vol.8, issue.2, 2013.

M. E. Johansson, D. Ambort, T. Pelaseyed, A. Schutte, J. K. Gustafsson et al.,

G. C. Hansson, Composition and functional role of the mucus layers in the intestine, Cell Mol Life Sci, vol.68, issue.22, pp.3635-3641, 2011.

, Appl Environ Microbiol, vol.81, issue.5, pp.1644-1651

E. Kieckens, J. Rybarczyk, R. W. Li, D. Vanrompay, and E. Cox, Potential immunosuppressive effects of Escherichia coli O157:H7 experimental infection on the bovine host, BMC Genomics, vol.17, issue.1, p.1049, 2016.

M. Kim, M. Morrison, and Z. Yu, Status of the phylogenetic diversity census of ruminal microbiomes, FEMS Microbiol Ecol, vol.76, issue.1, pp.49-63, 2011.

L. A. King, M. Gouali, P. Mariani-kurkdjian, and V. Vaillant, Surveillance du syndrome hémolytique et urémique post-diarrhéique chez les enfants de moins de 15 ans en France en 2012, & le réseau des néphroloques pédiatres, 2012.
DOI : 10.1016/s0929-693x(13)71303-4

L. A. King, E. Loukiadis, P. Mariani-kurkdjian, S. Haeghebaert, F. X. Weill et al., Foodborne transmission of sorbitol-fermenting Escherichia coli O157:[H7] via ground beef: an outbreak in northern France, Clin Microbiol Infect, vol.20, issue.12, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-02025475

L. A. King, M. Macé, P. Mariani-kurkdjian, M. Gouali, and V. Vaillant, Surveillance du syndrome hémolytique et urémique post-diarrhéique chez les enfants de moins de 15 ans en France en, 2011.
DOI : 10.1016/s0929-693x(13)71303-4

L. A. King, P. Mariani-kurkdjian, M. Gouali, and V. Vaillant, Surveillance du syndrome hémolytique et urémique post-diarrhéique chez les enfants de moins de 15 ans en France en 2013, & le réseau des néphrologues pédiatres, 2013.
DOI : 10.1016/s0929-693x(13)71303-4

T. King, S. Lucchini, J. C. Hinton, and K. Gobius, Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant-and strain-specific acid tolerance responses, Appl Environ Microbiol, vol.76, issue.19, pp.6514-6528, 2010.

E. Kintz, J. Brainard, L. Hooper, and P. Hunter, Transmission pathways for sporadic shiga-toxin producing E. coli infections: A systematic review and meta-analysis, Int J Hyg Environ Health, vol.220, issue.1, pp.57-67, 2017.
DOI : 10.1016/j.ijheh.2016.10.011

URL : https://doi.org/10.1016/j.ijheh.2016.10.011

S. Kittelmann and P. H. Janssen, Characterization of rumen ciliate community composition in domestic sheep, deer, and cattle, feeding on varying diets, by means of PCR-DGGE and clone libraries, FEMS Microbiol Ecol, vol.75, issue.3, pp.468-481, 2011.

S. Kittelmann, H. Seedorf, W. A. Walters, J. C. Clemente, R. Knight et al., Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities, PLoS One, vol.8, issue.2, p.47879, 2013.

R. Kolde, pheatmap: pretty heatmaps, 2015.

R. Kolenda, M. Burdukiewicz, and P. Schierack, A systematic review and meta-analysis of the epidemiology of pathogenic Escherichia coli of calves and the role of calves as reservoirs for human pathogenic, E. coli. Front Cell Infect Microbiol, vol.5, p.23, 2015.

A. U. Kresse, M. Rohde, and C. A. Guzman, The EspD protein of enterohemorrhagic Escherichia coli is required for the formation of bacterial surface appendages and is incorporated in the cytoplasmic membranes of target cells, Infect Immun, vol.67, issue.9, pp.4834-4842, 1999.

A. Kruger and P. M. Lucchesi, Shiga toxins and stx phages: highly diverse entities. Microbiology, pp.451-462, 2015.

I. T. Kudva, K. Blanch, and C. J. Hovde, Analysis of Escherichia coli O157:H7 survival in ovine or bovine manure and manure slurry, Appl Environ Microbiol, vol.64, issue.9, pp.3166-3174, 1998.

I. T. Kudva and E. A. Dean-nystrom, Bovine recto-anal junction squamous epithelial (RSE) cell adhesion assay for studying Escherichia coli O157 adherence, J Appl Microbiol, vol.111, issue.5, pp.1283-1294, 2011.
DOI : 10.1111/j.1365-2672.2011.05139.x

URL : https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2672.2011.05139.x

I. T. Kudva, R. W. Griffin, B. Krastins, D. A. Sarracino, S. B. Calderwood et al., Proteins other than the locus of enterocyte effacement-encoded proteins contribute to Escherichia coli O157:H7 adherence to bovine rectoanal junction stratified squamous epithelial cells, BMC Microbiol, vol.12, p.103, 2012.

I. T. Kudva, C. J. Hovde, and M. John, Adherence of non-O157 shiga toxin-producing Escherichia coli to bovine recto-anal junction squamous epithelial cells appears to be mediated by mechanisms distinct from those used by O157, Foodborne Pathog Dis, vol.10, issue.4, pp.375-381, 2013.

I. T. Kudva, T. B. Stanton, and J. D. Lippolis, The Escherichia coli O157:H7 bovine rumen fluid proteome reflects adaptive bacterial responses, BMC Microbiol, vol.14, p.48, 2014.
DOI : 10.1186/1471-2180-14-48

URL : https://bmcmicrobiol.biomedcentral.com/track/pdf/10.1186/1471-2180-14-48

J. H. Mermin and P. M. Griffin, Public health in crisis: outbreaks of Escherichia coli O157:H7 infections in Japan, Am J Epidemiol, vol.150, issue.8, pp.804-795, 1999.

R. A. Mir, T. A. Weppelmann, M. Elzo, S. Ahn, J. D. Driver et al., Colonization of beef cattle by shiga toxin-producing Escherichia coli during the first year of life: a cohort study, PLoS One, vol.11, issue.2, 2016.

R. A. Mir, T. A. Weppelmann, M. Kang, T. M. Bliss, N. Dilorenzo et al., Association between animal age and the prevalence of shiga toxin-producing Escherichia coli in a cohort of beef cattle, Vet Microbiol, vol.175, issue.2-4, pp.325-331, 2015.

R. L. Miranda, T. Conway, M. P. Leatham, D. E. Chang, W. E. Norris et al.,

P. S. Cohen, Glycolytic and gluconeogenic growth of Escherichia coli O157:H7 (EDL933) and E. coli K-12 (MG1655) in the mouse intestine, Infect Immun, vol.72, issue.3, pp.1666-1676, 2004.

L. Montagne, R. Toullec, and J. P. Lalles, Calf intestinal mucin: isolation, partial characterization, and measurement in ileal digesta with an enzyme-linked immunosorbent assay, J Dairy Sci, vol.83, issue.3, pp.507-517, 2000.
DOI : 10.3168/jds.s0022-0302(00)74910-1

A. P. Moran, A. Gupta, and L. Joshi, Sweet-talk: role of host glycosylation in bacterial pathogenesis of the gastrointestinal tract, Gut, vol.60, issue.10, pp.1412-1425, 2011.

C. G. Moreira and V. Sperandio, The epinephrine/norepinephrine/autoinducer-3 interkingdom signaling system in Escherichia coli O157:H7, Adv Exp Med Biol, vol.874, pp.247-261, 2016.
DOI : 10.1007/978-1-4419-5576-0_12

R. A. Moxley and G. R. Acuff, Peri-and postharvest factors in the control of shiga toxinproducing Escherichia coli in beef, Microbiol Spectr, vol.2, issue.6, 2014.

R. A. Moxley and D. R. Smith, Attaching-effacing Escherichia coli infections in cattle, Vet Clin North Am Food Anim Pract, vol.26, issue.1, pp.29-56, 2010.

S. Mukhopadhyay and A. D. Linstedt, Manganese blocks intracellular trafficking of shiga toxin and protects against shiga toxicosis, Science, vol.335, issue.6066, pp.332-335, 2012.
DOI : 10.1126/science.1215930

URL : http://europepmc.org/articles/pmc5367627?pdf=render

K. D. Munns, L. B. Selinger, K. Stanford, L. Guan, T. R. Callaway et al., Perspectives on super-shedding of Escherichia coli O157:H7 by cattle, Foodborne Pathog Dis, vol.12, issue.2, pp.89-103, 2015.

K. D. Munns, R. Zaheer, Y. Xu, K. Stanford, C. R. Laing et al.,

T. A. Mcallister, Comparative genomic analysis of Escherichia coli O157:H7 isolated from super-shedder and low-shedder cattle, PLoS One, vol.11, issue.3, p.151673, 2016.

N. Nakanishi, K. Tashiro, S. Kuhara, T. Hayashi, N. Sugimoto et al., Regulation of virulence by butyrate sensing in enterohaemorrhagic Escherichia coli, Microbiology, vol.155, pp.521-530, 2009.

P. Nart, S. W. Naylor, J. F. Huntley, I. J. Mckendrick, D. L. Gally et al., Responses of cattle to gastrointestinal colonization by Escherichia coli O157:H7, Infect Immun, vol.76, issue.11, pp.5366-5372, 2008.

J. P. Nataro and J. B. Kaper, Diarrheagenic Escherichia coli, Clin Microbiol Rev, vol.11, issue.1, pp.142-201, 1998.
DOI : 10.1128/cmr.11.2.403

URL : https://cmr.asm.org/content/cmr/11/2/403.full.pdf

S. W. Naylor, A. Flockhart, P. Nart, D. G. Smith, J. Huntley et al., Shedding of Escherichia coli O157:H7 in calves is reduced by prior colonization with the homologous strain, Appl Environ Microbiol, vol.73, issue.11, pp.3765-3767, 2007.

S. W. Naylor, D. L. Gally, and J. C. Low, Enterohaemorrhagic E. coli in veterinary medicine, Int J Med Microbiol, vol.295, issue.6-7, pp.419-441, 2005.

S. W. Naylor, J. C. Low, T. E. Besser, A. Mahajan, G. J. Gunn et al.,

D. L. Gally, Lymphoid follicle-dense mucosa at the terminal rectum is the principal site of colonization of enterohemorrhagic Escherichia coli O157:H7 in the bovine host, Infect Immun, vol.71, issue.3, pp.1505-1512, 2003.

S. W. Naylor, A. J. Roe, P. Nart, K. Spears, D. G. Smith et al., Escherichia coli O157:H7 forms attaching and effacing lesions at the terminal rectum of cattle and colonization requires the LEE4 operon, Microbiology, pp.2773-2781, 2005.

B. C. Neves, R. K. Shaw, G. Frankel, and S. Knutton, Polymorphisms within EspA filaments of enteropathogenic and enterohemorrhagic Escherichia coli, Infect Immun, vol.71, issue.4, pp.2262-2265, 2003.

F. A. Nicholson, S. J. Groves, and B. J. Chambers, Pathogen survival during livestock manure storage and following land application, Bioresour Technol, vol.96, issue.2, pp.135-143, 2005.

Y. D. Niu, Y. Xu, T. A. Mcallister, E. A. Rozema, T. P. Stephens et al.,

K. Stanford, Comparison of fecal versus rectoanal mucosal swab sampling for detecting Escherichia coli O157:H7 in experimentally inoculated cattle used in assessing bacteriophage as a mitigation strategy, J Food Prot, vol.71, issue.4, pp.691-698, 2008.

J. W. Njoroge, Y. Nguyen, M. M. Curtis, C. G. Moreira, and V. Sperandio, Virulence meets metabolism: Cra and KdpE gene regulation in enterohemorrhagic Escherichia coli, MBio, vol.3, issue.5, 2012.

S. B. O'brien, G. Duffy, E. Carney, J. J. Sheridan, D. A. Mcdowell et al., Prevalence and numbers of Escherichia coli O157 on bovine hides at a beef slaughter plant, J Food Prot, vol.68, issue.4, pp.660-665, 2005.

E. V. O'loughlin and R. M. Robins-browne, Effect of shiga toxin and shiga-like toxins on eukaryotic cells, Microbes Infect, vol.3, issue.6, pp.493-507, 2001.

M. Ogawa, K. Shimizu, K. Nomoto, R. Tanaka, T. Hamabata et al., Inhibition of in vitro growth of shiga toxin-producing Escherichia coli O157:H7 by probiotic Lactobacillus strains due to production of lactic acid, Int J Food Microbiol, vol.68, issue.1-2, pp.135-140, 2001.

I. D. Ogden, M. Macrae, and N. J. Strachan, Is the prevalence and shedding concentrations of E. coli O157 in beef cattle in Scotland seasonal, FEMS Microbiol Lett, vol.233, issue.2, pp.297-300, 2004.

T. Ohya and H. Ito, Experimental infection of calves with Escherichia coli O157:H7, J Vet Med Sci, vol.61, issue.10, pp.1187-1189, 1999.

T. Ohya, T. Marubashi, and H. Ito, Significance of fecal volatile fatty acids in shedding of Escherichia coli O157 from calves: experimental infection and preliminary use of a probiotic product, J Vet Med Sci, vol.62, issue.11, pp.1151-1155, 2000.

F. Omisakin, M. Macrae, I. D. Ogden, and N. J. Strachan, Concentration and prevalence of Escherichia coli O157 in cattle feces at slaughter, Appl Environ Microbiol, vol.69, issue.5, pp.2444-2447, 2003.

D. Orth, S. Ehrlenbach, J. Brockmeyer, A. B. Khan, G. Huber et al.,

R. Wurzner, , 2010.

, EspP, a serine protease of enterohemorrhagic Escherichia coli, impairs complement activation by cleaving complement factors C3/C3b and C5, Infect Immun, vol.78, issue.10, pp.4294-4301

N. Ottman, M. Davids, M. Suarez-diez, S. Boeren, P. J. Schaap et al., Genome-scale model and omics analysis of metabolic capacities of Akkermansia muciniphila reveal a preferential mucin-degrading lifestyle, Appl Environ Microbiol, issue.18, p.83, 2017.

Y. Ozutsumi, H. Hayashi, M. Sakamoto, H. Itabashi, and Y. Benno, Culture-independent analysis of fecal microbiota in cattle, Biosci Biotechnol Biochem, vol.69, issue.9, pp.1793-1797, 2005.

A. R. Pacheco, M. M. Curtis, J. M. Ritchie, D. Munera, M. K. Waldor et al., Fucose sensing regulates bacterial intestinal colonization, Nature, vol.492, issue.7427, pp.113-117, 2012.

R. Page and W. Peti, Toxin-antitoxin systems in bacterial growth arrest and persistence, Nat Chem Biol, vol.12, issue.4, pp.208-214, 2016.

C. T. Parker, J. L. Kyle, S. Huynh, M. Q. Carter, M. T. Brandl et al., Distinct transcriptional profiles and phenotypes exhibited by Escherichia coli O157:H7 isolates related to the 2006 spinach-associated outbreak, Appl Environ Microbiol, vol.78, issue.2, pp.455-463, 2012.

A. W. Paton, P. Srimanote, M. C. Woodrow, and J. C. Paton, Characterization of Saa, a novel autoagglutinating adhesin produced by locus of enterocyte effacement-negative shigatoxigenic Escherichia coli strains that are virulent for humans, Infect Immun, vol.69, issue.11, pp.6999-7009, 2001.

A. W. Paton, E. Voss, P. A. Manning, and J. C. Paton, Antibodies to lipopolysaccharide block adherence of shiga toxin-producing Escherichia coli to human intestinal epithelial (Henle 407) cells, Microb Pathog, vol.24, issue.1, pp.57-63, 1998.

K. Pedersen and L. Clark, A review of shiga toxin Eschrichia coli ans Salmonella enterica in cattle and free-ranging birds: potential association and epidemiological links, Human-Wildlife Conflicts, vol.1, issue.1, pp.68-77, 2007.

J. T. Penrod, C. C. Mace, and J. R. Roth, A pH-sensitive function and phenotype: evidence that EutH facilitates diffusion of uncharged ethanolamine in Salmonella enterica, J Bacteriol, vol.186, issue.20, pp.6885-6890, 2004.

N. T. Perna, G. F. Mayhew, G. Posfai, S. Elliott, M. S. Donnenberg et al., Molecular evolution of a pathogenicity island from enterohemorrhagic Escherichia coli O157:H7, Infect Immun, vol.66, issue.8, pp.3810-3817, 1998.

N. T. Perna, G. Plunkett, V. Burland, B. Mau, J. D. Glasner et al.,

F. R. Blattner, , 2001.

, Genome sequence of enterohaemorrhagic Escherichia coli O157:H7, Nature, vol.409, issue.6819, pp.529-533

A. K. Persad and J. T. Lejeune, Animal reservoirs of shiga toxin producing Escherichia coli, Microbiol Spectr, vol.2, issue.4, 2014.

R. E. Peterson, T. J. Klopfenstein, R. A. Moxley, G. E. Erickson, S. Hinkley et al.,

D. R. Smith, Effect of a vaccine product containing type III secreted proteins on the probability of Escherichia coli O157:H7 fecal shedding and mucosal colonization in feedlot cattle, J Food Prot, vol.70, issue.11, pp.2568-2577, 2007.

A. D. Phillips, S. Navabpour, S. Hicks, G. Dougan, T. Wallis et al., , 2000.

, Enterohaemorrhagic Escherichia coli O157:H7 target Peyer's patches in humans and cause attaching/effacing lesions in both human and bovine intestine, Gut, vol.47, issue.3, pp.377-381

C. Picozzi, D. Antoniani, I. Vigentini, and R. Foschino, Genotypic characterization and biofilm formation of shiga toxin-producing Escherichia coli, FEMS Microbiol Lett, vol.364, issue.2, 2016.

R. Pifer and V. Sperandio, The interplay between the microbiota and enterohemorrhagic Escherichia coli, Microbiol Spectr, vol.2, issue.5, 2014.

J. F. Pohlenz and E. A. Dean-nystrom, Colonisation of Escherichia coli O157:H7 on squamous epithelial cells at the rectal-anal junction, Vet Rec, vol.155, issue.8, p.248, 2004.

N. Pradel, V. Livrelli, C. De-champs, J. B. Palcoux, A. Reynaud et al.,

C. Forestier, Prevalence and characterization of Shiga toxin-producing Escherichia coli isolated from cattle, food, and children during a one-year prospective study in France, J Clin Microbiol, vol.38, issue.3, pp.1023-1031, 2000.

G. A. Preidis, C. Hill, R. L. Guerrant, B. S. Ramakrishna, G. W. Tannock et al., , 2011.

. Probiotics, enteric and diarrheal diseases, and global health, Gastroenterology, vol.140, issue.1, pp.8-14

C. E. Price and A. J. Driessen, Biogenesis of membrane bound respiratory complexes in Escherichia coli, Biochim Biophys Acta, issue.6, pp.748-766, 2010.

S. B. Price, J. C. Wright, F. J. Degraves, M. P. Castanie-cornet, and J. W. Foster, Acid resistance systems required for survival of Escherichia coli O157:H7 in the bovine gastrointestinal tract and in apple cider are different, Appl Environ Microbiol, vol.70, issue.8, pp.4792-4799, 2004.

I. M. Pruimboom-brees, T. W. Morgan, M. R. Ackermann, E. D. Nystrom, J. E. Samuel et al., Cattle lack vascular receptors for Escherichia coli O157:H7 shiga toxins, Proc Natl Acad Sci, issue.19, pp.10325-10329, 2000.

S. Puttamreddy, N. A. Cornick, and F. C. Minion, , 2010.

, Genome-wide transposon mutagenesis reveals a role for pO157 genes in biofilm development in Escherichia coli O157:H7 EDL933, vol.78, pp.2377-2384

. R-core-team, R: A language and environment for statistical computing, 2016.

M. A. Rasmussen and T. A. Casey, Environmental and food safety aspects of Escherichia coli O157:H7 infections in cattle, Crit Rev Microbiol, vol.27, issue.2, pp.57-73, 2001.

M. A. Rasmussen, W. C. Cray, . Jr, T. A. Casey, and S. C. Whipp, Rumen contents as a reservoir of enterohemorrhagic Escherichia coli, FEMS Microbiol Lett, vol.114, issue.1, pp.79-84, 1993.

S. Raynaud, P. Boscher, P. Picant, B. Mathieu, C. Degand et al., Prévalence, origine, circulation et persistance des Escherichia coli producteurs de shiga-toxines (STEC) dans les élevages bovins français, Renc Rech Ruminants, vol.12, pp.379-392, 2005.

N. C. Reading, D. A. Rasko, A. G. Torres, and V. Sperandio, The two-component system QseEF and the membrane protein QseG link adrenergic and stress sensing to bacterial pathogenesis, Proc Natl Acad Sci U S A, vol.106, issue.14, pp.5889-5894, 2009.

M. A. Rendon, Z. Saldana, A. L. Erdem, V. Monteiro-neto, A. Vazquez et al.,

J. A. Giron, Commensal and pathogenic Escherichia coli use a common pilus adherence factor for epithelial cell colonization, Proc Natl Acad Sci U S A, vol.104, issue.25, pp.10637-10642, 2007.

J. D. Riff, J. W. Callahan, and P. M. Sherman, Cholesterol-enriched membrane microdomains are required for inducing host cell cytoskeleton rearrangements in response to attachingeffacing Escherichia coli, Infect Immun, vol.73, issue.11, pp.7113-7125, 2005.

L. W. Riley, R. S. Remis, S. D. Helgerson, H. B. Mcgee, J. G. Wells et al.,

M. L. Cohen, Hemorrhagic colitis associated with a rare Escherichia coli serotype, N Engl J Med, vol.308, issue.12, pp.681-685, 1983.

M. A. Rivero, J. A. Passucci, E. M. Rodriguez, and A. E. Parma, Role and clinical course of verotoxigenic Escherichia coli infections in childhood acute diarrhoea in Argentina, J Med Microbiol, vol.59, pp.345-352, 2010.

C. M. Robinson, J. F. Sinclair, M. J. Smith, and A. D. Brien, Shiga toxin of enterohemorrhagic Escherichia coli type O157:H7 promotes intestinal colonization, Proc Natl Acad Sci U S A, vol.103, issue.25, pp.9667-9672, 2006.

A. J. Roe, C. Currie, D. G. Smith, and D. L. Gally, Analysis of type 1 fimbriae expression in verotoxigenic Escherichia coli: a comparison between serotypes O157 and O26, Microbiology, pp.145-152, 2001.

F. Rogerie, A. Marecat, S. Gambade, F. Dupond, P. Beaubois et al., Characterization of shiga toxin producing E. coli and O157 serotype E. coli isolated in France from healthy domestic cattle, Int J Food Microbiol, vol.63, issue.3, pp.217-223, 2001.

M. H. Rostagno, Can stress in farm animals increase food safety risk?, Foodborne Pathog Dis, vol.6, issue.7, pp.767-776, 2009.
DOI : 10.1089/fpd.2009.0315

J. M. Rounds, C. E. Rigdon, L. J. Muhl, M. Forstner, G. T. Danzeisen et al., Non-O157 shiga toxin-producing Escherichia coli associated with venison, Emerg Infect Dis, vol.18, issue.2, pp.279-282, 2012.

M. V. Rumi, K. Irino, N. Deza, M. J. Huguet, and A. B. Bentancor, First isolation in Argentina of a highly virulent shiga toxin-producing Escherichia coli O145:NM from a domestic cat, J Infect Dev Ctries, vol.6, issue.4, pp.358-363, 2012.

J. B. Russell and J. L. Rychlik, Factors that alter rumen microbial ecology, Science, vol.292, issue.5519, pp.1119-1122, 2001.
DOI : 10.1126/science.1058830

J. H. Ryu and L. R. Beuchat, Biofilm formation by Escherichia coli O157:H7 on stainless steel: effect of exopolysaccharide and Curli production on its resistance to chlorine, Appl Environ Microbiol, vol.71, issue.1, pp.247-254, 2005.

S. Sabouri, Z. Sepehrizadeh, S. Amirpour-rostami, and M. Skurnik, A minireview on the in vitro and in vivo experiments with anti-Escherichia coli O157:H7 phages as potential biocontrol and phage therapy agents, Int J Food Microbiol, vol.243, pp.52-57, 2017.

P. Saeedi, M. Yazdanparast, E. Behzadi, A. H. Salmanian, S. L. Mousavi et al., A review on strategies for decreasing E. coli O157:H7 risk in animals. Microb Pathog, vol.103, pp.186-195, 2017.
DOI : 10.1016/j.micpath.2017.01.001

M. Saha, J. K. Mcdaniel, and X. L. Zheng, Thrombotic thrombocytopenic purpura: pathogenesis, diagnosis, and potential novel therapeutics, J Thromb Haemost, 2017.
DOI : 10.1111/jth.13764

URL : https://onlinelibrary.wiley.com/doi/pdf/10.1111/jth.13764

J. Sambrook, E. F. Fritsch, and T. Maniatis, Current protocols in molecular biology, Molecular cloning: A laboratory manual, vol.1, p.1626, 1989.

M. W. Sanderson, T. E. Besser, J. M. Gay, C. C. Gay, and D. D. Hancock, Fecal Escherichia coli O157:H7 shedding patterns of orally inoculated calves, Vet Microbiol, vol.69, issue.3, pp.199-205, 1999.
DOI : 10.1016/s0378-1135(99)00106-6

K. Sandvig, J. Bergan, A. B. Dyve, T. Skotland, and M. L. Torgersen, Endocytosis and retrograde transport of shiga toxin, Toxicon, vol.56, issue.7, pp.1181-1185, 2010.

T. Saraoui, S. Parayre, G. Guernec, V. Loux, J. Montfort et al., A unique in vivo experimental approach reveals metabolic adaptation of the probiotic Propionibacterium freudenreichii to the colon environment, BMC Genomics, vol.14, p.911, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01209705

F. Scheutz, Taxonomy meets public health: the case of shiga toxin-producing Escherichia coli, Microbiol Spectr, vol.2, issue.3, 2014.

F. Scheutz, L. D. Teel, L. Beutin, D. Pierard, G. Buvens et al., Multicenter evaluation of a sequence-based protocol for subtyping shiga toxins and standardizing Stx nomenclature, J Clin Microbiol, vol.50, issue.9, pp.2951-2963, 2012.

C. L. Schultz, T. S. Edrington, T. R. Callaway, S. B. Schroeder, D. M. Hallford et al.,

D. J. Nisbet, The influence of melatonin on growth of E. coli O157:H7 in pure culture and exogenous melatonin on faecal shedding of E. coli O157:H7 in experimentally infected wethers, Lett Appl Microbiol, vol.43, issue.1, pp.105-110, 2006.

C. L. Schultz, T. S. Edrington, S. B. Schroeder, D. M. Hallford, K. J. Genovese et al.,

D. J. Nisbet, Effect of the thyroid on faecal shedding of E. coli O157:H7 and Escherichia coli in naturally infected yearling beef cattle, J Appl Microbiol, vol.99, issue.5, pp.1176-1180, 2005.

A. Segura, P. Auffret, C. Klopp, Y. Bertin, and E. Forano, Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastrointestinal tract, Stand Genomic Sci, vol.12, p.61, 2017.

R. Serra-moreno, J. Jofre, and M. Muniesa, Insertion site occupancy by stx2 bacteriophages depends on the locus availability of the host strain chromosome, J Bacteriol, vol.189, issue.18, pp.6645-6654, 2007.

N. Shaikh, N. J. Holt, J. R. Johnson, and P. I. Tarr, Fim operon variation in the emergence of Enterohemorrhagic Escherichia coli: an evolutionary and functional analysis, FEMS Microbiol Lett, vol.273, issue.1, pp.58-63, 2007.

V. K. Sharma and S. M. Bearson, Evaluation of the impact of quorum sensing transcriptional regulator SdiA on long-term persistence and fecal shedding of Escherichia coli O157:H7 in weaned calves, Microb Pathog, vol.57, pp.21-26, 2013.

V. K. Sharma, R. E. Sacco, R. A. Kunkle, S. M. Bearson, and D. E. Palmquist, Correlating levels of type III secretion and secreted proteins with fecal shedding of Escherichia coli O157:H7 in cattle, Infect Immun, vol.80, issue.4, pp.1333-1342, 2012.

H. Sheng, H. J. Knecht, I. T. Kudva, and C. J. Hovde, Application of bacteriophages to control intestinal Escherichia coli O157:H7 levels in ruminants, Appl Environ Microbiol, vol.72, issue.8, pp.5359-5366, 2006.

H. Sheng, J. Y. Lim, H. J. Knecht, J. Li, and C. J. Hovde, Role of Escherichia coli O157:H7 virulence factors in colonization at the bovine terminal rectal mucosa, Infect Immun, vol.74, issue.8, pp.4685-4693, 2006.

H. Sheng, Y. N. Nguyen, C. J. Hovde, and V. Sperandio, SdiA aids enterohemorrhagic Escherichia coli carriage by cattle fed a forage or grain diet, Infect Immun, vol.81, issue.9, pp.3472-3478, 2013.

H. Sheng, S. Shringi, K. N. Baker, S. A. Minnich, C. J. Hovde et al., Standardized Escherichia coli O157:H7 exposure studies in cattle provide evidence that bovine factors do not drive increased summertime colonization, Appl Environ Microbiol, vol.82, issue.3, pp.964-971, 2015.

P. M. Sherman, K. C. Johnson-henry, H. P. Yeung, P. S. Ngo, J. Goulet et al., Probiotics reduce enterohemorrhagic Escherichia coli O157:H7-and enteropathogenic E. coli O127:H6-induced changes in polarized T84 epithelial cell monolayers by reducing bacterial adhesion and cytoskeletal rearrangements, Infect Immun, vol.73, issue.8, pp.5183-5188, 2005.

R. Shin, M. Suzuki, and Y. Morishita, Influence of intestinal anaerobes and organic acids on the growth of enterohaemorrhagic Escherichia coli O157:H7, J Med Microbiol, vol.51, issue.3, pp.201-206, 2002.

J. F. Sinclair and A. D. Brien, Intimin types alpha, beta, and gamma bind to nucleolin with equivalent affinity but lower avidity than to the translocated intimin receptor, J Biol Chem, vol.279, issue.32, pp.33751-33758, 2004.

D. Smith, M. Blackford, S. Younts, R. Moxley, J. Gray et al.,

T. Klopfenstein, Ecological relationships between the prevalence of cattle shedding Escherichia coli O157:H7 and characteristics of the cattle or conditions of the feedlot pen, J Food Prot, vol.64, issue.12, pp.1899-1903, 2001.

D. G. Smith, S. W. Naylor, and D. L. Gally, Consequences of EHEC colonisation in humans and cattle, Int J Med Microbiol, vol.292, issue.3-4, pp.169-183, 2002.

K. E. Smith, P. R. Wilker, P. L. Reiter, E. B. Hedican, J. B. Bender et al., Antibiotic treatment of Escherichia coli O157 infection and the risk of hemolytic uremic syndrome, Pediatr Infect Dis J, vol.31, issue.1, pp.37-41, 2012.

T. A. Snider, A. J. Fabich, T. Conway, and K. D. Clinkenbeard, E. coli O157:H7 catabolism of intestinal mucin-derived carbohydrates and colonization, Vet Microbiol, vol.136, issue.1-2, pp.150-154, 2009.
URL : https://hal.archives-ouvertes.fr/in2p3-00356269

H. T. Solheim, C. Sekse, A. M. Urdahl, Y. Wasteson, and L. L. Nesse, Biofilm as an environment for dissemination of stx genes by transduction, Appl Environ Microbiol, vol.79, issue.3, pp.896-900, 2013.

U. Sonnenborn and J. Schuldes, The non-pathogenic Escherichia coli strain Nissle 1917features of versatile probiotic, Microbial Ecology in Health and Disease, vol.21, pp.122-158, 2009.

V. Sperandio, SdiA sensing of acyl-homoserine lactones by enterohemorrhagic E. coli (EHEC) serotype O157:H7 in the bovine rumen, Gut Microbes, vol.1, issue.6, pp.432-435, 2010.

V. Sperandio, A. G. Torres, J. A. Giron, and J. B. Kaper, Quorum sensing is a global regulatory mechanism in enterohemorrhagic Escherichia coli O157:H7, J Bacteriol, vol.183, issue.17, pp.5187-5197, 2001.

R. A. Spooner and J. M. Lord, How ricin and shiga toxin reach the cytosol of target cells: retrotranslocation from the endoplasmic reticulum, Curr Top Microbiol Immunol, vol.357, pp.19-40, 2012.

K. Stanford, R. P. Johnson, T. W. Alexander, T. A. Mcallister, and T. Reuter, Influence of season and feedlot location on prevalence and virulence factors of seven serogroups of Escherichia coli in feces of Western-Canadian slaughter cattle, PLoS One, vol.11, issue.8, 2016.

B. Stecher, The roles of inflammation, nutrient availability and the commensal microbiota in enteric pathogen infection, Microbiol Spectr, issue.3, p.3, 2015.

B. Stecher and W. D. Hardt, The role of microbiota in infectious disease, Trends Microbiol, vol.16, issue.3, pp.107-114, 2008.

M. P. Stevens and G. M. Frankel, The locus of enterocyte effacement and associated virulence factors of enterohemorrhagic Escherichia coli, Microbiol Spectr, vol.2, issue.4, 2014.

M. P. Stevens, A. J. Roe, I. Vlisidou, P. M. Van-diemen, R. M. La-ragione et al.,

T. S. Wallis, Mutation of toxB and a truncated version of the efa-1 gene in Escherichia coli O157:H7 influences the expression and secretion of locus of enterocyte effacement-encoded proteins but not intestinal colonization in calves or sheep, Infect Immun, vol.72, issue.9, pp.5402-5411, 2004.

M. P. Stevens, P. M. Van-diemen, G. Frankel, A. D. Phillips, and T. S. Wallis, Efa1 influences colonization of the bovine intestine by shiga toxin-producing Escherichia coli serotypes O5 and O111, Infect Immun, vol.70, issue.9, pp.5158-5166, 2002.

S. R. Steyert, J. W. Sahl, C. M. Fraser, L. D. Teel, F. Scheutz et al., Comparative genomics and stx phage characterization of LEE-negative shiga toxin-producing Escherichia coli, Front Cell Infect Microbiol, vol.2, p.133, 2012.

I. Stojiljkovic, M. Cobeljic, and K. Hantke, Escherichia coli K-12 ferrous iron uptake mutants are impaired in their ability to colonize the mouse intestine, FEMS Microbiol Lett, vol.108, issue.1, pp.111-115, 1993.

L. K. Su, C. P. Lu, Y. Wang, D. M. Cao, J. H. Sun et al., Lysogenic infection of a shiga toxin 2-converting bacteriophage changes host gene expression, 2010.

, Mol Biol (Mosk), vol.44, issue.1, pp.60-73

T. L. Talarico and W. J. Dobrogosz, Chemical characterization of an antimicrobial substance produced by Lactobacillus reuteri, Antimicrob Agents Chemother, vol.33, issue.5, pp.674-679, 1989.

Y. Taniguchi, P. J. Choi, G. W. Li, H. Chen, M. Babu et al.,

X. S. Xie, Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells, Science, vol.329, issue.5991, pp.533-538, 2010.

P. I. Tarr, S. S. Bilge, J. C. Vary, . Jr, S. Jelacic et al., Iha: a novel Escherichia coli O157:H7 adherence-conferring molecule encoded on a recently acquired chromosomal island of conserved structure, Infect Immun, vol.68, issue.3, pp.1400-1407, 2000.

I. Tatsuno, M. Horie, H. Abe, T. Miki, K. Makino et al., toxB gene on pO157 of enterohemorrhagic Escherichia coli O157:H7 is required for full epithelial cell adherence phenotype, Infect Immun, vol.69, issue.11, pp.6660-6669, 2001.

V. L. Tesh, Induction of apoptosis by shiga toxins, Future Microbiol, vol.5, issue.3, pp.431-453, 2010.

D. E. Thomas and E. J. Elliott, Interventions for preventing diarrhea-associated hemolytic uremic syndrome: systematic review, vol.13, p.799, 2013.

K. M. Thomas, M. S. Mccann, M. M. Collery, A. Logan, P. Whyte et al., Tracking verocytotoxigenic Escherichia coli O157, O26, O111, O103 and O145 in Irish cattle, Int J Food Microbiol, vol.153, issue.3, pp.288-296, 2012.

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, vol.103, issue.40, pp.14941-14946, 2006.

A. G. Torres, K. J. Kanack, C. B. Tutt, V. Popov, and J. B. Kaper, Characterization of the second long polar (LP) fimbriae of Escherichia coli O157:H7 and distribution of LP fimbriae in other pathogenic E. coli strains, FEMS Microbiol Lett, vol.238, issue.2, pp.333-344, 2004.

A. G. Torres and J. B. Kaper, Multiple elements controlling adherence of enterohemorrhagic Escherichia coli O157:H7 to HeLa cells, Infect Immun, vol.71, issue.9, pp.4985-4995, 2003.

A. G. Torres, N. T. Perna, V. Burland, A. Ruknudin, F. R. Blattner et al., Characterization of Cah, a calcium-binding and heat-extractable autotransporter protein of enterohaemorrhagic Escherichia coli, Mol Microbiol, vol.45, issue.4, pp.951-966, 2002.

R. Tozzoli, L. Grande, V. Michelacci, R. Fioravanti, D. Gally et al.,

S. Morabito, Identification and characterization of a peculiar vtx2-converting phage frequently present in verocytotoxin-producing Escherichia coli O157 isolated from human infections, Infect Immun, vol.82, issue.7, pp.3023-3032, 2014.

Y. D. Tremblay, S. Hathroubi, and M. Jacques, , 2014.

, Can J Vet Res, vol.78, issue.2, pp.110-116

L. A. Trotz-williams, N. J. Mercer, J. M. Walters, A. M. Maki, and R. P. Johnson, Pork implicated in a shiga toxin-producing Escherichia coli O157:H7 outbreak in Ontario, Canada. Can J Public Health, vol.103, issue.5, pp.322-326, 2012.

K. J. Turnbull and K. Gerdes, HicA toxin of Escherichia coli derepresses hicAB transcription to selectively produce HicB antitoxin, Mol Microbiol, vol.104, issue.5, pp.781-792, 2017.

G. A. Uhlich, KatP contributes to OxyR-regulated hydrogen peroxide resistance in Escherichia coli serotype O157:H7. Microbiology, pp.3589-3598, 2009.

G. Unden and J. Bongaerts, Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors, Biochim Biophys Acta, vol.1320, issue.3, pp.217-234, 1997.

G. Unden, A. Strecker, A. Kleefeld, O. B. Kim, P. M. Van-diemen et al., Identification of enterohemorrhagic Escherichia coli O26:H-genes required for intestinal colonization in calves, Infect Immun, vol.7, issue.1, pp.1735-1743, 2005.

J. Van-donkersgoed, J. Berg, A. Potter, D. Hancock, T. Besser et al.,

S. Klashinsky, Environmental sources and transmission of Escherichia coli O157 in feedlot cattle, Can Vet J, vol.42, issue.9, pp.714-720, 2001.

S. K. Vanaja, A. C. Springman, T. E. Besser, T. S. Whittam, and S. D. Manning, Differential expression of virulence and stress fitness genes between Escherichia coli O157:H7 strains with clinical or bovine-biased genotypes, Appl Environ Microbiol, vol.76, issue.1, pp.60-68, 2010.

. O. Vdsciences and . Vertébrés,

C. Venegas-vargas, S. Henderson, A. Khare, R. E. Mosci, J. D. Lehnert et al.,

S. D. Manning, Factors associated with shiga toxin-producing Escherichia coli shedding by dairy and beef cattle, Appl Environ Microbiol, vol.82, issue.16, pp.5049-5056, 2016.

C. Vernozy-rozand, M. P. Montet, F. Lequerrec, E. Serillon, B. Tilly et al.,

Y. Richard, Prevalence of verotoxin-producing Escherichia coli (VTEC) in slurry, farmyard manure and sewage sludge in France, J Appl Microbiol, vol.93, issue.3, pp.473-478, 2002.

S. Vidovic and D. R. Korber, Escherichia coli O157: Insights into the adaptive stress physiology and the influence of stressors on epidemiology and ecology of this human pathogen, Crit Rev Microbiol, vol.42, issue.1, pp.83-93, 2016.

S. Vidovic, A. K. Mangalappalli-illathu, and D. R. Korber, Prolonged cold stress response of Escherichia coli O157 and the role of RpoS, Int J Food Microbiol, vol.146, issue.2, pp.163-169, 2011.

S. Vidovic, A. K. Mangalappalli-illathu, H. Xiong, and D. R. Korber, Heat acclimation and the role of RpoS in prolonged heat shock of Escherichia coli O157, Food Microbiol, vol.30, issue.2, pp.457-464, 2012.

D. A. Vilte, M. Larzabal, S. Garbaccio, M. Gammella, B. C. Rabinovitz et al., Reduced faecal shedding of Escherichia coli O157:H7 in cattle following systemic vaccination with gamma-intimin C 280 and EspB proteins, Vaccine, vol.29, issue.23, pp.3962-3968, 2011.

I. Vlisidou, F. Dziva, R. M. La-ragione, A. Best, J. Garmendia et al.,

M. P. Stevens, Role of intimin-tir interactions and the tir-cytoskeleton coupling protein in the colonization of calves and lambs by Escherichia coli O157:H7, Infect Immun, vol.74, issue.1, pp.758-764, 2006.

I. Vlisidou, M. Lyte, P. M. Van-diemen, P. Hawes, P. Monaghan et al., The neuroendocrine stress hormone norepinephrine augments Escherichia coli O157:H7-induced enteritis and adherence in a bovine ligated ileal loop model of infection, Infect Immun, vol.72, issue.9, pp.5446-5451, 2004.

P. Vogeleer, Y. D. Tremblay, G. Jubelin, M. Jacques, and J. Harel, Biofilm-forming abilities of shiga toxin-producing Escherichia coli isolates associated with human infections, Appl Environ Microbiol, vol.82, issue.5, pp.1448-1458, 2015.

P. Vogeleer, Y. D. Tremblay, A. A. Mafu, M. Jacques, and J. Harel, Life on the outside: role of biofilms in environmental persistence of shiga-toxin producing Escherichia coli, Front Microbiol, vol.5, p.317, 2014.

H. Vu-khac and N. A. Cornick, Prevalence and genetic profiles of Shiga toxin-producing Escherichia coli strains isolated from buffaloes, cattle, and goats in central Vietnam, Vet Microbiol, vol.126, issue.4, pp.356-363, 2008.

P. L. Wagner, J. Livny, M. N. Neely, D. W. Acheson, D. I. Friedman et al., Bacteriophage control of shiga toxin 1 production and release by Escherichia coli, Mol Microbiol, vol.44, issue.4, pp.957-970, 2002.

P. L. Wagner, M. N. Neely, X. Zhang, D. W. Acheson, M. K. Waldor et al., Role for a phage promoter in shiga toxin 2 expression from a pathogenic Escherichia coli strain, J Bacteriol, vol.183, issue.6, pp.2081-2085, 2001.

G. Wang, T. Zhao, and M. P. Doyle, Fate of enterohemorrhagic Escherichia coli O157:H7 in bovine feces, Appl Environ Microbiol, vol.62, issue.7, pp.2567-2570, 1996.

O. Wang, T. A. Mcallister, G. Plastow, K. Stanford, B. Selinger et al., Hindgut mucosa-associated microbiome interacting with host regulating Escherichia coli O157:H7 shedding in cattle, Appl Environ Microbiol, 2017.
DOI : 10.1128/aem.01738-17

S. Wang, K. Deng, S. Zaremba, X. Deng, C. Lin et al., Transcriptomic response of Escherichia coli O157:H7 to oxidative stress, Appl Environ Microbiol, vol.75, issue.19, pp.6110-6123, 2009.

X. Wang, D. M. Lord, S. H. Hong, W. Peti, M. J. Benedik et al., Type II toxin/antitoxin MqsR/MqsA controls type V toxin/antitoxin GhoT/GhoS, Environ Microbiol, vol.15, issue.6, pp.1734-1744, 2013.
DOI : 10.1111/1462-2920.12063

URL : http://europepmc.org/articles/pmc3620836?pdf=render

Y. Watanabe, K. Ozasa, J. H. Mermin, P. M. Griffin, K. Masuda et al., Factory outbreak of Escherichia coli O157:H7 infection in Japan, Emerg Infect Dis, vol.5, issue.3, pp.424-428, 1999.

J. E. Wells, E. D. Berry, and V. H. Varel, Effects of common forage phenolic acids on Escherichia coli O157:H7 viability in bovine feces, Appl Environ Microbiol, vol.71, issue.12, pp.7974-7979, 2005.

J. E. Wells, M. Kim, J. L. Bono, L. A. Kuehn, and A. K. Benson, Meat Science and Muscle Biology Symposium: Escherichia coli O157:H7, diet, and fecal microbiome in beef cattle, J Anim Sci, vol.92, issue.4, pp.1345-1355, 2014.
DOI : 10.2527/jas.2013-7282

J. E. Wells, M. Kim, J. L. Bono, L. A. Kuehn, and A. K. Benson, MEAT SCIENCE AND MUSCLE BIOLOGY SYMPOSIUM: Escherichia coli O157:H7, diet, and fecal microbiome in beef cattle, J Anim Sci, vol.92, pp.1345-1355, 2014.
DOI : 10.2527/jas.2013-7282

J. G. Wells, B. R. Davis, I. K. Wachsmuth, L. W. Riley, R. S. Remis et al., Laboratory investigation of hemorrhagic colitis outbreaks associated with a rare Escherichia coli serotype, J Clin Microbiol, vol.18, issue.3, pp.512-520, 1983.

T. J. Wells, T. N. Mcneilly, M. Totsika, A. Mahajan, D. L. Gally et al., The Escherichia coli O157:H7 EhaB autotransporter protein binds to laminin and collagen I and induces a serum IgA response in O157:H7 challenged cattle, Environ Microbiol, vol.11, issue.7, pp.1803-1814, 2009.

T. J. Wells, O. Sherlock, L. Rivas, A. Mahajan, S. A. Beatson et al.,

M. A. Schembri, EhaA is a novel autotransporter protein of enterohemorrhagic Escherichia coli O157:H7 that contributes to adhesion and biofilm formation, Environ Microbiol, vol.10, issue.3, pp.589-604, 2008.

M. E. Wickham, C. Lupp, M. Mascarenhas, A. Vazquez, B. K. Coombes et al., Bacterial genetic determinants of non-O157 STEC outbreaks and hemolytic-uremic syndrome after infection, J Infect Dis, vol.194, issue.6, pp.819-827, 2006.
DOI : 10.1086/506620

URL : https://academic.oup.com/jid/article-pdf/194/6/819/18012366/194-6-819.pdf

H. ;. Wickhman, D. L. Pearl, and J. T. Lejeune, Multiple-locus variable-nucleotide tandem repeat subtype analysis implicates European starlings as biological vectors for Escherichia coli O157:H7 in Ohio, USA, J Appl Microbiol, vol.111, issue.4, pp.982-988, 2009.

A. R. Wong, J. S. Pearson, M. D. Bright, D. Munera, K. S. Robinson et al.,

E. L. Hartland, Insights on Escherichia coli biofilm formation and inhibition from wholetranscriptome profiling, Environ Microbiol, vol.80, issue.6, pp.1-15, 2009.

M. J. Woodward, D. Gavier-widen, I. M. Mclaren, C. Wray, M. Sozmen et al., Infection of gnotobiotic calves with Escherichia coli O157:H7 strain A84, Vet Rec, vol.144, issue.17, pp.466-470, 1999.

J. Xicohtencatl-cortes, V. Monteiro-neto, M. A. Ledesma, D. M. Jordan, O. Francetic et al.,

J. A. Giron, Intestinal adherence associated with type IV pili of enterohemorrhagic Escherichia coli O157:H7, J Clin Invest, vol.117, issue.11, pp.3519-3529, 2007.

J. Xicohtencatl-cortes, V. Monteiro-neto, Z. Saldana, M. A. Ledesma, J. L. Puente et al., The type 4 pili of enterohemorrhagic Escherichia coli O157:H7 are multipurpose structures with pathogenic attributes, J Bacteriol, vol.191, issue.1, pp.411-421, 2009.

J. Xicohtencatl-cortes, Z. Saldana, W. Deng, E. Castaneda, E. Freer et al.,

J. A. Giron, Bacterial macroscopic rope-like fibers with cytopathic and adhesive properties, J Biol Chem, vol.285, issue.42, pp.32336-32342, 2010.

J. Xicohtencatl-cortes, E. Sanchez-chacon, Z. Saldana, E. Freer, and J. A. Giron, Interaction of Escherichia coli O157:H7 with leafy green produce, J Food Prot, vol.72, issue.7, pp.1531-1537, 2009.

Y. Xu, E. Dugat-bony, R. Zaheer, L. Selinger, R. Barbieri et al., Escherichia coli O157:H7 super-shedder and non-shedder feedlot steers harbour distinct fecal bacterial communities, PLoS One, vol.9, issue.5, p.98115, 2014.
DOI : 10.1371/journal.pone.0098115

URL : https://hal.archives-ouvertes.fr/hal-01195479

Z. Yang, J. Kovar, J. Kim, J. Nietfeldt, D. R. Smith et al.,

A. K. Benson, Identification of common subpopulations of non-sorbitol-fermenting, beta-glucuronidasenegative Escherichia coli O157:H7 from bovine production environments and human clinical samples, Appl Environ Microbiol, vol.70, issue.11, pp.6846-6854, 2004.

S. M. Younts-dahl, G. D. Osborn, M. L. Galyean, J. D. Rivera, G. H. Loneragan et al., Reduction of Escherichia coli O157 in finishing beef cattle by various doses of Lactobacillus acidophilus in direct-fed microbials, J Food Prot, vol.68, issue.1, pp.6-10, 2005.