I. Goldstein, F. Wallet, J. Robert, and M. H. Becquemin, Lung Tissue Concentrations of Nebulized Amikacin during Mechanical Ventilation in Piglets with Healthy Lungs, American Journal of Respiratory and Critical Care Medicine, vol.165, issue.2, pp.171-175, 2002.
DOI : 10.1164/ajrccm.165.2.2107025

L. Golshahi, K. D. Seed, J. J. Dennis, and W. H. Finlay, Complex, Journal of Aerosol Medicine and Pulmonary Drug Delivery, vol.21, issue.4, pp.351-360, 2008.
DOI : 10.1089/jamp.2008.0701

J. Gu, X. Liu, Y. Li, and W. Han, A Method for Generation Phage Cocktail with Great Therapeutic Potential, PLoS ONE, vol.22, issue.3, pp.31698-22396736, 2012.
DOI : 10.1371/journal.pone.0031698.t001

H. Hadas, M. Einav, I. Fishov, and A. Zaritsky, Bacteriophage T4 Development Depends on the Physiology of its Host Escherichia Coli, Microbiology, vol.143, issue.1, pp.179-185, 1997.
DOI : 10.1099/00221287-143-1-179

M. Hankin, L'action bactéricide des eaux de la Jumna et du Gange sur le vibrion du choléra, Ann Inst Pasteur, vol.10, pp.511-523, 1896.

G. Harris, R. Kuo-lee, C. K. Lam, and G. Kanzaki, A Mouse Model of Acinetobacter baumannii-Associated Pneumonia Using a Clinically Isolated Hypervirulent Strain, Antimicrobial Agents and Chemotherapy, vol.57, issue.8, pp.3601-3613, 2013.
DOI : 10.1128/AAC.00944-13

G. F. Hatfull and R. W. Hendrix, Bacteriophages and their genomes, Current Opinion in Virology, vol.1, issue.4, pp.298-303, 2011.
DOI : 10.1016/j.coviro.2011.06.009

R. H. Heineman and J. J. Bull, TESTING OPTIMALITY WITH EXPERIMENTAL EVOLUTION: LYSIS TIME IN A BACTERIOPHAGE, Evolution, vol.56, issue.7, pp.1695-1709, 2007.
DOI : 10.1074/jbc.272.10.6599

I. R. Henderson, P. Owen, and J. P. Nataro, Molecular switches - the ON and OFF of bacterial phase variation, Molecular Microbiology, vol.196, issue.5, pp.919-932, 1999.
DOI : 10.1016/0966-842X(96)81498-3

R. W. Hendrix, Bacteriophages: Evolution of the Majority, Theoretical Population Biology, vol.61, issue.4, pp.471-480, 2002.
DOI : 10.1006/tpbi.2002.1590

S. Henken, J. Bohling, A. D. Ogunniyi, and J. C. Paton, Evaluation of Biophotonic Imaging To Estimate Bacterial Burden in Mice Infected with Highly Virulent Compared to Less Virulent Streptococcus pneumoniae Serotypes, Antimicrobial Agents and Chemotherapy, vol.54, issue.8, pp.3155-3160, 2010.
DOI : 10.1128/AAC.00310-10

M. Henry, L. M. Bobay, A. Chevallereau, and E. Saussereau, The search for therapeutic bacteriophages uncovers one new subfamily and two new genera of pseudomonasinfecting myoviridae, PLoS One, vol.10, issue.1, pp.117163-25629728, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01233568

M. Henry, R. Lavigne, and L. Debarbieux, Predicting in vivo efficacy to guide the choice of therapeutic bacteriophages to treat pulmonary infections, Antimicrob Agents Chemother, p.24041900, 2013.

K. M. Hillman, T. Riordan, S. M. O-'farrell, and S. Tabaqchali, Colonization of the gastric contents in critically patients, Critical Care Medicine, vol.10, issue.7, pp.444-447, 1982.
DOI : 10.1097/00003246-198207000-00005

T. M. Hooton, Uncomplicated Urinary Tract Infection, New England Journal of Medicine, vol.366, issue.11, pp.1028-1037, 2012.
DOI : 10.1056/NEJMcp1104429

P. Horvath and R. Barrangou, CRISPR/Cas, the Immune System of Bacteria and Archaea, Science, vol.327, issue.5962, pp.167-170, 2010.
DOI : 10.1126/science.1179555

S. Hudault, J. Guignot, and A. L. Servin, Escherichia coli strains colonising the gastrointestinal tract protect germfree mice against Salmonella typhimurium infection, Gut, vol.49, issue.1, pp.47-55, 2001.
DOI : 10.1136/gut.49.1.47

W. E. Huff, G. R. Huff, N. C. Rath, and J. M. Balog, Therapeutic efficacy of bacteriophage and Baytril (enrofloxacin) individually and in combination to treat colibacillosis in broilers, Poultry Science, vol.83, issue.12, pp.1944-1947, 2004.
DOI : 10.1093/ps/83.12.1944

K. A. Hughes, I. W. Sutherland, J. Clark, and M. V. Jones, Bacteriophage and associated polysaccharide depolymerases - novel tools for study of bacterial biofilms, Journal of Applied Microbiology, vol.85, issue.3, pp.583-590, 1998.
DOI : 10.1046/j.1365-2672.1998.853541.x

C. Hulo, E. De-castro, P. Masson, and L. Bougueleret, ViralZone: a knowledge resource to understand virus diversity, Nucleic Acids Research, vol.39, issue.Database, pp.576-582, 2011.
DOI : 10.1093/nar/gkq901

P. Hyman and S. T. Abedon, Practical Methods for Determining Phage Growth Parameters, Methods Mol Biol, vol.501, pp.175-202, 2009.
DOI : 10.1007/978-1-60327-164-6_18

J. Ibanez, A. Penafiel, J. M. Raurich, and P. Marse, Gastroesophageal reflux in intubated patients receiving enteral nutrition: effect of supine and semirecumbent positions, 1992.

C. J. Inchley, The actvity of mouse Kupffer cells following intravenous injection of T4 bacteriophage, Clin Exp Immunol, vol.5, issue.1, pp.173-187, 1969.

C. Jacqueline, A. Roquilly, C. Desessard, and D. Boutoille, Efficacy of ceftolozane in a murine model of Pseudomonas aeruginosa acute pneumonia: in vivo antimicrobial activity and impact on host inflammatory response, Journal of Antimicrobial Chemotherapy, vol.68, issue.1, pp.177-183, 2013.
DOI : 10.1093/jac/dks343

A. Jaiswal, H. Koley, A. Ghosh, and A. Palit, Efficacy of cocktail phage therapy in treating Vibrio cholerae infection in??rabbit model, Microbes and Infection, vol.15, issue.2, pp.152-156, 2013.
DOI : 10.1016/j.micinf.2012.11.002

M. T. Kuipers, T. Van-der-poll, M. J. Schultz, and C. W. Wieland, Bench-to-bedside review: Damage-associated molecular patterns in the onset of ventilator-induced lung injury, Critical Care, vol.15, issue.6, pp.235-22216838, 2011.
DOI : 10.1097/CCM.0b013e3181b07b78

S. Kumari, Bacteriophage Treatment of Burn Wound Infection Caused by Pseudomonas aeruginosa PAO in BALB/c Mice, American Journal of Biomedical Sciences, vol.1, issue.4, pp.385-394, 2009.
DOI : 10.5099/aj090400385

S. Kumari, K. Harjai, and S. Chhibber, Efficacy of bacteriophage treatment in murine burn wound infection induced by klebsiella pneumoniae, J Microbiol Biotechnol, vol.19, issue.6, pp.622-628, 2009.

S. Kumari, K. Harjai, and S. Chhibber, Evidence to Support the Therapeutic Potential of Bacteriophage Kpn5 in Burn Wound Infection Caused by Klebsiella pneumoniae in BALB/c Mice, Journal of Microbiology and Biotechnology, vol.20, issue.5, pp.935-941, 2010.
DOI : 10.4014/jmb.0909.09010

S. Kumari, K. Harjai, and S. Chhibber, Topical treatment of Klebsiella pneumoniae B5055 induced burn wound infection in mice using natural products, J Infect Dev Ctries, vol.4, issue.6, pp.367-377, 2010.

T. Kwan, J. Liu, M. Dubow, and P. Gros, The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages, Proceedings of the National Academy of Sciences, vol.102, issue.14, pp.5174-5179, 2005.
DOI : 10.1073/pnas.0501140102

T. Kwan, J. Liu, M. Dubow, and P. Gros, Comparative genomic analysis of 18, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00069313

B. Kwiatkowski, B. Boschek, H. Thiele, and S. Stirm, Substrate specificity of two bacteriophage-associated endo-N-acetylneuraminidases, J Virol, vol.45, issue.1, pp.367-374, 1983.

L. La-combe and B. , Epidémiologie et physiopathologie de la colonisation et des infections pulmonaires à Escherichia coli : premiers résultats de l'étude multicentrique COLOCOLI (congrès de la Société de Réanimation de Langue Française, 2014.

S. J. Labrie, J. E. Samson, and S. Moineau, Bacteriophage resistance mechanisms, Nature Reviews Microbiology, vol.153, issue.5, pp.317-327, 2010.
DOI : 10.1038/nrmicro2315

G. L. Lau, C. C. Sieo, W. S. Tan, and M. Hair-bejo, Efficacy of a bacteriophage isolated from chickens as a therapeutic agent for colibacillosis in broiler chickens, Poultry Science, vol.89, issue.12, pp.2589-2596, 2010.
DOI : 10.3382/ps.2010-00904

K. B. Laupland, Incidence of bloodstream infection: a review of population-based studies, Clinical Microbiology and Infection, vol.19, issue.6, pp.492-500, 2013.
DOI : 10.1111/1469-0691.12144

S. Lax and J. A. Gilbert, Hospital-associated microbiota and implications for nosocomial infections, Trends in Molecular Medicine, vol.21, issue.7, pp.427-432, 2015.
DOI : 10.1016/j.molmed.2015.03.005

J. R. Meyer, D. T. Dobias, J. S. Weitz, and J. E. Barrick, Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda, Science, vol.335, issue.6067, pp.428-432, 2012.
DOI : 10.1126/science.1214449

R. Miedzybrodzki, J. Borysowski, B. Weber-dabrowska, and W. Fortuna, Clinical Aspects of Phage Therapy, Adv Virus Res, vol.83, pp.73-121, 2012.
DOI : 10.1016/B978-0-12-394438-2.00003-7

P. Miernikiewicz, K. Dabrowska, A. Piotrowicz, and B. Owczarek, T4 Phage and Its Head Surface Proteins Do Not Stimulate Inflammatory Mediator Production, PLoS ONE, vol.222, issue.1, pp.71036-2013, 2013.
DOI : 10.1371/journal.pone.0071036.t004

R. W. Miller, E. J. Skinner, A. Sulakvelidze, and G. F. Mathis, Bacteriophage Therapy for Control of Necrotic Enteritis of Broiler Chickens Experimentally Infected with Clostridium perfringens, Avian Diseases, vol.54, issue.1, pp.33-40, 2010.
DOI : 10.1637/8953-060509-Reg.1

T. Minonishi, H. Kinoshita, M. Hirayama, and S. Kawahito, The supine-to-prone position change induces modification of endotracheal tube cuff pressure accompanied by tube displacement, Journal of Clinical Anesthesia, vol.25, issue.1, pp.28-31, 2013.
DOI : 10.1016/j.jclinane.2012.05.007

A. Mora, G. Dahbi, C. Lopez, and R. Mamani, Virulence Patterns in a Murine Sepsis Model of ST131 Escherichia coli Clinical Isolates Belonging to Serotypes O25b:H4 and O16:H5 Are Associated to Specific Virotypes, PLoS ONE, vol.21, issue.1, pp.87025-2014, 2014.
DOI : 10.1371/journal.pone.0087025.t004

E. Morello, E. Saussereau, D. Maura, and M. Huerre, Pulmonary Bacteriophage Therapy on Pseudomonas aeruginosa Cystic Fibrosis Strains: First Steps Towards Treatment and Prevention, PLoS ONE, vol.72, issue.Pt 10, pp.16963-21347240, 2011.
DOI : 10.1371/journal.pone.0016963.t001

URL : https://hal.archives-ouvertes.fr/pasteur-01425539

C. E. Morin and J. B. Kaper, vaccine strain CVD 103-HgR, FEMS Immunology & Medical Microbiology, vol.57, issue.1, pp.69-79, 2009.
DOI : 10.1111/j.1574-695X.2009.00580.x

M. Hooke, A. Sordelli, D. O. Cerquetti, M. C. Vogt, and A. J. , Quantitative determination of bacterial replication in vivo, Infect Immun, vol.49, issue.2, pp.424-427, 1985.

J. Muscedere, O. Rewa, K. Mckechnie, and X. Jiang, Subglottic secretion drainage for the prevention of ventilator-associated pneumonia: A systematic review and meta-analysis*, Critical Care Medicine, vol.39, issue.8, 2011.
DOI : 10.1097/CCM.0b013e318218a4d9

N. Mushtaq, M. B. Redpath, J. P. Luzio, and P. W. Taylor, Treatment of experimental Escherichia coli infection with recombinant bacteriophage-derived capsule depolymerase, Journal of Antimicrobial Chemotherapy, vol.56, issue.1, pp.160-165, 2005.
DOI : 10.1093/jac/dki177

N. Nau, R. Eiffert, and H. , Minimizing the release of proinflammatory and toxic bacterial products within the host: A promising approach to improve outcome in life-threatening infections, FEMS Immunology & Medical Microbiology, vol.44, issue.1, pp.1-16, 2005.
DOI : 10.1016/j.femsim.2005.01.001

A. Negroni, M. Costanzo, R. Vitali, and F. Superti, Characterization of adherent-invasive Escherichia coli isolated from pediatric patients with inflammatory bowel disease, Inflammatory Bowel Diseases, vol.18, issue.5, pp.913-924, 2012.
DOI : 10.1002/ibd.21899

H. M. Nguyen and C. Kang, Lysis Delay and Burst Shrinkage of Coliphage T7 by Deletion of Terminator T?? Reversed by Deletion of Early Genes, Journal of Virology, vol.88, issue.4, pp.2107-2115, 2014.
DOI : 10.1128/JVI.03274-13

M. H. Nicolas-chanoine, X. Bertrand, and J. Y. Madec, Escherichia coli ST131, an Intriguing Clonal Group, Clinical Microbiology Reviews, vol.27, issue.3, pp.543-574, 2014.
DOI : 10.1128/CMR.00125-13

URL : https://hal.archives-ouvertes.fr/hal-01061609

L. J. Norcia, A. M. Silvia, and S. F. Hayashi, Studies on Time-Kill Kinetics of Different Classes of Antibiotics Against Veterinary Pathogenic Bacteria Including Pasteurella, Actinobacillus and Escherichia coli., The Journal of Antibiotics, vol.52, issue.1, pp.52-60, 1999.
DOI : 10.7164/antibiotics.52.52

O. O-'riordan, T. G. Palmer, L. B. Smaldone, and G. C. , Aerosol deposition in mechanically ventilated patients. Optimizing nebulizer delivery., American Journal of Respiratory and Critical Care Medicine, vol.149, issue.1, pp.214-219, 1994.
DOI : 10.1164/ajrccm.149.1.8111585

H. D. Ochs, R. H. Buckley, R. H. Kobayashi, and A. L. Kobayashi, Antibody responses to bacteriophage phi X174 in patients with adenosine deaminase deficiency, Blood, vol.80, issue.5, pp.1163-1171, 1992.

M. Ohnishi, K. Kurokawa, and T. Hayashi, Diversification of Escherichia coli genomes: are bacteriophages the major contributors?, Trends in Microbiology, vol.9, issue.10, pp.481-485, 2001.
DOI : 10.1016/S0966-842X(01)02173-4

P. C. Okhuysen and H. L. Dupont, (EAEC): A Cause of Acute and Persistent Diarrhea of Worldwide Importance, The Journal of Infectious Diseases, vol.202, issue.4, pp.503-505, 2010.
DOI : 10.1086/654895

A. Oliveira, R. Sereno, and J. Azeredo, In vivo efficiency evaluation of a phage cocktail in controlling severe colibacillosis in confined conditions and experimental poultry houses, Veterinary Microbiology, vol.146, issue.3-4, pp.3-4, 2010.
DOI : 10.1016/j.vetmic.2010.05.015

V. M. Olkkonen and D. H. Bamford, Quantitation of the adsorption and penetration stages of bacteriophage ??6 infection, Virology, vol.171, issue.1, pp.229-238, 1989.
DOI : 10.1016/0042-6822(89)90530-8

F. Orskov and I. Orskov, serotyping and disease in man and animals, Canadian Journal of Microbiology, vol.38, issue.7, pp.699-704, 1992.
DOI : 10.1139/m92-115

R. Overbeek, R. Olson, G. D. Pusch, and G. J. Olsen, The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST), Nucleic Acids Research, vol.42, issue.D1, pp.206-214, 2014.
DOI : 10.1093/nar/gkt1226

L. Papazian, J. M. Forel, A. Gacouin, and C. Penot-ragon, Neuromuscular Blockers in Early Acute Respiratory Distress Syndrome, New England Journal of Medicine, vol.363, issue.12, pp.1107-1116, 2010.
DOI : 10.1056/NEJMoa1005372

D. L. Paterson and R. A. Bonomo, Extended-Spectrum Beta-Lactamases, Seminars in Respiratory and Critical Care Medicine, vol.24, issue.1, pp.657-686, 2005.
DOI : 10.1055/s-2003-37919

J. H. Paul and M. B. Sullivan, Marine phage genomics: what have we learned?, Current Opinion in Biotechnology, vol.16, issue.3, pp.299-307, 2005.
DOI : 10.1016/j.copbio.2005.03.007

R. J. Payne and V. A. Jansen, Understanding Bacteriophage Therapy as a Density-dependent Kinetic Process, Journal of Theoretical Biology, vol.208, issue.1, pp.37-48, 2001.
DOI : 10.1006/jtbi.2000.2198

M. L. Pedulla, M. E. Ford, J. M. Houtz, and T. Karthikeyan, Origins of Highly Mosaic Mycobacteriophage Genomes, Cell, vol.113, issue.2, pp.171-182, 2003.
DOI : 10.1016/S0092-8674(03)00233-2

G. Peirano, P. A. Bradford, K. M. Kazmierczak, and R. E. Badal, ST131, Emerging Infectious Diseases, vol.20, issue.11, pp.1928-1931, 2014.
DOI : 10.3201/eid2011.141388

J. Penders, C. Thijs, C. Vink, and F. F. Stelma, Factors Influencing the Composition of the Intestinal Microbiota in Early Infancy, PEDIATRICS, vol.118, issue.2, pp.511-521, 2006.
DOI : 10.1542/peds.2005-2824

P. J. Petersen, N. V. Jacobus, W. J. Weiss, and R. T. Testa, In vitro and in vivo activities of LJC10,627, a new carbapenem with stability to dehydropeptidase I., Antimicrobial Agents and Chemotherapy, vol.35, issue.1, pp.203-207, 1991.
DOI : 10.1128/AAC.35.1.203

B. Picard, J. S. Garcia, S. Gouriou, and P. Duriez, The link between phylogeny and virulence in Escherichia coli extraintestinal infection, Infect Immun, vol.67, issue.2, pp.546-553, 1999.

M. K. Pietila, T. A. Demina, N. S. Atanasova, and H. M. Oksanen, Archaeal viruses and bacteriophages: comparisons and contrasts, Trends in Microbiology, vol.22, issue.6, pp.334-344, 2014.
DOI : 10.1016/j.tim.2014.02.007

J. P. Pirnay, B. G. Blasdel, L. Bretaudeau, and A. Buckling, Quality and Safety Requirements for Sustainable Phage Therapy Products, Pharmaceutical Research, vol.313, issue.7, pp.2173-2179, 2015.
DOI : 10.1007/s11095-014-1617-7

J. D. Pitout and K. B. Laupland, Extended-spectrum ??-lactamase-producing Enterobacteriaceae: an emerging public-health concern, The Lancet Infectious Diseases, vol.8, issue.3, pp.159-166, 2008.
DOI : 10.1016/S1473-3099(08)70041-0

H. C. Polk, . Jr, and A. A. Miles, Enhancement of bacterial infection by ferric iron: kinetics, mechanisms, and surgical significance, Surgery, vol.70, issue.1, pp.71-77, 1971.

G. P. Smith, Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface, Science, vol.228, issue.4705, pp.1315-1317, 1985.
DOI : 10.1126/science.4001944

G. L. Snider, Historical perspective on mechanical ventilation: from simple life support system to ethical dilemma Critical Care Units: A Descriptive Analysis, Am Rev Respir Dis Society of Critical Care Medicine, vol.140, issue.2, 1989.

J. S. Soothill, Bacteriophage prevents destruction of skin grafts by Pseudomonas aeruginosa, Burns, vol.20, issue.3, pp.209-211, 1994.
DOI : 10.1016/0305-4179(94)90184-8

H. Sous and I. Hirsch, Bactericidal activity of phenoxymethylpenicillin in an in-vitro model simulating tissue kinetics, Journal of Antimicrobial Chemotherapy, vol.15, issue.suppl A, pp.233-239, 1985.
DOI : 10.1093/jac/15.suppl_A.233

B. J. Stoll, N. I. Hansen, P. J. Sanchez, and R. G. Faix, Early Onset Neonatal Sepsis: The Burden of Group B Streptococcal and E. coli Disease Continues, PEDIATRICS, vol.127, issue.5, pp.817-826, 2011.
DOI : 10.1542/peds.2010-2217

P. Stordeur and J. Mainil, La colibacillose aviaire, Annales de Médecine Vétérinaire, vol.146, pp.11-18, 2002.

Z. J. Storms, L. Smith, D. Sauvageau, and D. G. Cooper, Modeling bacteriophage attachment using adsorption efficiency, Biochemical Engineering Journal, vol.64, pp.22-29, 2012.
DOI : 10.1016/j.bej.2012.02.007

M. J. Sullivan, N. K. Petty, and S. A. Beatson, Easyfig: a genome comparison visualizer, Bioinformatics, vol.27, issue.7, pp.1009-1010, 2011.
DOI : 10.1093/bioinformatics/btr039

I. W. Sutherland, Polysaccharide lyases, FEMS Microbiology Reviews, vol.16, issue.4, pp.323-347, 1995.
DOI : 10.1111/j.1574-6976.1995.tb00179.x

C. A. Suttle, The significance of viruses to mortality in aquatic microbial communities, Microbial Ecology, vol.31, issue.2, pp.237-243, 1994.
DOI : 10.1007/BF00166813

T. Takata, K. Aizawa, A. Shimizu, and S. Sakakibara, Optimization of dose and dose regimen of biapenem based on pharmacokinetic and pharmacodynamic analysis, Journal of Infection and Chemotherapy, vol.10, issue.2, pp.76-85, 2004.
DOI : 10.1007/s10156-003-0292-0

I. Takemura-uchiyama, J. Uchiyama, M. Osanai, and N. Morimoto, Experimental phage therapy against lethal lung-derived septicemia caused by Staphylococcus aureus in mice, Microbes and Infection, vol.16, issue.6, pp.512-517, 2014.
DOI : 10.1016/j.micinf.2014.02.011

C. C. Teneback, T. C. Scanlon, M. J. Wargo, and J. L. Bement, Bioengineered Lysozyme Reduces Bacterial Burden and Inflammation in a Murine Model of Mucoid Pseudomonas aeruginosa Lung Infection, Antimicrobial Agents and Chemotherapy, vol.57, issue.11, pp.5559-5564, 2013.
DOI : 10.1128/AAC.00500-13

E. Terezakis, I. Needleman, N. Kumar, and D. Moles, The impact of hospitalization on oral health: a systematic review, Journal of Clinical Periodontology, vol.17, issue.(R, pp.628-636, 2009.
DOI : 10.1111/j.1600-051X.2011.01727.x

M. Wilkinson and M. A. Woodhead, Guidelines for community-acquired pneumonia in the ICU, Current Opinion in Critical Care, vol.10, issue.1, pp.59-64, 2004.
DOI : 10.1097/00075198-200402000-00010

D. R. Wilson and B. B. Finlay, Phage display: applications, innovations, and issues in phage and host biology, Canadian Journal of Microbiology, vol.44, issue.4, pp.313-329, 1998.
DOI : 10.1139/w98-015

K. E. Wommack and R. R. Colwell, Virioplankton: Viruses in Aquatic Ecosystems, Microbiology and Molecular Biology Reviews, vol.64, issue.1, pp.69-114, 2000.
DOI : 10.1128/MMBR.64.1.69-114.2000

C. A. Woodall, Electroporation of E. coli, Methods Mol Biol, vol.235, pp.55-69, 2003.
DOI : 10.1385/1-59259-409-3:55

A. Wright, C. H. Hawkins, E. E. Anggard, and D. R. Harper, ; a preliminary report of efficacy, Clinical Otolaryngology, vol.8, issue.4, pp.349-357, 2009.
DOI : 10.1111/j.1749-4486.2009.01973.x

Y. Yarmolinsky, M. B. Sternberg, and N. , Bacteriophage P1. The bacteriophages, R. Calendar, vol.1, pp.291-438, 1998.

P. J. Young, M. Rollinson, G. Downward, and S. Henderson, Leakage of fluid past the tracheal tube cuff in a benchtop model, British Journal of Anaesthesia, vol.78, issue.5, pp.557-562, 1997.
DOI : 10.1093/bja/78.5.557

Z. Zilberberg, M. D. Epstein, and S. K. , Acute Lung Injury in the Medical ICU, American Journal of Respiratory and Critical Care Medicine, vol.157, issue.4, pp.1159-1164, 1998.
DOI : 10.1164/ajrccm.157.4.9704088

P. S. Zolfaghari and D. L. Wyncoll, The tracheal tube: gateway to ventilator-associated pneumonia, Critical Care, vol.15, issue.5, pp.310-21996487, 2011.
DOI : 10.1086/526438

J. Emerson, M. Rosenfeld, S. Mcnamara, R. B. Gibson, and R. , Pseudomonas aeruginosa and other predictors of mortality and morbidity in young children with cystic fibrosis, Pediatric Pulmonology, vol.95, issue.2, pp.91-100, 2002.
DOI : 10.1002/ppul.10127

R. Henry, C. Mellis, and L. Petrovic, MucoidPseudomonas aeruginosa is a marker of poor survival in cystic fibrosis, Pediatric Pulmonology, vol.96, issue.3, pp.158-161, 1992.
DOI : 10.1002/ppul.1950120306

N. Hoiby, Recent advances in the treatment of Pseudomonas aeruginosainfections in cystic fibrosis, BMC Medicine, vol.6, issue.suppl. 33, p.32, 2011.
DOI : 10.1016/j.jcf.2007.02.001

C. Hansen, T. Pressler, and N. Hoiby, Early aggressive eradication therapy for intermittent Pseudomonas aeruginosa airway colonization in cystic fibrosis patients: 15??years experience, Journal of Cystic Fibrosis, vol.7, issue.6, pp.523-530, 2008.
DOI : 10.1016/j.jcf.2008.06.009

P. Croughs, B. Li, J. Hoogkamp-korstanje, and E. Stobberingh, Thirteen years of antibiotic susceptibility surveillance of Pseudomonas aeruginosa from intensive care units and urology services in the Netherlands, European Journal of Clinical Microbiology & Infectious Diseases, vol.54, issue.11, pp.283-288, 2013.
DOI : 10.1007/s10096-012-1741-4

A. Reyes, M. Haynes, and N. Hanson, Viruses in the faecal microbiota of monozygotic twins and their mothers, Nature, vol.11, issue.7304, pp.334-338, 2010.
DOI : 10.1038/nature09199

F. Rodriguez-valera, A. Martin-cuadrado, and B. Rodriguez-brito, Explaining microbial population genomics through phage predation, Nature Reviews Microbiology, vol.62, issue.11, pp.828-836, 2009.
DOI : 10.1038/nrmicro2235

P. Gomez and A. Buckling, Bacteria-Phage Antagonistic Coevolution in Soil, Science, vol.332, issue.6025, pp.106-109, 2011.
DOI : 10.1126/science.1198767

R. Matos, N. Lapaque, and L. Rigottier-gois, Enterococcus faecalis Prophage Dynamics and Contributions to Pathogenic Traits, PLoS Genetics, vol.7, issue.6, p.1003539, 2013.
DOI : 10.1371/journal.pgen.1003539.s007

URL : https://hal.archives-ouvertes.fr/hal-01190746

J. Barr, R. Auro, and M. Furlan, Bacteriophage adhering to mucus provide a non-host-derived immunity, Proceedings of the National Academy of Sciences, vol.110, issue.26, pp.10771-10776, 2013.
DOI : 10.1073/pnas.1305923110

F. Herelle, Sur un microbe invisible antagoniste des bacilles dysent eriques. Les Comptes rendus de l'Acad emie des sciences, pp.373-375, 1917.

W. Summers, Bacteriophage Therapy, Annual Review of Microbiology, vol.55, issue.1, pp.437-451, 2001.
DOI : 10.1146/annurev.micro.55.1.437

S. Abedon, S. Kuhl, B. Blasdel, and E. Kutter, Phage treatment of human infections, CMI Saussereau et al. Effectiveness of bacteriophages in CF sputa O989, pp.66-85, 2011.
DOI : 10.1016/S0041-1345(03)00525-6

N. Chanishvili, Phage Therapy???History from Twort and d'Herelle Through Soviet Experience to Current Approaches, Adv Virus Res, vol.83, pp.3-40, 2012.
DOI : 10.1016/B978-0-12-394438-2.00001-3

D. Maura and L. Debarbieux, Bacteriophages as twenty-first century antibacterial tools for food and medicine, Applied Microbiology and Biotechnology, vol.34, issue.4, pp.851-859, 2011.
DOI : 10.1007/s00253-011-3227-1

URL : https://hal.archives-ouvertes.fr/pasteur-01425532

K. Thiel, Old dogma, new tricks???21st Century phage therapy, Nature Biotechnology, vol.22, issue.1, pp.31-36, 2004.
DOI : 10.1038/nbt0104-31

D. Alemayehu, P. Casey, and O. Mcauliffe, Bacteriophages phimr299-2 and phinh-4 can eliminate Pseudomonas aeruginosa in the murine lung and on cystic fibrosis lung airway cells, MBio, vol.3, pp.29-41, 2012.

L. Debarbieux, D. Leduc, and M. D. , Lung Infections, The Journal of Infectious Diseases, vol.201, issue.7, pp.1096-1104, 2010.
DOI : 10.1086/651135

URL : https://hal.archives-ouvertes.fr/pasteur-01425464

M. Henry, R. Lavigne, and L. Debarbieux, Predicting In Vivo Efficacy of Therapeutic Bacteriophages Used To Treat Pulmonary Infections, Antimicrobial Agents and Chemotherapy, vol.57, issue.12, pp.5961-5968, 2013.
DOI : 10.1128/AAC.01596-13

E. Morello, E. Saussereau, D. Maura, M. Huerre, L. Touqui et al., Pulmonary Bacteriophage Therapy on Pseudomonas aeruginosa Cystic Fibrosis Strains: First Steps Towards Treatment and Prevention, PLoS ONE, vol.72, issue.Pt 10, p.16963, 2011.
DOI : 10.1371/journal.pone.0016963.t001

URL : https://hal.archives-ouvertes.fr/pasteur-01425539

J. Lu, C. Perng, S. Lee, and C. Wan, Use of pcr with universal primers and restriction endonuclease digestions for detection and identification of common bacterial pathogens in cerebrospinal fluid, J Clin Microbiol, vol.38, pp.2076-2080, 2000.

E. Mowat, S. Paterson, and J. Fothergill, Pseudomonas aeruginosa population diversity and turnover in cystic fibrosis chronic infections

M. Workentine, C. Sibley, and B. Glezerson, Phenotypic Heterogeneity of Pseudomonas aeruginosa Populations in a Cystic Fibrosis Patient, PLoS ONE, vol.33, issue.1, p.60225, 2013.
DOI : 10.1371/journal.pone.0060225.s010

N. Hoyland-kroghsbo, R. Maerkedahl, and S. Svenningsen, A Quorum-Sensing-Induced Bacteriophage Defense Mechanism, mBio, vol.4, issue.1, pp.362-00312, 2013.
DOI : 10.1128/mBio.00362-12

L. Debarbieux, Bacterial sensing of bacteriophages in communities: the search for the Rosetta stone, Current Opinion in Microbiology, vol.20, pp.125-130, 2014.
DOI : 10.1016/j.mib.2014.05.015

J. Pirnay, D. Vos, D. Verbeken, and G. , The Phage Therapy Paradigm: Pr??t-??-Porter or Sur-mesure?, Pharmaceutical Research, vol.2, issue.4, pp.934-937, 2011.
DOI : 10.1007/s11095-010-0313-5

B. Chan, S. Abedon, and C. Loc-carrillo, Phage cocktails and the future of phage therapy, Future Microbiology, vol.8, issue.6, pp.769-783, 2013.
DOI : 10.2217/fmb.13.47

J. Fagon, J. Chastre, and A. Hance, Nosocomial pneumonia in ventilated patients: A cohort study evaluating attributable mortality and hospital stay, The American Journal of Medicine, vol.94, issue.3, pp.281-288, 1993.
DOI : 10.1016/0002-9343(93)90060-3

D. Heyland, D. Cook, and L. Griffith, The Attributable Morbidity and Mortality of Ventilator-Associated Pneumonia in the Critically Ill Patient, American Journal of Respiratory and Critical Care Medicine, vol.159, issue.4, pp.1249-12561965, 1993.
DOI : 10.1164/ajrccm.159.4.9807050

A. Torres, R. Aznar, and J. Gatell, Incidence, Risk, and Prognosis Factors of Nosocomial Pneumonia in Mechanically Ventilated Patients, American Review of Respiratory Disease, vol.142, issue.3, pp.523-528, 1990.
DOI : 10.1164/ajrccm/142.3.523

D. Center and . Control, Antibiotic resistance threats in the United States Available at: http://www.cdc.gov/drugresistance/ threat-report-2013 International study of the prevalence and outcomes of infection in intensive care units, JAMA, vol.302, pp.2323-2329, 2009.

M. Hamet, A. Pavon, and F. Dalle, Candida spp. airway colonization could promote antibiotic-resistant bacteria selection in patients with suspected ventilator-associated pneumonia, Intensive Care Medicine, vol.58, issue.8, pp.1272-1279, 2012.
DOI : 10.1007/s00134-012-2584-2

J. Messika, F. Magdoud, and O. Clermont, Pathophysiology of Escherichia coli ventilator-associated pneumonia: implication of highly virulent extraintestinal pathogenic strains, Intensive Care Medicine, vol.70, issue.12, pp.2007-2016, 2012.
DOI : 10.1007/s00134-012-2699-5

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

J. Lynch, N. Clark, and G. Zhanel, Evolution of antimicrobial resistance among Enterobacteriaceae (focus on extended spectrum ??-lactamases and carbapenemases), Expert Opinion on Pharmacotherapy, vol.67, issue.12, pp.199-210, 2013.
DOI : 10.1016/j.mib.2011.07.026

J. Ricard, New therapies for pneumonia, Current Opinion in Pulmonary Medicine, vol.18, issue.3, pp.181-186, 2012.
DOI : 10.1097/MCP.0b013e3283520fec

D. Roux and J. Ricard, Novel Therapies for Pseudomonas aeruginosa Pneumonia, Infectious Disorders - Drug Targets, vol.11, issue.4, pp.389-394, 2011.
DOI : 10.2174/187152611796504836

A. Fauci and H. Marston, The Perpetual Challenge of Antimicrobial Resistance, JAMA, vol.311, issue.18, pp.1853-1854, 2014.
DOI : 10.1001/jama.2014.2465

H. Brüssow, What is needed for phage therapy to become a reality in Western medicine?, Virology, vol.434, issue.2, pp.138-142, 2012.
DOI : 10.1016/j.virol.2012.09.015

S. Matsuzaki, J. Uchiyama, and I. Takemura-uchiyama, Perspective: The age of the phage, Nature, vol.347, issue.7498, p.9, 2014.
DOI : 10.1038/509S9a

L. Carmody, J. Gill, and E. Summer, Pulmonary Infection, The Journal of Infectious Diseases, vol.201, issue.2, pp.264-271, 2010.
DOI : 10.1086/649227

S. Chhibber, S. Kaur, and S. Kumari, Therapeutic potential of bacteriophage in treating Klebsiella pneumoniae B5055-mediated lobar pneumonia in mice, Journal of Medical Microbiology, vol.57, issue.12, pp.1508-1513, 2008.
DOI : 10.1099/jmm.0.2008/002873-0

S. Chhibber, T. Kaur, and S. Kaur, Co-Therapy Using Lytic Bacteriophage and Linezolid: Effective Treatment in Eliminating Methicillin Resistant Staphylococcus aureus (MRSA) from Diabetic Foot Infections, PLoS ONE, vol.25, issue.3, p.56022, 2013.
DOI : 10.1371/journal.pone.0056022.t002

L. Debarbieux, D. Leduc, and D. Maura, Lung Infections, The Journal of Infectious Diseases, vol.201, issue.7, pp.1096-1104, 2010.
DOI : 10.1086/651135

URL : https://hal.archives-ouvertes.fr/pasteur-01425464

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

C. Morin and J. Kaper, vaccine strain CVD 103-HgR, FEMS Immunology & Medical Microbiology, vol.57, issue.1, pp.69-79, 2009.
DOI : 10.1111/j.1574-695X.2009.00580.x

K. Rhee, H. Cheng, and A. Harris, T1810 Determination of Spatial and Temporal Colonization of Enteropathogenic E. coli and Enterohemorrhagic E. coli in Mice Using Bioluminescent In Vivo Imaging, Gastroenterology, vol.138, issue.5, pp.34-41, 2011.
DOI : 10.1016/S0016-5085(10)62688-1

F. Herelle, Sur un microbe invisible antagoniste des bacilles dysentériques, C R Acad Sci Paris, vol.165, pp.373-375, 1917.

P. Boulanger, Purification of Bacteriophages and SDS-PAGE Analysis of Phage Structural Proteins from Ghost Particles, Methods Mol Biol, vol.502, pp.227-238, 2009.
DOI : 10.1007/978-1-60327-565-1_13

D. Pickard, Preparation of Bacteriophage Lysates and Pure DNA, Methods Mol Biol, vol.502, pp.3-9, 2009.
DOI : 10.1007/978-1-60327-565-1_1

J. Tsonos, E. Adriaenssens, and J. Klumpp, Complete Genome Sequence of the Novel Escherichia coli Phage phAPEC8, Journal of Virology, vol.86, issue.23, pp.13117-13118, 2012.
DOI : 10.1128/JVI.02374-12

B. Kwiatkowski, B. Boschek, and H. Thiele, Substrate specificity of two bacteriophage-associated endo-N-acetylneuraminidases, J Virol, vol.45, pp.367-374, 1983.

W. Johanson, A. Pierce, and J. Sanford, Changing Pharyngeal Bacterial Flora of Hospitalized Patients, New England Journal of Medicine, vol.281, issue.21, pp.1137-1140, 1969.
DOI : 10.1056/NEJM196911202812101

W. Johanson, . Jr, A. Pierce, and J. Sanford, Nosocomial Respiratory Infections with Gram-Negative Bacilli, Annals of Internal Medicine, vol.77, issue.5, pp.701-706, 1972.
DOI : 10.7326/0003-4819-77-5-701

J. Ricard and D. Roux, Candida colonization in ventilated ICU patients: no longer a bystander!, Intensive Care Medicine, vol.18, issue.8, pp.1243-1245, 2012.
DOI : 10.1007/s00134-012-2587-z

W. Ho, H. Gan, and K. Yap, Genome Sequence of Multidrug-Resistant Escherichia coli EC302/04, Isolated from a Human Tracheal Aspirate, Journal of Bacteriology, vol.194, issue.23, pp.6691-6692, 2012.
DOI : 10.1128/JB.01804-12

C. Köhler and U. Dobrindt, What defines extraintestinal pathogenic Escherichia coli?, International Journal of Medical Microbiology, vol.301, issue.8, pp.642-647, 2011.
DOI : 10.1016/j.ijmm.2011.09.006

S. Herold, T. Tabar, and H. Janssen, Exudate Macrophages Attenuate Lung Injury by the Release of IL-1 Receptor Antagonist in Gram-negative Pneumonia, American Journal of Respiratory and Critical Care Medicine, vol.183, issue.10, pp.1380-1390, 2011.
DOI : 10.1164/rccm.201009-1431OC

D. Greenwood, In Vitro Veritas? Antimicrobial Susceptibility Tests and Their Clinical Relevance, Journal of Infectious Diseases, vol.144, issue.4, pp.380-385, 1981.
DOI : 10.1093/infdis/144.4.380

M. Henry, R. Lavigne, and L. Debarbieux, Predicting In Vivo Efficacy of Therapeutic Bacteriophages Used To Treat Pulmonary Infections, Antimicrobial Agents and Chemotherapy, vol.57, issue.12, pp.5961-5968, 2013.
DOI : 10.1128/AAC.01596-13

J. Bull, G. Otto, and I. Molineux, In Vivo Growth Rates Are Poorly Correlated with Phage Therapy Success in a Mouse Infection Model, Antimicrobial Agents and Chemotherapy, vol.56, issue.2, pp.949-954, 2012.
DOI : 10.1128/AAC.05842-11

M. Duplessis, C. Lévesque, and S. Moineau, Characterization of Streptococcus thermophilus Host Range Phage Mutants, Applied and Environmental Microbiology, vol.72, issue.4, pp.3036-3041, 2006.
DOI : 10.1128/AEM.72.4.3036-3041.2006

U. Qimron, B. Marintcheva, and S. Tabor, Genomewide screens for Escherichia coli genes affecting growth of T7 bacteriophage, Proceedings of the National Academy of Sciences, vol.103, issue.50, pp.19039-19044, 2006.
DOI : 10.1073/pnas.0609428103

J. Uchiyama, I. Takemura, and M. Satoh, Improved Adsorption of an Enterococcus faecalis Bacteriophage ??EF24C with a Spontaneous Point Mutation, PLoS ONE, vol.6, issue.10, pp.26648-432107, 2011.
DOI : 10.1371/journal.pone.0026648.s007

J. Bondy-denomy, A. Pawluk, and K. Maxwell, Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system, Nature, vol.74, issue.7432, pp.429-432, 2013.
DOI : 10.1038/nature11723

K. Seed, D. Lazinski, and S. Calderwood, A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity, Nature, vol.64, issue.7438, pp.489-491, 2013.
DOI : 10.1038/nature11927

C. Sauve, E. Azoulay-dupuis, and P. Moine, Efficacies of cefotaxime and ceftriaxone in a mouse model of pneumonia induced by two penicillin-and cephalosporin-resistant strains of Streptococcus pneumoniae @@@@@@@@@@@@@@@@@@ qnrA1, qnrB1 and qnrS1 on the efficacy of ciprofloxacin and levofloxacin in an experimental pneumonia model caused by Escherichia coli with or without the GyrA mutation Ser83Leu, Antimicrob Agents Chemother J Antimicrob Chemother, vol.40, issue.68, pp.2829-28341609, 1996.

F. Docobo-pérez, P. Nordmann, and J. Domínguez-herrera, Efficacies of colistin and tigecycline in mice with experimental pneumonia due to NDM-1-producing strains of Klebsiella pneumoniae and Escherichia coli, International Journal of Antimicrobial Agents, vol.39, issue.3, pp.251-254, 2012.
DOI : 10.1016/j.ijantimicag.2011.10.012

J. Knudsen, K. Fuursted, and N. Frimodt-møller, Comparison of the effect of cefepime with four cephalosporins against pneumococci with various susceptibilities to penicillin, in vitro and in the mouse peritonitis model, Journal of Antimicrobial Chemotherapy, vol.40, issue.5, pp.679-686, 1997.
DOI : 10.1093/jac/40.5.679

B. Chan and S. Abedon, Phage Therapy Pharmacology, Adv Appl Microbiol, vol.78, pp.1-23, 2012.
DOI : 10.1016/B978-0-12-394805-2.00001-4

D. Craven and K. Steger, Epidemiology of Nosocomial Pneumonia, Chest, vol.108, issue.2, pp.1-16, 1995.
DOI : 10.1378/chest.108.2_Supplement.1S

A. Letarov and E. Kulikov, The bacteriophages in human- and animal body-associated microbial communities, Journal of Applied Microbiology, vol.4, issue.1, pp.1-13, 2009.
DOI : 10.1111/j.1365-2672.2009.04143.x

J. Méndez, A. Audicana, and M. Cancer, Assessment of drinking water quality using indicator bacteria and bacteriophages, J Water Health, vol.2, pp.201-214, 2004.

P. Miernikiewicz, K. D?browska, and A. Piotrowicz, T4 Phage and Its Head Surface Proteins Do Not Stimulate Inflammatory Mediator Production, PLoS ONE, vol.222, issue.1, p.71036, 2013.
DOI : 10.1371/journal.pone.0071036.t004

K. D?browska, P. Miernikiewicz, and A. Piotrowicz, Immunogenicity Studies of Proteins Forming the T4 Phage Head Surface, Journal of Virology, vol.88, issue.21, pp.12551-12557, 2014.
DOI : 10.1128/JVI.02043-14

C. Loc-carrillo and S. Abedon, Pros and cons of phage therapy, Bacteriophage, vol.14, issue.2, pp.111-114, 2011.
DOI : 10.4161/bact.1.2.15680

S. Abedon, S. Kuhl, and B. Blasdel, Phage treatment of human infections, Bacteriophage, vol.7, issue.2, pp.66-85, 2011.
DOI : 10.1016/S0041-1345(03)00525-6

E. Morello, E. Saussereau, and D. Maura, Pulmonary Bacteriophage Therapy on Pseudomonas aeruginosa Cystic Fibrosis Strains: First Steps Towards Treatment and Prevention, PLoS ONE, vol.72, issue.Pt 10, p.16963, 2011.
DOI : 10.1371/journal.pone.0016963.t001

URL : https://hal.archives-ouvertes.fr/pasteur-01425539

D. Alemayehu, P. Casey, and O. Mcauliffe, Bacteriophages ?MR299-2 and ?NH-4 can eliminate Pseudomonas aeruginosa in the murine lung and on cystic fibrosis lung airway cells, MBio, vol.3, pp.29-41, 2012.