B. Burrowes, D. Harper, J. Anderson, M. Mcconville, and M. Enright, Bacteriophage therapy: potential uses in the control of antibiotic-resistant pathogens, Expert Review of Anti-infective Therapy, vol.9, issue.9, pp.775-785, 2011.
DOI : 10.1586/eri.11.90

E. Saussereau and L. Debarbieux, Bacteriophages in the Experimental Treatment of Pseudomonas aeruginosa Infections in Mice, Adv Virus Res, vol.83, pp.123-141, 2012.
DOI : 10.1016/B978-0-12-394438-2.00004-9

S. Mccallin, A. Sarker, S. Barretto, C. Sultana, S. Berger et al., Safety analysis of a Russian phage cocktail: From MetaGenomic analysis to oral application in healthy human subjects, Virology, vol.443, issue.2, pp.187-196, 2013.
DOI : 10.1016/j.virol.2013.05.022

H. Brussow, 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

L. Debarbieux, D. Leduc, D. Maura, E. Morello, and A. Criscuolo, 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

E. Morello, E. Saussereau, D. Maura, M. Huerre, and L. Touqui, Pulmonary Bacteriophage Therapy on Pseudomonas aeruginosa Cystic Fibrosis Strains: First Steps Towards Treatment and Prevention, PLoS ONE, vol.72, issue.Pt 10, p.21347240, 2011.
DOI : 10.1371/journal.pone.0016963.t001
URL : https://hal.archives-ouvertes.fr/pasteur-01425539

G. Pier and R. Ramphal, Pseudomonas aeruginosa Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases, pp.2835-2860, 2009.

M. Zilberberg and A. Shorr, Prevalence of multidrug-resistant pseudomonas aeruginosa and carbapenem-resistant enterobacteriaceae among specimens from hospitalized patients with pneumonia and bloodstream infections in the United States from 2000 to 2009, Journal of Hospital Medicine, vol.8, pp.559-563, 2013.
DOI : 10.1002/jhm.2080

O. Ciofu, C. Hansen, and N. Hoiby, Respiratory bacterial infections in cystic fibrosis, Current Opinion in Pulmonary Medicine, vol.19, issue.3, pp.251-258, 2013.
DOI : 10.1097/MCP.0b013e32835f1afc

B. Williams, J. Dehnbostel, and T. Blackwell, Pseudomonas aeruginosa: Host defence in lung diseases, Respirology, vol.151, issue.5, pp.1037-1056, 2010.
DOI : 10.1111/j.1440-1843.2010.01819.x

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. Saussereau, I. Vachier, R. Chiron, B. Godbert, and I. Sermet, Effectiveness of bacteriophages in the sputum of cystic fibrosis patients, Clinical Microbiology and Infection, vol.20, issue.12, 2014.
DOI : 10.1111/1469-0691.12712

J. Garbe, B. Bunk, M. Rohde, and M. Schobert, Sequencing and Characterization of Pseudomonas aeruginosa phage JG004, BMC Microbiology, vol.11, issue.1, p.21569567, 2011.
DOI : 10.1128/JB.187.9.3002-3012.2005

C. Essoh, Y. Blouin, G. Loukou, A. Cablanmian, and S. Lathro, The Susceptibility of Pseudomonas aeruginosa Strains from Cystic Fibrosis Patients to Bacteriophages, PLoS ONE, vol.192, issue.4, p.23637754, 2013.
DOI : 10.1371/journal.pone.0060575.s008
URL : https://hal.archives-ouvertes.fr/hal-00822766

S. Lu, S. Le, Y. Tan, J. Zhu, and M. Li, Genomic and Proteomic Analyses of the Terminally Redundant Genome of the Pseudomonas aeruginosa Phage PaP1: Establishment of Genus PaP1-Like Phages, PLoS ONE, vol.354, issue.5, p.23675441, 2013.
DOI : 10.1371/journal.pone.0062933.s001

J. Uchiyama, M. Rashel, I. Takemura, S. Kato, and T. Ujihara, Genetic characterization of Pseudomonas aeruginosa bacteriophage KPP10, Archives of Virology, vol.49, issue.4, pp.733-738, 2012.
DOI : 10.1007/s00705-011-1210-x

B. Toussaint, I. Delic-attree, and P. Vignais, Pseudomonas aeruginosa Contains an IHF-like Protein That Binds to the algD Promoter, Biochemical and Biophysical Research Communications, vol.196, issue.1, pp.416-421, 1993.
DOI : 10.1006/bbrc.1993.2265

R. Lavigne, P. Darius, E. Summer, D. Seto, and P. Mahadevan, Classification of Myoviridae bacteriophages using protein sequence similarity, BMC Microbiology, vol.9, issue.1, p.224, 2009.
DOI : 10.1186/1471-2180-9-224

P. Ceyssens, J. Noben, H. Ackermann, J. Verhaegen, D. Vos et al., Survey of Pseudomonas aeruginosa and its phages: de novo peptide sequencing as a novel tool to assess the diversity of worldwide collected viruses, Environmental Microbiology, vol.11, 2009.

J. Gill, J. Berry, W. Russell, L. Lessor, and D. Escobar-garcia, The Caulobacter crescentus phage phiCbK: genomics of a canonical phage, BMC Genomics, vol.13, issue.1, p.23050599, 2012.
DOI : 10.1128/JVI.01579-12

X. Jiang, H. Jiang, C. Li, S. Wang, and Z. Mi, Sequence characteristics of T4-like bacteriophage IME08 benome termini revealed by high throughput sequencing, Virology Journal, vol.8, issue.1, p.21524290, 0194.
DOI : 10.1093/nar/18.10.3090

J. He, R. Baldini, E. Deziel, M. Saucier, and Q. Zhang, The broad host range pathogen Pseudomonas aeruginosa strain PA14 carries two pathogenicity islands harboring plant and animal virulence genes, Proceedings of the National Academy of Sciences, vol.101, issue.8, pp.2530-2535, 2004.
DOI : 10.1073/pnas.0304622101

M. Wolfgang, B. Kulasekara, X. Liang, D. Boyd, and K. Wu, Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa, Proceedings of the National Academy of Sciences, vol.100, issue.14, pp.8484-8489, 2003.
DOI : 10.1073/pnas.0832438100

B. Tümmler, Clonal Variations in Pseudomonas aeruginosa, Pseudomonas, 2006.
DOI : 10.1007/0-387-28881-3_2

E. Rocha and A. Danchin, Base composition bias might result from competition for metabolic resources, Trends in Genetics, vol.18, issue.6, pp.291-294, 2002.
DOI : 10.1016/S0168-9525(02)02690-2

M. Bailly-bechet, M. Vergassola, and E. Rocha, Causes for the intriguing presence of tRNAs in phages, Genome Research, vol.17, issue.10, pp.1486-1495, 2007.
DOI : 10.1101/gr.6649807
URL : https://hal.archives-ouvertes.fr/hal-00434705

R. Lavigne, D. Seto, P. Mahadevan, H. Ackermann, and A. Kropinski, Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools, Research in Microbiology, vol.159, issue.5, pp.406-414, 2008.
DOI : 10.1016/j.resmic.2008.03.005

S. Santos, A. Kropinski, P. Ceyssens, H. Ackermann, and A. Villegas, Genomic and Proteomic Characterization of the Broad-Host-Range Salmonella Phage PVP-SE1: Creation of a New Phage Genus, Journal of Virology, vol.85, issue.21, pp.11265-11273, 2011.
DOI : 10.1128/JVI.01769-10

L. Truncaite, E. Simoliunas, A. Zajanckauskaite, L. Kaliniene, and R. Mankeviciute, Bacteriophage vB_EcoM_FV3: a new member of ???rV5-like viruses???, Archives of Virology, vol.67, issue.12, pp.2431-2435, 2012.
DOI : 10.1007/s00705-012-1449-x

A. Kropinski, T. Waddell, J. Meng, K. Franklin, and H. Ackermann, The host-range, genomics and proteomics of Escherichia coli O157:H7 bacteriophage rV5, Virology Journal, vol.10, issue.1, pp.76-23497209, 2013.
DOI : 10.1021/pr015504q

R. Juhala, M. Ford, R. Duda, A. Youlton, and G. Hatfull, Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages, Journal of Molecular Biology, vol.299, issue.1, pp.27-51, 2000.
DOI : 10.1006/jmbi.2000.3729

R. Frampton, C. Taylor, H. Moreno, A. Visnovsky, S. Petty et al., Identification of Bacteriophages for Biocontrol of the Kiwifruit Canker Phytopathogen Pseudomonas syringae pv. actinidiae, Applied and Environmental Microbiology, vol.80, issue.7, pp.2216-2228, 2014.
DOI : 10.1128/AEM.00062-14

S. Zuber, C. Ngom-bru, C. Barretto, A. Bruttin, and H. Brussow, Genome Analysis of Phage JS98 Defines a Fourth Major Subgroup of T4-Like Phages in Escherichia coli, Journal of Bacteriology, vol.189, issue.22, pp.8206-8214, 2007.
DOI : 10.1128/JB.00838-07

J. Martinsohn, M. Radman, and M. Petit, The lambda red proteins promote efficient recombination between diverged sequences: implications for bacteriophage genome mosaicism, PLoS Genet, vol.4, p.18451987, 2008.
URL : https://hal.archives-ouvertes.fr/inserm-00496049

A. Lopes, J. Amarir-bouhram, G. Faure, M. Petit, and R. Guerois, Detection of novel recombinases in bacteriophage genomes unveils Rad52, Rad51 and Gp2.5 remote homologs, Nucleic Acids Research, vol.38, issue.12, pp.3952-3962, 2010.
DOI : 10.1093/nar/gkq096

L. Bobay, M. Touchon, and E. Rocha, Manipulating or Superseding Host Recombination Functions: A Dilemma That Shapes Phage Evolvability, PLoS Genetics, vol.18, issue.1, p.24086157, 2013.
DOI : 10.1371/journal.pgen.1003825.s010
URL : https://hal.archives-ouvertes.fr/pasteur-01374955

M. De-paepe, G. Hutinet, O. Son, J. Amarir-bouhram, and S. Schbath, Temperate Phages Acquire DNA from Defective Prophages by Relaxed Homologous Recombination: The Role of Rad52-Like Recombinases, PLoS Genetics, vol.57, issue.5, p.24603854, 2014.
DOI : 10.1371/journal.pgen.1004181.s012
URL : https://hal.archives-ouvertes.fr/hal-01134590

S. Eddy, Accelerated Profile HMM Searches, PLoS Computational Biology, vol.21, issue.10, p.22039361, 2011.
DOI : 10.1371/journal.pcbi.1002195.g006

F. Rohwer and R. Edwards, The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage, Journal of Bacteriology, vol.184, issue.16, pp.4529-4535, 2002.
DOI : 10.1128/JB.184.16.4529-4535.2002

P. Mahadevan, J. King, and D. Seto, CGUG: in silico proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to ca. 1.9 Mb, BMC Research Notes, vol.2, issue.1, 2009.
DOI : 10.1186/1756-0500-2-168

M. Krupovic and D. Bamford, Double-stranded DNA viruses: 20 families and only five different architectural principles for virion assembly, Current Opinion in Virology, vol.1, issue.2, pp.118-124, 2011.
DOI : 10.1016/j.coviro.2011.06.001

A. Comeau, D. Tremblay, S. Moineau, T. Rattei, and A. Kushkina, Phage Morphology Recapitulates Phylogeny: The Comparative Genomics of a New Group of Myoviruses, PLoS ONE, vol.20, issue.7, p.22792219, 2012.
DOI : 10.1371/journal.pone.0040102.s005
URL : https://hal.archives-ouvertes.fr/hal-00787616

P. Ceyssens, T. Glonti, N. Kropinski, R. Lavigne, and N. Chanishvili, Phenotypic and genotypic variations within a single bacteriophage species, Virology Journal, vol.8, issue.1, pp.134-21429206, 2011.
DOI : 10.1016/j.virusres.2005.05.014

G. Verbeken, J. Pirnay, R. Lavigne, S. Jennes, D. Vos et al., Call for a Dedicated European Legal Framework for Bacteriophage Therapy, Archivum Immunologiae et Therapiae Experimentalis, vol.34, issue.Pt 7, pp.117-129, 2014.
DOI : 10.1007/s00005-014-0269-y

I. Huys, J. Pirnay, R. Lavigne, S. Jennes, D. Vos et al., Paving a regulatory pathway for phage therapy, EMBO reports, vol.4, issue.11, pp.951-954, 2013.
DOI : 10.1038/embor.2013.163

G. Verbeken, I. Huys, J. Pirnay, S. Jennes, and N. Chanishvili, Taking Bacteriophage Therapy Seriously: A Moral Argument, BioMed Research International, vol.32, issue.3, pp.621316-621326, 2014.
DOI : 10.1016/j.jhin.2007.10.006

R. Aziz, S. Devoid, T. Disz, R. Edwards, and C. Henry, SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models, PLoS ONE, vol.40, issue.10, p.23110173, 2012.
DOI : 10.1371/journal.pone.0048053.s001

K. Rutherford, J. Parkhill, J. Crook, T. Horsnell, and P. Rice, Artemis: sequence visualization and annotation, Bioinformatics, vol.16, issue.10, pp.944-945, 2000.
DOI : 10.1093/bioinformatics/16.10.944

T. Lowe and S. Eddy, tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence, Nucleic Acids Research, vol.25, issue.5, pp.955-964, 1997.
DOI : 10.1093/nar/25.5.0955

J. Soding, A. Biegert, and A. Lupas, The HHpred interactive server for protein homology detection and structure prediction, Nucleic Acids Research, vol.33, issue.Web Server, pp.244-248, 2005.
DOI : 10.1093/nar/gki408

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

I. Milne, G. Stephen, M. Bayer, P. Cock, and L. Pritchard, Using Tablet for visual exploration of second-generation sequencing data, Briefings in Bioinformatics, vol.14, issue.2, pp.193-202, 2013.
DOI : 10.1093/bib/bbs012

R. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340

R. Finn, J. Clements, and S. Eddy, HMMER web server: interactive sequence similarity searching, Nucleic Acids Research, vol.39, issue.suppl, pp.29-37, 2011.
DOI : 10.1093/nar/gkr367

A. Criscuolo and S. Gribaldo, BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evolutionary Biology, vol.10, issue.1, p.20626897, 2010.
DOI : 10.1186/1471-2148-10-210

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, and W. Hordijk, New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-321, 2010.
DOI : 10.1093/sysbio/syq010
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

R. Lavigne, J. Noben, K. Hertveldt, P. Ceyssens, and Y. Briers, The structural proteome of Pseudomonas aeruginosa bacteriophage ??KMV, Microbiology, vol.152, issue.2, pp.529-534, 2006.
DOI : 10.1099/mic.0.28431-0

M. Moak and I. Molineux, Peptidoglycan hydrolytic activities associated with bacteriophage virions, Molecular Microbiology, vol.51, issue.4, pp.1169-1183, 2004.
DOI : 10.1046/j.1365-2958.2003.03894.x