S. T. Abedon, Phage therapy: various perspectives on how to improve the art, Methods in Molecular Biology, vol.1734, pp.113-127, 2018.

S. S. Ali, J. C. Whitney, J. Stevenson, H. Robinson, P. L. Howell et al., Structural insights into the regulation of foreign genes in Salmonella by the Hha/ H-NS complex, The Journal of Biological Chemistry, vol.288, pp.13356-13369, 2013.

A. Alonso, M. G. Pucciarelli, N. Figueroa-bossi, and F. Portillo, Increased excision of the Salmonella prophage ST64B caused by a deficiency in Dam methylase, Journal of Bacteriology, vol.187, pp.7901-7911, 2005.

D. Andres, U. Gohlke, N. K. Broeker, S. Schulze, W. Rabsch et al., An essential serotype recognition pocket on phage P22 tailspike protein forces Salmonella enterica serovar Paratyphi A O-antigen fragments to bind as nonsolution conformers, Glycobiology, vol.23, pp.486-494, 2013.

, Prophages in Salmonella enterica 11

, © 2018 The Authors. Molecular Microbiology Published by John Wiley & Sons Ltd, vol.0, pp.1-14

D. Andres, C. Hanke, U. Baxa, A. Seul, S. Barbirz et al., Tailspike interactions with lipopolysaccharide effect DNA ejection from phage P22 particles in vitro, The Journal of Biological Chemistry, vol.285, pp.36768-36775, 2010.

P. Argos, A. Landy, K. Abremski, J. B. Egan, E. Haggardljungquist et al., The integrase family of site-specific recombinases: regional similarities and global diversity, The EMBO Journal, vol.5, pp.433-440, 1986.

P. M. Ashton, S. V. Owen, L. Kaindama, W. P. Rowe, C. R. Lane et al., Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa, 2017.

, Genome Medicine, vol.9, p.92

N. L. Bachmann, N. K. Petty, N. L. Ben-zakour, J. M. Szubert, J. Savill et al., Genome analysis and CRISPR typing of Salmonella enterica serovar Virchow, BMC Genomics, p.389, 2014.

R. Balbontín, N. Figueroa-bossi, J. Casadesús, and L. Bossi, Insertion hot spot for horizontally acquired DNA within a bidirectional small-RNA locus in Salmonella enterica, Journal of Bacteriology, vol.190, pp.4075-4078, 2008.

R. Balbontín, G. Rowley, M. G. Pucciarelli, J. López-garrido, Y. Wormstone et al., DNA adenine methylation regulates virulence gene expression in Salmonella enterica serovar Typhimurium, Journal of Bacteriology, vol.188, pp.8160-8168, 2006.

R. C. Baños, S. Aznar, C. Madrid, and A. Juárez, Differential functional properties of chromosomaland plasmid-encoded H-NS proteins, Research in Microbiology, vol.162, pp.382-385, 2011.

R. C. Baños, A. Vivero, S. Aznar, J. García, M. Pons et al., Differential regulation of horizontally acquired and core genome genes by the bacterial modulator H-NS, PLoS Genetics, vol.5, p.1000513, 2009.

B. L. Bearson, H. K. Allen, B. W. Brunelle, I. S. Lee, S. R. Casjens et al., The agricultural antibiotic carbadox induces phage-mediated gene transfer in Salmonella, Frontiers in Microbiology, vol.5, p.52, 2014.

B. L. Bearson and B. W. Brunelle, Fluoroquinolone induction of phage-mediated gene transfer in multidrug-resistant Salmonella, International Journal of Antimicrobial Agents, vol.46, pp.201-204, 2015.

B. Silva, J. Storms, Z. Sauvageau, and D. , Host receptors for bacteriophage adsorption, FEMS Microbiology Letters, p.363, 2016.

L. Bobay, E. P. Rocha, C. Touchon, and M. , The adaptation of temperate bacteriophages to their host genomes, Molecular Biology and Evolution, vol.30, pp.737-751, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01374945

L. Bobay, M. Touchon, and E. P. Rocha, Pervasive domestication of defective prophages by bacteria, Proceedings of the National Academy of Sciences, vol.111, pp.12127-12132, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01374961

L. Bossi, J. A. Fuentes, G. Mora, and N. Figueroa-bossi, Prophage contribution to bacterial population dynamics, Journal of Bacteriology, vol.185, pp.6467-6471, 2003.

K. Botstein, K. K. Lew, V. Jarvik, and C. A. Swanson, Role of antirepressor in the bipartite control of repression and immunity by bacteriophage P22, Journal of Molecular Biology, vol.91, pp.439-462, 1975.

E. F. Boyd, Bacteriophage-encoded bacterial virulence factors and phage-pathogenicity island interactions, Advances in Virus Research, vol.82, pp.91-118, 2012.

E. F. Boyd and H. Brüssow, Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved, Trends in Microbiology, vol.10, pp.521-529, 2002.

E. F. Boyd, M. R. Carpenter, and N. Chowdhury, Mobile effector proteins on phage genomes, Bacteriophage, vol.2, pp.139-148, 2012.

J. S. Boyd, The symbiotic bacteriophages of Salmonella typhimurium, The Journal of Pathology and Bacteriology, vol.62, pp.501-517, 1950.

S. E. Broadbent, M. R. Davies, and M. W. Van-der-woude, Phase variation controls expression of Salmonella lipopolysaccharide modification genes by a DNA methylation-dependent mechanism, Molecular Microbiology, vol.77, pp.337-353, 2010.

N. F. Brown, B. K. Coombes, J. L. Bishop, M. E. Wickham, M. J. Lowden et al., Salmonella phage ST64B encodes a member of the SseK/NleB effector family, PLoS One, vol.6, p.17824, 2011.

C. P. Brussaard, S. W. Wilhelm, F. Thingstad, M. G. Weinbauer, G. Bratbak et al., Global-scale processes with a nanoscale drive: the role of marine viruses, The ISME Journal, vol.2, pp.575-578, 2008.

H. Brüssow, C. Canchaya, and W. Hardt, Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion, Microbiology and Molecular Biology Reviews, vol.68, pp.560-602, 2004.

B. Busby, D. M. Kristensen, and E. V. Koonin, Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens, Environmental Microbiology, vol.15, pp.307-312, 2012.

A. Campbell, Comparative molecular biology of lambdoid phages, Annual Review of Microbiology, vol.48, pp.193-222, 1994.

S. E. Carden, G. T. Walker, J. Honeycutt, K. Lugo, T. Pham et al., Pseudogenization of the secreted effector gene ssei confers rapid systemic dissemination of S. Typhimurium ST313 within migratory dendritic cells, Cell Host & Microbe, vol.21, pp.182-194, 2017.

C. J. Cardinale, R. S. Washburn, V. R. Tadigotla, L. M. Brown, M. E. Gottesman et al., Termination factor Rho and its cofactors NusA and NusG silence foreign, DNA in E. coli. Science, vol.320, pp.935-938, 2008.
DOI : 10.1126/science.1152763

URL : http://europepmc.org/articles/pmc4059013?pdf=render

J. Casadesús, Bacterial DNA methylation and methylomes, Advances in Experimental Medicine and Biology, vol.945, pp.35-61, 2016.

S. Casjens, Prophages and bacterial genomics: what have we learned so far? Molecular Microbiology, vol.49, pp.277-300, 2003.
DOI : 10.1046/j.1365-2958.2003.03580.x

URL : https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-2958.2003.03580.x

S. R. Casjens and J. H. Grose, Contributions of P2-and P22-like prophages to understanding the enormous diversity and abundance of tailed bacteriophages, Virology, vol.496, pp.255-276, 2016.

W. Cenens, A. Makumi, S. K. Govers, R. Lavigne, and A. Aertsen, Viral transmission dynamics at single-cell resolution reveal transiently immune subpopulations caused by a carrier state association, PLoS Genetics, p.1005770, 2015.
DOI : 10.1371/journal.pgen.1005770

URL : https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1005770&type=printable

W. Cenens, A. Makumi, M. T. Mebrhatu, R. Lavigne, and A. Aertsen, Phage-host interactions during pseudolysogeny: lessons from the Pid/dgo interaction, Bacteriophage, vol.3, p.25029, 2013.

W. Cenens, M. T. Mebrhatu, A. Makumi, P. Ceyssens, R. Lavigne et al., Expression of a novel P22 ORFan gene reveals the phage carrier state in Salmonella Typhimurium, PLoS Genetics, vol.9, p.1003269, 2013.

Y. Chen, I. Golding, S. Sawai, L. Guo, and E. C. Cox, Population fitness and the regulation of Escherichia coli genes by bacterial viruses, PLoS Biology, vol.3, p.229, 2005.

M. R. Clokie and . Kropinski, Bacteriophages: Methods and Protocols, 2009.

A. M. Colgan, C. Kröger, M. Diard, W. Hardt, J. L. Puente et al., The impact of 18 ancestral and horizontally-acquired regulatory proteins upon the transcriptome and sRNA landscape of Salmonella enterica serovar Typhimurium, PLoS Genetics, vol.12, 2016.

B. K. Coombes, M. E. Wickham, N. F. Brown, S. Lemire, L. Bossi et al., Genetic and molecular analysis of GogB, a phage-encoded type III-secreted substrate in Salmonella enterica serovar typhimurium with autonomous expression from its associated phage, Journal of Molecular Biology, vol.348, pp.817-830, 2005.

I. Cota, M. A. Sánchez-romero, S. B. Hernández, M. G. Pucciarelli, F. García-del-portillo et al., Epigenetic control of Salmonella enterica O-antigen chain length: a tradeoff between virulence and bacteriophage resistance, PLoS Genetics, vol.11, issue.11, p.1005667, 2015.

S. G. Cresawn, M. Bogel, N. Day, D. Jacobs-sera, R. W. Hendrix et al., Phamerator: a bioinformatic tool for comparative bacteriophage genomics, BMC Bioinformatics, vol.12, p.395, 2011.
DOI : 10.1186/1471-2105-12-395

URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-12-395

D. 'alessandro, B. Pérez-escanda, V. Balestrazzi, L. Iriarte, A. Pickard et al., A novel prophage identified in strains from Salmonella enterica serovar enteritidis is a phylogenetic signature of the lineage ST-1974, 2018.

D. Ari, R. Casadesús, and J. , Underground metabolism, BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology, vol.20, pp.181-186, 1998.

K. H. Darwin and V. L. Miller, The putative invasion protein chaperone SicA acts together with InvF to activate the expression of Salmonella typhimurium virulence genes, Molecular Microbiology, vol.35, pp.949-960, 2000.

E. V. Davies, C. Winstanley, J. L. Fothergill, and C. E. James, The role of temperate bacteriophages in bacterial infection, FEMS Microbiology Letters, vol.363, p.15, 2016.

M. R. Davies, S. E. Broadbent, S. R. Harris, N. R. Thomson, and M. W. Van-der-woude, Horizontally acquired glycosyltransferase operons drive Salmonellae lipopolysaccharide diversity, PLoS Genetics, vol.9, p.1003568, 2013.
DOI : 10.1371/journal.pgen.1003568

URL : https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1003568&type=printable

M. De-paepe, G. Hutinet, O. Son, J. Amarir-bouhram, S. Schbath et al., Temperate phages acquire DNA from defective prophages by relaxed homologous recombination: the role of Rad52-like recombinases, PLoS Genetics, vol.10, p.1004181, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01134590

A. D. Dearborn and T. Dokland, Mobilization of pathogenicity islands by Staphylococcus aureus strain Newman bacteriophages, Bacteriophage, vol.2, pp.70-78, 2012.
DOI : 10.4161/bact.20632

URL : https://www.tandfonline.com/doi/pdf/10.4161/bact.20632?needAccess=true

M. Diard, E. Bakkeren, J. K. Cornuault, K. Moor, A. Hausmann et al., Inflammation boosts bacteriophage transfer between Salmonella spp, Science, vol.355, pp.1211-1215, 2017.
DOI : 10.1126/science.aaf8451

URL : https://hal.archives-ouvertes.fr/hal-01607431

C. J. Dorman, H-NS, the genome sentinel, Nature Reviews Microbiology, vol.5, pp.157-161, 2007.
DOI : 10.1038/nrmicro1598

C. U. Duerr, S. F. Zenk, C. Chassin, J. Pott, D. Gütle et al., O-antigen delays lipopolysaccharide recognition and impairs antibacterial host defense in murine intestinal epithelial cells, PLoS Pathogens, vol.5, p.1000567, 2009.
DOI : 10.1371/journal.ppat.1000567

URL : https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1000567&type=printable

K. Ehrbar and W. Hardt, Bacteriophage-encoded type III effectors in Salmonella enterica subspecies 1 serovar Typhimurium. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, vol.5, pp.1-9, 2005.

F. Enault, A. Briet, L. Bouteille, S. Roux, M. B. Sullivan et al., Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses, The ISME Journal, vol.11, pp.237-247, 2017.
DOI : 10.1038/ismej.2016.90

URL : https://hal.archives-ouvertes.fr/hal-01557484

M. R. Evans, R. C. Fink, A. Vazquez-torres, S. Porwollik, J. Jones-carson et al., Analysis of the ArcA regulon in anaerobically grown Salmonella enterica sv, Typhimurium. BMC Microbiology, p.58, 2011.

R. Feiner, T. Argov, L. Rabinovich, N. Sigal, I. Borovok et al., A new perspective on lysogeny: prophages as active regulatory switches of bacteria, Nature Reviews Microbiology, vol.13, pp.641-650, 2015.

X. Feng, D. Walthers, R. Oropeza, and L. J. Kenney, The response regulator SsrB activates transcription and binds to a region overlapping OmpR binding sites at Salmonella pathogenicity island 2, Molecular Microbiology, vol.54, pp.823-835, 2004.
DOI : 10.1111/j.1365-2958.2004.04317.x

N. Figueroa-bossi and L. Bossi, Inducible prophages contribute to Salmonella virulence in mice, Molecular Microbiology, vol.33, pp.167-176, 1999.
DOI : 10.1046/j.1365-2958.1999.01461.x

URL : https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-2958.1999.01461.x

N. Figueroa-bossi and L. Bossi, Resuscitation of a defective prophage in Salmonella cocultures, Journal of Bacteriology, vol.186, pp.4038-4041, 2004.

N. Figueroa-bossi, E. Coissac, P. Netter, and L. Bossi, Unsuspected prophage-like elements in Salmonella typhimurium, Molecular Microbiology, vol.25, pp.161-173, 1997.

N. Figueroa-bossi, S. Uzzau, D. Maloriol, and L. Bossi, Variable assortment of prophages provides a transferable repertoire of pathogenic determinants in Salmonella, Molecular Microbiology, vol.39, pp.260-271, 2001.

R. C. Fink, M. R. Evans, S. Porwollik, A. Vazquez-torres, J. Jones-carson et al., FNR is a global regulator of virulence and anaerobic metabolism in Salmonella enterica Serovar Typhimurium (ATCC 14028s), Journal of Bacteriology, vol.189, pp.2262-2273, 2007.

L. Fortier and O. Sekulovic, Importance of prophages to evolution and virulence of bacterial pathogens, Virulence, vol.4, pp.354-365, 2013.

L. García-pastor, E. Puerta-fernández, and J. Casadesús, Bistability and phase variation in Salmonella enterica, Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 2018.

E. B. Gilcrease and S. R. Casjens, The genome sequence of Escherichia coli tailed phage D6 and the diversity of Enterobacteriales circular plasmid prophages, Virology, vol.515, pp.203-214, 2018.

, Prophages in Salmonella enterica, vol.13

, © 2018 The Authors. Molecular Microbiology Published by John Wiley & Sons Ltd, vol.0, pp.1-14

D. L. Hammarlöf, C. Kröger, S. V. Owen, R. Canals, L. Lacharme-lora et al., Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella, Proceedings of the National Academy of Sciences, vol.115, pp.2614-2623, 2018.

G. F. Hatfull, Dark matter of the biosphere: the amazing world of bacteriophage diversity, Journal of Virology, vol.89, pp.8107-8110, 2015.

G. F. Hatfull, D. Jacobs-sera, J. G. Lawrence, W. H. Pope, D. A. Russell et al., Comparative genomic analysis of 60 mycobacteriophage genomes: genome clustering, gene acquisition, and gene size, Journal of Molecular Biology, vol.397, pp.119-143, 2010.

S. B. Hernández, I. Cota, A. Ducret, L. Aussel, J. Casadesús et al., The homolog of the gene bstA of the BTP1 Phage from Salmonella enterica Serovar Typhimurium ST313 is an antivirulence gene in, Salmonella enterica Serovar Dublin. Infection and Immunity, vol.8, p.86, 2012.

A. Herrero-fresno, I. Wallrodt, P. Leekitcharoenphon, J. E. Olsen, F. M. Aarestrup et al., The role of the st313-td Gene in virulence of Salmonella Typhimurium ST313, PLOS One, vol.9, p.84566, 2014.

T. Hershko-shalev, A. Odenheimer-bergman, M. Elgrablyweiss, T. Ben-zvi, S. Govindarajan et al., Gifsy-1 prophage IsrK with dual function as small and messenger RNA modulates vital bacterial machineries, PLOS Genetics, vol.12, p.1005975, 2016.

T. D. Ho and J. M. Slauch, Characterization of grvA, an antivirulence gene on the gifsy-2 phage in Salmonella enterica serovar typhimurium, Journal of Bacteriology, vol.183, pp.611-620, 2001.

M. Hoffmann, S. Zhao, J. Pettengill, Y. Luo, S. R. Monday et al., Comparative genomic analysis and virulence differences in closely related salmonella enterica serotype heidelberg isolates from humans, retail meats, and animals, Genome Biology and Evolution, vol.6, pp.1046-1068, 2014.

S. L. Jaslow, K. D. Gibbs, W. F. Fricke, L. Wang, K. J. Pittman et al., Salmonella activation of STAT3 signaling by SarA effector promotes intracellular replication and production of IL-10, Cell Reports, vol.23, pp.3525-3536, 2018.

F. Kamal and J. J. Dennis, Burkholderia cepacia complex phage-antibiotic synergy (PAS): antibiotics stimulate lytic phage activity, Applied and Environmental Microbiology, vol.81, pp.1132-1138, 2015.

J. Kaur and S. K. Jain, Role of antigens and virulence factors of Salmonella enterica serovar Typhi in its pathogenesis, Microbiological Research, vol.167, pp.199-210, 2012.

M. Kim and S. Ryu, Antirepression system associated with the life cycle switch in the temperate podoviridae phage SPC32H, Journal of Virolog, vol.87, pp.11775-11786, 2013.

S. Kim, K. Ryu, D. Biswas, and J. Ahn, Survival, prophage induction, and invasive properties of lysogenic Salmonella Typhimurium exposed to simulated gastrointestinal conditions, Archives of Microbiology, vol.196, pp.655-659, 2014.

E. Kintz, M. R. Davies, D. L. Hammarlöf, R. Canals, J. C. Hinton et al., A BTP1 prophage gene present in invasive non-typhoidal Salmonella determines composition and length of the O-antigen of the lipopolysaccharide, Molecular Microbiology, vol.96, pp.263-275, 2015.

B. Kraushaar, J. A. Hammerl, M. Kienöl, M. L. Heinig, N. Sperling et al., Acquisition of virulence factors in livestock-associated MRSA: lysogenic conversion of CC398 strains by virulence gene-containing phages, Scientific Reports, vol.7, 2004.

C. Kröger, A. Colgan, S. Srikumar, K. Händler, S. K. Sivasankaran et al., An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium, Cell Host & Microbe, vol.14, pp.683-695, 2013.

A. M. Kropinski, I. V. Kovalyova, S. J. Billington, A. N. Patrick, B. D. Butts et al., The genome of epsilon15, a serotype-converting, Group E1 Salmonella enterica-specific bacteriophage, Virology, vol.369, pp.234-244, 2007.

S. Lemire, N. Figueroa-bossi, L. Bossi, C. Lévi-meyrueis, V. Monteil et al., Bacteriophage crosstalk: coordination of prophage induction by trans-acting antirepressors, Nucleic Acids Research, vol.7, pp.1456-1468, 2011.
DOI : 10.1371/journal.pgen.1002149

URL : https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1002149&type=printable

M. Levine, S. Truesdell, T. Ramakrishnan, and M. J. Bronson, Dual control of lysogeny by bacteriophage P22: an antirepressor locus and its controlling elements, Journal of Molecular Biology, vol.91, pp.421-438, 1975.
DOI : 10.1016/0022-2836(75)90270-3

URL : https://deepblue.lib.umich.edu/bitstream/2027.42/22123/1/0000550.pdf

M. Lewis, A tale of two repressors-a historical perspective, Journal of Molecular Biology, vol.409, pp.14-27, 2011.

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, pp.3952-3962, 2010.

S. Lucchini, G. Rowley, M. D. Goldberg, D. Hurd, M. Harrison et al., H-NS mediates the silencing of laterally acquired genes in bacteria, PLoS Pathogens, vol.2, p.81, 2006.

R. Menouni, G. Hutinet, M. Petit, and M. Ansaldi, Bacterial genome remodeling through bacteriophage recombination, FEMS Microbiology Letters, vol.362, pp.1-10, 2015.
DOI : 10.1093/femsle/fnu022

URL : https://hal.archives-ouvertes.fr/hal-01204494

S. Mirold, W. Rabsch, H. Tschäpe, and W. D. Hardt, Transfer of the Salmonella type III effector sopE between unrelated phage families, Journal of Molecular Biology, vol.312, pp.7-16, 2001.

A. Nadeem and L. M. Wahl, Prophage as a genetic reservoir: promoting diversity and driving innovation in the host community, Evolution: International Journal of Organic Evolution, vol.71, pp.2080-2089, 2017.

W. W. Navarre, T. A. Halsey, D. Walthers, J. Frye, M. Mcclelland et al., Co-regulation of Salmonella enterica genes required for virulence and resistance to antimicrobial peptides by SlyA and PhoP/ PhoQ, Molecular Microbiology, vol.56, pp.492-508, 2005.

W. W. Navarre, M. Mcclelland, S. J. Libby, and F. C. Fang, Silencing of xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA, Genes & Development, vol.21, pp.1456-1471, 2007.

W. W. Navarre, S. Porwollik, Y. Wang, M. Mcclelland, H. Rosen et al., Molecular Microbiology, 0, 1-14 foreign DNA with low GC content by the H-NS protein in Salmonella, Science, vol.313, pp.236-238, 2006.

L. P. Nedialkova, M. Sidstedt, M. B. Koeppel, S. Spriewald, D. Ring et al., Temperate phages promote colicin-dependent fitness of Salmonella enterica serovar Typhimurium, Environmental Microbiology, vol.18, pp.1591-1603, 2015.
DOI : 10.1111/1462-2920.13077

P. H. Oliveira, M. Touchon, J. Cury, and E. P. Rocha, The chromosomal organization of horizontal gene transfer in bacteria, Nature Communications, vol.8, p.841, 2017.

S. V. Owen, N. Wenner, R. Canals, A. Makumi, D. L. Hammarlöf et al., Characterization of the prophage repertoire of African Salmonella Typhimurium ST313 reveals high levels of spontaneous induction of novel phage BTP1, Frontiers in Microbiology, vol.8, p.235, 2017.

A. V. Pilar, S. A. Reid-yu, C. A. Cooper, D. T. Mulder, and B. K. Coombes, GogB is an anti-inflammatory effector that limits tissue damage during Salmonella infection through interaction with human FBXO22 and Skp1, PLoS Pathogens, vol.8, p.1002773, 2012.
DOI : 10.1371/journal.ppat.1002773

URL : https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1002773&type=printable

S. Porwollik, R. M. Wong, Y. Mcclelland, and M. , Evolutionary genomics of Salmonella: gene acquisitions revealed by microarray analysis, Proceedings of the National Academy of Sciences, vol.99, pp.8956-8961, 2002.
DOI : 10.1073/pnas.122153699

URL : http://www.pnas.org/content/99/13/8956.full.pdf

L. Rabinovich, N. Sigal, I. Borovok, R. Nir-paz, and A. A. Herskovits, Prophage excision activates Listeria competence genes that promote phagosomal escape and virulence, Cell, vol.150, pp.792-802, 2012.
DOI : 10.1016/j.cell.2012.06.036

URL : https://doi.org/10.1016/j.cell.2012.06.036

K. Ranade and A. R. Poteete, Superinfection exclusion (sieB) genes of bacteriophages P22 and lambda, Journal of Bacteriology, vol.175, pp.4712-4718, 1993.
DOI : 10.1128/jb.175.15.4712-4718.1993

URL : https://jb.asm.org/content/jb/175/15/4712.full.pdf

C. Rinke, P. Schwientek, A. Sczyrba, N. N. Ivanova, I. J. Anderson et al., Insights into the phylogeny and coding potential of microbial dark matter, Nature, vol.499, pp.431-437, 2013.

S. Roux, F. Enault, B. L. Hurwitz, and M. B. Sullivan, VirSorter: mining viral signal from microbial genomic data, PeerJournal, vol.3, p.985, 2015.
DOI : 10.7717/peerj.985

URL : https://hal.archives-ouvertes.fr/hal-01557667

S. Roux, S. J. Hallam, T. Woyke, and M. B. Sullivan, Viral dark matter and virus-host interactions resolved from publicly available microbial genomes, 2015.
DOI : 10.7554/elife.08490

URL : https://doi.org/10.7554/elife.08490

R. T. Sauer, J. Pan, P. Hopper, K. Hehir, J. Brown et al., Primary structure of the phage P22 repressor and its gene c2, Biochemistry, vol.20, pp.3591-3598, 1981.
DOI : 10.1021/bi00515a044

J. Shah, P. T. Desai, and B. C. Weimer, Genetic mechanisms underlying the pathogenicity of cold-stressed Salmonella enterica Serovar Typhimurium in cultured intestinal epithelial cells, Applied and Environmental Microbiology, vol.80, pp.6943-6953, 2014.

K. E. Shearwin, A. M. Brumby, and J. B. Egan, The tum protein of coliphage 186 is an antirepressor, Journal of Biological Chemistry, vol.273, pp.5708-5715, 1998.

J. M. Slauch, A. A. Lee, M. J. Mahan, and J. J. Mekalanos, Molecular characterization of the oafA locus responsible for acetylation of Salmonella typhimurium O-antigen: oafA is a member of a family of integral membrane trans-acylases, Journal of Bacteriology, vol.178, pp.5904-5909, 1996.

Q. Sun, Y. A. Knirel, J. Wang, X. Luo, S. N. Senchenkova et al., Serotype-converting bacteriophage SfII encodes an acyltransferase protein that mediates 6-O-acetylation of GlcNAc in Shigella flexneri O-antigens, conferring on the host a novel O-antigen epitope, Journal of Bacteriology, vol.196, pp.3656-3666, 2014.

M. M. Susskind and D. Botstein, Superinfection exclusion by lambda prophage in lysogens of Salmonella typhimurium, Virology, vol.100, pp.212-216, 1980.

M. M. Susskind, D. Botstein, and A. Wright, Superinfection exclusion by P22 prophage in lysogens of Salmonella typhimurium. III. Failure of superinfecting phage DNA to enter sieA+ lysogens, Virology, vol.62, pp.350-366, 1974.

C. A. Suttle, Marine viruses-major players in the global ecosystem, Nature Reviews Microbiology, vol.5, pp.801-812, 2007.
DOI : 10.1038/nrmicro1750

URL : https://hal.archives-ouvertes.fr/hal-01663342

A. M. Tomljenovic-berube, B. Henriksbo, S. Porwollik, C. A. Cooper, B. R. Tuinema et al., Mapping and regulation of genes within Salmonella pathogenicity island 12 that contribute to in vivo fitness of, Salmonella enterica Serovar Typhimurium. Infection and Immunity, vol.81, pp.2394-2404, 2013.

M. Touchon and E. P. Rocha, The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella, PLoS One, vol.5, p.11126, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-01374940

S. C. Tucker and J. E. Galán, Complex function for SicA, a Salmonella enterica serovar typhimurium type III secretion-associated chaperone, Journal of Bacteriology, vol.182, pp.2262-2268, 2000.

A. Vivero, R. C. Baños, J. F. Mariscotti, J. C. Oliveros, F. García-del-portillo et al., Modulation of horizontally acquired genes by the Hha-YdgT proteins in Salmonella enterica serovar Typhimurium, Journal of Bacteriology, vol.190, pp.1152-1156, 2008.

P. Vonaesch, M. E. Sellin, S. Cardini, V. Singh, M. Barthel et al., The Salmonella Typhimurium effector protein SopE transiently localizes to the early SCV and contributes to intracellular replication, Cellular Microbiology, vol.16, pp.1723-1735, 2014.

A. Wernicki, A. Nowaczek, and R. Urban-chmiel, Bacteriophage therapy to combat bacterial infections in poultry, Virology Journal, vol.14, p.179, 2017.
DOI : 10.1186/s12985-017-0849-7

URL : https://virologyj.biomedcentral.com/track/pdf/10.1186/s12985-017-0849-7

F. W. Whipple, E. F. Hou, and A. Hochschild, Amino acid-amino acid contacts at the cooperativity interface of the bacteriophage lambda and P22 repressors, Genes & Development, vol.12, pp.2791-2802, 1998.

M. J. Worley, K. H. Ching, and F. Heffron, Salmonella SsrB activates a global regulon of horizontally acquired genes, Molecular Microbiology, vol.36, pp.749-761, 2000.

Z. Yang, A. Soderholm, T. W. Lung, C. Giogha, M. M. Hill et al., SseK3 is a Salmonella effector that binds TRIM32 and modulates the host's NF-?B signalling activity, PLoS One, vol.10, p.138529, 2015.

H. Yoon, C. Ansong, J. N. Adkins, and F. Heffron, Discovery of Salmonella virulence factors translocated via outer membrane vesicles to murine macrophages, Infection and Immunity, vol.79, pp.2182-2192, 2011.

N. D. Zinder and J. Lederberg, Genetic exchange in Salmonella, Journal of Bacteriology, vol.64, pp.679-699, 1952.

Q. Zou, Q. Li, H. Zhu, Y. Feng, Y. Li et al., SPC-P1: a pathogenicity-associated prophage of Salmonella paratyphi C, BMC Genomics, p.729, 2010.