F. Lowy, Infections, New England Journal of Medicine, vol.339, issue.8, pp.520-532, 1998.
DOI : 10.1056/NEJM199808203390806

S. Herbert, A. Ziebandt, K. Ohlsen, T. Schäfer, M. Hecker et al., Repair of Global Regulators in Staphylococcus aureus 8325 and Comparative Analysis with Other Clinical Isolates, Infection and Immunity, vol.78, issue.6, pp.2877-2889, 2010.
DOI : 10.1128/IAI.00088-10

R. Novick and M. Richmond, Nature and interactions of the genetic elements governing penicillinase synthesis in Staphylococcus aureus, J. Bacteriol, vol.90, pp.467-480, 1965.

A. Gillaspy, V. Worrell, J. Orvis, B. Roe, D. Dyer et al., Staphylococcus aureus NCTC8325 genome, Gram-positive pathogens, pp.381-412, 2006.

J. Drake, B. Charlesworth, D. Charlesworth, and J. Crow, Rates of spontaneous mutation, Genetics, vol.148, pp.1667-1686, 1998.

C. Goerke, M. Y. Papenberg, S. Dasbach, S. Dietz, K. Ziebach et al., Increased frequency of genomic alterations in Staph- crossmark Genome Announcements, pp.855-869, 2004.

J. Rolain, P. François, D. Hernandez, F. Bittar, H. Richet et al., Genomic analysis of an emerging multiresistant Staphylococcus aureus strain rapidly spreading in cystic fibrosis patients revealed the presence of an antibiotic inducible bacteriophage, Biology Direct, vol.4, issue.1, 2009.
DOI : 10.1186/1745-6150-4-1
URL : https://hal.archives-ouvertes.fr/hal-01478692

B. Young, T. Golubchik, E. Batty, R. Fung, H. Larner-svensson et al., Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease, Proceedings of the National Academy of Sciences, vol.109, issue.12, pp.4550-4555, 2012.
DOI : 10.1073/pnas.1113219109

M. Lohse, A. Bolger, A. Nagel, A. Fernie, J. Lunn et al., RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics, Nucleic Acids Research, vol.40, issue.W1, pp.622-627, 2012.
DOI : 10.1093/nar/gks540

A. Bankevich, S. Nurk, D. Antipov, A. Gurevich, M. Dvorkin et al., SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing, Journal of Computational Biology, vol.19, issue.5, pp.455-477, 2012.
DOI : 10.1089/cmb.2012.0021

S. Nurk, A. Bankevich, D. Antipov, A. Gurevich, A. Korobeynikov et al., Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products, Journal of Computational Biology, vol.20, issue.10, pp.714-737, 2013.
DOI : 10.1089/cmb.2013.0084

S. Angiuoli, A. Gussman, W. Klimke, G. Cochrane, D. Field et al., Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation, OMICS: A Journal of Integrative Biology, vol.12, issue.2, pp.137-1410017, 2008.
DOI : 10.1089/omi.2008.0017

Y. Zhou, Y. Liang, K. Lynch, J. Dennis, and D. Wishart, PHAST: A Fast Phage Search Tool, Nucleic Acids Research, vol.39, issue.suppl, pp.347-352, 2011.
DOI : 10.1093/nar/gkr485

I. Grissa, G. Vergnaud, and C. Pourcel, CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats, Nucleic Acids Research, vol.35, issue.Web Server, pp.52-57, 2007.
DOI : 10.1093/nar/gkm360
URL : https://hal.archives-ouvertes.fr/hal-00194414