Gillis, AnnikaRonse, LouisLouisRonse2025-07-012025-07-012025-06-1020252025-06-10https://hdl.handle.net/2078.2/43283The emergence of multidrug-resistant "Staphylococcus" strains represents a major global health concern, reducing the effectiveness of conventional antibiotic treatments. In response, alternative strategies are being explored, including phage therapy. However, still little is known about the antiviral defense systems arsenal of the genus "Staphylococcus", and how these systems interact with each other and horizontally spread between species. In this study, we analyzed 3 132 complete staphylococcal genomes from the NCBI database to identify and characterize the distribution of phage defense systems and correlate them with mobile genetic elements using DefenseFinder and PADLOC (for defense systems detection) and Virsorter2 (for prophages detection). In the analyzed genomes, 37 748 systems were predicted as part of the "Staphylococcus" defense arsenal, including 73 different types with the most prevalent being Restriction-Modification (RM) systems. Staphylococci encode on average 12 defense systems. The results of this work highlight the diversity and uneven distribution of phage defense systems between "Staphylococcus" species. Defense strategies in these bacteria are varied, with on average four abortive infection and three non-abortive infection systems per genomes. Prophages represent about 9% of total length of genomes, and plasmids 1%, while 11% of defense systems were predicted inside mobile genetic elements (MGEs). Some systems like Abi2DF or FS_Sma, found at high frequency in the staphylococcal genomes, were predicted more than 30% in MGEs, suggesting a high mobility of these systems. These findings provide new insights into the adaptive landscape of "Staphylococcus" species and may guide future efforts in antimicrobial development. However, further analyses on a more exhaustive list of MGEs encoded on defense islands may be interesting for future work on the subject.text::thesis::master thesis