Temperate bacteriophage SapYZUs7 alters Staphylococcus aureus fitness balance by regulating expression of phage resistance, virulence and antimicrobial resistance gene.

Temperate bacteriophages are crucial for maintaining the pathogenicity and fitness of S. aureus, which also show promise as a biocontrol agent for S. aureus. However, the fitness benefit and cost of lysogeny by S. aureus temperate phages and their underlying mechanisms remain unexplored. In this study, phage resistance, virulence, antimicrobial resistance (AMR), transcriptome, and metabolome of phage SapYZUs7 lysogenic and non-lysogenic S. aureus strains were compared. Whole-genome analysis revealed that SapYZUs7 harbouring smaII associated with a single-protein MazF-like antiphage system could be integrated into the genome of S. aureus isolates. Notably, lysogenic S. aureus exhibited higher phage resistance, a lower growth rate, and inhibited metabolic activity compared to the parental strains, indicating interference of phage reproduction by smaII. Moreover, prophages carrying smaII are widely distributed across S. aureus and harboured other virulence factor (VF) and AMR genes. Besides, the SapYZUs7-integration increased phagocytosis resistance but decreased adhesion, biofilm formation, and AMR. The combined use of SapYZUs7 and antibiotics exhibited a better bactericidal effect than SapYZUs7 or the antibiotics alone. Consistently, integrated omics analysis suggested that SapYZUs7-lysogeny downregulated multiple VF and AMR genes. Our analysis suggests that SmaII drives mutualistic phage-host interactions through lysogenic conversion. The fitness cost of SapYZUs7-integration is the downregulated expression of VF and AMR genes, serving as an alternative candidate as a biocontrol agent for methicillin-resistant S. aureus and multidrug-resistant S. aureus.