Mobile genetic elements drive a plasmid fusion and deletion lifecycle shaping evolution and antimicrobial resistance.

Plasmids are key drivers of bacterial adaptation, yet the mechanisms that generate their diversity remain poorly understood. Here, we show that mobile genetic elements (MGEs) orchestrate a fusion-deletion life cycle that repeatedly remodels plasmids in Staphylococcus aureus. Large-scale genomic analyses reveal that multireplicon plasmids are widespread and strongly enriched in transposases. Using experimental assays, we demonstrate that rare MGE-mediated fusion events, via homologous recombination or transposition, combine distinct plasmids into single multireplicon elements, expanding gene content and transfer potential. Antibiotic pressure selectively enriches these fused plasmids, rescuing bacterial populations under stress, whereas opposing selective forces, including phage predation, favour deletion derivatives that preserve essential functions and phage transmissibility. This cyclical process generates dynamic plasmid repertoires with conserved backbones and diverse accessory modules. We propose that MGE-driven fusion-deletion cycles represent a general principle of plasmid evolution, explaining the rapid emergence and persistence of multidrug-resistant plasmids across bacterial pathogens.