Prophage-mediated lysogenic conversion drives virulence evolution and genomic plasticity in Streptococcus suis serotype 9

Streptococcus suis serotype 9 is an emerging zoonotic pathogen threatening pig production and public health. Here, we combined comparative genomics of 16 strains, including clinical isolate SS2401, to elucidate the role of prophages in shaping genomic plasticity and virulence evolution. The pan-genome was open (α = 0.375), highlighting extensive genetic diversity. Prophages were prevalent (56.25% of strains), significantly correlated with larger genomes, and exhibited two integration modes: direct insertion as genomic islands and integration at recombination hotspots associated with large-scale inversions. Phylogenetic analysis of the terminase large subunit (TerL) and whole-genome sequences revealed multiple independent acquisitions, with three prophages in SS2401 originating from distinct lineages ("one strain, multiple sources"). Recombination analysis detected 1,432 events across the core genome, indicating frequent horizontal gene exchange. The virulence gene sly (suilysin) was carried as a gene cassette within prophage Phi2401a. Notably, we identified integrase-deficient but otherwise intact prophages that may function as "gene prisons," stably fixing virulence traits. These findings demonstrate that prophages act as dual drivers of genomic architecture and as dynamic reservoirs for virulence genes, providing a framework for understanding bacterial adaptation and informing surveillance strategies in the swine industry.IMPORTANCEStreptococcus suis serotype 9 poses a significant threat to pig farming and public health worldwide. This study reveals that prophages are not passive passengers but active architects of genomic plasticity and virulence evolution in this pathogen. We demonstrate that prophages contribute to genome expansion, facilitate large-scale chromosomal rearrangements, and carry key virulence genes such as sly. The discovery of a "one strain, multiple sources" acquisition pattern and the "gene prison" model explains how virulence traits can be stably maintained and disseminated. These findings redefine prophages as dual drivers of bacterial evolution, providing new insights for surveillance and intervention strategies in the swine industry.