Prophage diversity in poultry-associated <i>Salmonella enterica</i> from Ecuador: a case study using an <i>in-silico</i> terminase-based approach

Prophages can constitute up to 30% of the accessory genome in <i>Salmonella</i> enterica, acting as major drivers of virulence evolution and antimicrobial resistance; however, their diversity and functional contribution in Ecuadorian poultry-associated lineages remain unexplored. Here, we analyzed 142 S. <i>enterica</i> genomes from poultry and clinical sources to systematically characterize prophage diversity and cargo gene content. Genomes were assembled using SPAdes and screened with Phigaro and PHASTEST, while virulence-associated genes were identified through VFDB and VirulenceFinder. We identified a high prevalence of <i>Peduovirus</i> pro483 in S. <i>Infantis</i> isolates, carrying cargo proteins such as metalloendopeptidase, whereas related S. <i>Enteritidis</i> strains harbored distinct cargo elements, including cytosine-specific methyltransferases, consistent with independent horizontal acquisition events. Notably, <i>Enterobacteria</i> phage ST104 was detected in S. <i>Typhimurium</i> isolates encoding superinfection exclusion proteins (SieA and SieB), suggesting enhanced resistance to secondary phage infection and potential competitive advantages within microbial communities. Collectively, these findings provide the first comprehensive characterization of prophage diversity in S. enterica from Ecuadorian poultry production systems and underscore the role of prophages as dynamic contributors to lineage-specific adaptation, virulence potential, and public health risk.