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

Prophages can constitute up to 30% of the accessory genome in Salmonella 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. enterica 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 Peduovirus pro483 in S. Infantis isolates, carrying cargo proteins such as metalloendopeptidase, whereas related S. Enteritidis strains harbored distinct cargo elements, including cytosine-specific methyltransferases, consistent with independent horizontal acquisition events. Notably, Enterobacteria phage ST104 was detected in S. Typhimurium 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.