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

## TL;DR

This study explores prophage diversity in Salmonella from Ecuadorian poultry, revealing how these genetic elements contribute to virulence and resistance.

## Contribution

The first comprehensive characterization of prophage diversity in Ecuadorian poultry-associated Salmonella enterica.

## Key findings

- Peduovirus pro483 is prevalent in S. Infantis isolates, carrying metalloendopeptidase cargo proteins.
- S. Enteritidis strains contain cytosine-specific methyltransferases, indicating independent horizontal gene transfer.
- Enterobacteria phage ST104 in S. Typhimurium encodes proteins that may enhance resistance to secondary phage infections.

## Abstract

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.