ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Phage Biology
This article is part of the Research TopicPhage-Based Interventions in Livestock: From Genomics to Translational ApplicationsView all 6 articles
Prophage diversity in poultry-associated Salmonella enterica from Ecuador: a case study using an in-silico terminase-based approach
Provisionally accepted
- 1Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
- 2The University of North Carolina at Chapel Hill, Chapel Hill, United States
- 3Unidad de Investigación de Enfermedades Transmitidas por Alimentos y Resistencia a los Antimicrobianos (UNIETAR), Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, QUITO, Ecuador
- 4Instituto de Microbiologia, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
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Prophages contribute up to 30% of the accessory genome in Salmonella enterica, significantly influencing virulence and antimicrobial resistance; however, their diversity in Ecuadorian poultry isolates remains poorly understood. To address this, 142 S. enterica genomes from poultry and clinical sources were assembled using SPAdes and analyzed for prophage content using Phigaro, and PHASTEST, with virulence genes identified through VFDB and VirulenceFinder. The analysis revealed high prevalence of Peduovirus pro483 in S. Infantis isolates carrying cargo proteins like metalloendopeptidase, while related S. Enteritidis isolates carried different cargo genes such as cytosine-specific methyltransferases, suggesting distinct horizontal transfer events. Additionally, Enterobacteria phage ST104 was identified in S. Typhimurium harboring superinfection exclusion proteins (SieA, SieB) that likely enhance host phage resistance. These findings represent the first characterization of prophage diversity in Ecuadorian poultry farms, highlighting the critical role these elements play in strain adaptation and their broader implications for public health. To our knowledge, this is the first study to describe prophage diversity in S. enterica strains isolated from Ecuadorian poultry farms, providing insights into their potential role in strain adaptation and public health relevance.
Keywords: Genomes, In-silico, Prophages, S. enterica, serovar Infantis
Received: 11 Sep 2025; Accepted: 10 Feb 2026.
Copyright: © 2026 Quelal-Madrid, Armijos, Vinueza-Burgos, Mejia and Zapata Mena. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Sonia Zapata Mena
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