Evaluación de la diversidad genómica y las relaciones filogenéticas de Salmonella enterica aislada a partir de pollo comercializado en mercados de la ciudad de Ambato mediante secuenciación de Tercera Generación

Abstract

Salmonellosis is one of the most important foodborne diseases worldwide, with S. enterica being one of the main pathogens associated with the poultry production chain. In Ecuador, the commercialization of chicken in traditional markets constitutes a potential source of exposure, especially in cities such as Ambato, where information on the genomic characterization of circulating strains is limited. The present study evaluated the genetic diversity and phylogenetic relationships of 12 S. enterica strains isolated from chicken carcasses and giblets marketed in Ambato markets. The strains were sequenced using Oxford Nanopore technology and characterized through bioinformatics tools to determine serotypes, sequence types, virulence genes, antimicrobial resistance genes, plasmids, and prophages. Phylogenetic relationships were established through comparative analysis of single nucleotide polymorphisms with reference strains. The genomes showed completeness levels ranging from 95.52 percent to 100 percent. Eleven isolates belonged to the Infantis serotype and one to the Kentucky serotype. All strains carried genes associated with resistance to aminoglycosides and sulfonamides, whereas blaCTX-M-65 was detected in seven isolates. Phylogenetic analysis revealed the circulation of a predominant clonal lineage of S. Infantis related to poultry isolates previously reported in Ecuador. The results demonstrate the presence of multidrug-resistant strains of epidemiological importance and highlight the value of third-generation sequencing for strengthening genomic surveillance under the One Health approach.