Caracterización de genomas completos de aislamientos de Salmonella spp. aisladas de muestras de agua del canal de riego Mocha-Quero-Ladrillos mediante secuenciación de tercera generación

Abstract

The presence of Salmonella enterica in the Mocha-Quero-Ladrillos irrigation canal represents a significant public health risk, as this water resource is used in agricultural activities and can serve as a vehicle for the transfer of pathogens to plant-based food products. The detection of the microorganism at multiple points along the system revealed that the canal functions as a reservoir capable of supporting the survival and dispersion of this pathogen in non-clinical environments, thereby increasing its potential impact on food safety and public health. To characterize the isolates, microbiological techniques and biochemical verification were applied, complemented by third-generation sequencing using Oxford Nanopore and specialized bioinformatic pipelines. This approach enabled the generation of complete genome assemblies and the identification of coding regions, mobile genetic elements, virulence factors, and intrinsic resistance determinants, including an aminoglycoside acetyltransferase conferring resistance to tobramycin and kanamycin. In silico serotyping confirmed that all isolates corresponded to the serovar Salmonella Typhimurium, while genomic parameters described their organization, variability, and degree of fragmentation. The phylogenetic analysis, integrating forty-nine isolates from different sources, demonstrated that the nine environmental strains from the canal exhibit a close evolutionary relationship with zoonotic sublineages ST19 and ST1649 associated with animal and food-related matrices in Ecuador. These findings indicate that the genotypes present in the canal are not exclusive aquatic variants but rather lineages circulating across multiple ecological niches.