Análisis genómico de Escherichia coli portadoras de genes de resistencia mcr-1 y blaOXA-48 de origen ambiental ecuatoriano utilizando secuenciación de tercera generación

Abstract

The present research emphasizes the importance of analyzing antimicrobial resistance (AMR) both globally and in Ecuador, focusing on the analysis of two complete genome sequences of E. coli strains (62A and 17A) of environmental origin, which harbor resistance genes. The relevance of this work in global public health is significant, highlighting the urgency to address this issue. Using the Oxford Nanopore Technologies (ONT) sequencing technique and bioinformatics tools, a detailed characterization of the chromosomes and plasmids of the strains was achieved. The analysis was carried out on the platform of the Center for Genomic Epidemiology (CGE-DTU), allowing the identification of resistance genes, virulence factors, plasmids, sequence types, including multilocus sequence typing (MLST). Additionally, the genetic environment was studied using DiGAling and phylogeny through the cgMLST method of the Galaxy platform, using the iTOL tool for visualization. The results revealed that both strains have an approximate genomic size of 4.8 Mb, and the resistance genes are located on IncFII type plasmids. They also share phylogenetic profiles and antibiotic resistance, particularly highlighting the E. coli 17A strain, being the first in Ecuador reported with the blaOXA-48 gene. These discoveries are vital for the surveillance and control of E. coli, underscoring the importance of an integrated One Health approach, which considers the relationship between human, animal, and environmental health; allowing for coordinated strategies against the challenges of antibiotic resistance.