Genomic Insights into Colistin and Tigecycline Resistance in ESBL-Producing and Harboring Genes in Ecuador.

() and () are resistant to third-generation cephalosporins (3GCs), carbapenems, colistin, and tigecycline, making them a major public health priority, mainly within the developing world. However, their genomic epidemiology and possible determinants of resistance remain to be elucidated. Thus, this study aimed to perform a genomic characterization of and , both of which are resistant to last-line antibiotics, isolated from humans, poultry, and a dairy farm environment within Ecuador. This study analyzed nine 3GC-resistant isolates harboring the -1 gene (six from poultry farms, two from human infections, and one from dairy farm compost), together with ten isolated colistin- and carbapenem-resistant clinical samples. The isolates of human origin belonged to ST609 and phylogroup A, while the poultry and compost isolates belonged to phylogroups A, B1, E, and F. Diverse STs of the isolates included ST13 (five isolates), ST258 (four isolates), and ST86 (one isolate). Within the isolates, , , , and genes were identified. This study also identified and (the latter in a carbapenem-susceptible isolate). In , the plasmid-borne -1.1 gene was identified across all isolates within an IncI2 plasmid. Tigecycline-reduced susceptibility or resistance was related to missense amino acid substitutions coded in the and A genes. Within , and , on the one hand, and and , on the other, were associated with 3GC and carbapenem resistance, respectively. The allele was identified in a ~10 kb Tn transposon (). In , sequence data and phenotypic analysis linked a nonsense amino acid substitution coded in the (K3*) gene and missense amino acid substitutions coded in the , A, , , , , and genes to colistin resistance. Meanwhile, tigecycline resistance was linked to nonsense and missense amino acid substitutions coded within the sequence. Additionally, this study identified several integron structures, including Int191 (), which was the most prevalent integron (Int) among and isolates in this study, followed by Int0 () and Int18 (). These results contribute to the genomic epidemiology of MDR and in our setting and to the worldwide epidemiology in the One Health approach.