Genomic Insights into Colistin and Tigecycline Resistance in ESBL-Producing Escherichia coli and Klebsiella pneumoniae Harboring bla_KPC Genes in Ecuador

Introduction: Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) 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 E. coli and K. pneumoniae, both of which are resistant to last-line antibiotics, isolated from humans, poultry, and a dairy farm environment within Ecuador. Methods: This study analyzed nine 3GC-resistant E. coli isolates harboring the mcr-1 gene (six from poultry farms, two from human infections, and one from dairy farm compost), together with ten isolated colistin- and carbapenem-resistant K. pneumoniae clinical samples. Results: The E. coli 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 K. pneumoniae isolates included ST13 (five isolates), ST258 (four isolates), and ST86 (one isolate). Within the E. coli isolates, bla_CTX-M-55, bla_CTX-M-65, bla_CTX-M-15, and bla_CTX-M-2 genes were identified. This study also identified bla_CMY-2 and bla_KPC-3 (the latter in a carbapenem-susceptible isolate). In E. coli, the plasmid-borne mcr-1.1 gene was identified across all E. coli isolates within an IncI2 plasmid. Tigecycline-reduced susceptibility or resistance was related to missense amino acid substitutions coded in the marA and acrA genes. Within K. pneumoiae, bla_CTX-M-15 and bla_CTX-M-65, on the one hand, and bla_KPC-2 and bla_KPC-3, on the other, were associated with 3GC and carbapenem resistance, respectively. The bla_KPC-2 allele was identified in a ~10 kb Tn4401 transposon (tnpR–tnpA–istA–istB–bla_KPC-2–tnpA). In K pneumoniae, sequence data and phenotypic analysis linked a nonsense amino acid substitution coded in the mgrB (K3*) gene and missense amino acid substitutions coded in the marA, acrA, arnB, eptA, pmrB, pmrJ, and phoQ genes to colistin resistance. Meanwhile, tigecycline resistance was linked to nonsense and missense amino acid substitutions coded within the ramR sequence. Additionally, this study identified several integron structures, including Int191 (5′CS-dfrA14-3′CS), which was the most prevalent integron (Int) among E. coli and K. pneumoniae isolates in this study, followed by Int0 (5′CS-3′CS) and Int18 (5′CS-dfrA1-3′CS). Conclusions: These results contribute to the genomic epidemiology of MDR E. coli and K. pneumoniae in our setting and to the worldwide epidemiology in the One Health approach.