Co-occurrence of bla KPC and bla OXA−48 genes in Klebsiella pneumoniae isolates from a tertiary-care hospital in Ecuador and evidence of emerging genotypic–phenotypic AMR inconsistencies

Abstract Background Antimicrobial resistance (AMR) is a growing threat to public health, especially in low- and middle-income countries. This study aimed to identify multidrug-resistant (MDR) pathogens in clinical samples from a tertiary hospital in Ecuador, evaluate their phenotypic antibiotic susceptibility, and compare these findings with genotypic resistance patterns. Methods Clinical samples were collected from an Ecuadorian reference hospital from September 2022 to September 2023. Bacterial identification and susceptibility testing were performed using the VITEK-2 system. After genomic DNA extraction, key resistance genes (bla KPC, bla NDM, bla VIM, bla OXA−48, bla CTX−M and bla IMP−1) were identified via multiplex PCR with TaqMan probes. Phenotypic and genotypic data were integrated using bioinformatics tools. Results The 216 bacterial isolates analyzed exhibited resistance phenotypes, primarily to carbapenems and third-generation cephalosporins. Klebsiella pneumoniae was the most prevalent resistant species (59.7%), followed by Pseudomonas aeruginosa (11.6%) and Serratia marcescens (8.3%). However, 20.8% of the isolates phenotypically resistant to carbapenems did not carry any of the targeted carbapenemase genes. The bla KPC gene was most common (70.8%), followed by bla NDM (9.7%) and bla VIM (2.8%). Ten isolates harbored gene combinations, including, to our knowledge, the first reported co-occurrence of bla KPC and bla OXA−48 in K. pneumoniae in Ecuador.Neither bla IMP−1 nor bla CTX−M was detected in any of the evaluated isolates. Conclusions There is strong concordance between carbapenemase genes and the MDR phenotype, some of which are newly reported in Ecuador. However, the absence of gene detection in some resistant isolates suggests the presence of alternative resistance mechanisms. Integrating phenotypic and molecular methods that target locally prevalent resistance genes improves the accuracy of AMR detection and supports better diagnosis and infection control in hospital settings.