Molecular epidemiology and resistance mechanisms of carbapenem-resistant Gram-negative bacilli in a referral hospital in Lima, Peru
Abstract
Abstract Background Carbapenem-resistant Gram-negative bacilli (CR-GNB) represent a significant public health threat, as they are associated with high mortality in healthcare settings. Carbapenemase production is the predominant resistance mechanism, and horizontal gene transfer drives the rapid dissemination of antimicrobial resistance (AMR). Objectives This study aimed to characterize the phenotypic and genotypic AMR profiles of CR-GNB isolated from patients at Arzobispo Loayza National Hospital (Lima, Peru) between October 2021 and January 2022. Methods We conducted a cross-sectional study and collected clinical and epidemiological data from patients with bacterial infections. MALDI-TOF identified pathogens, and antimicrobial susceptibility was interpreted according to CLSI guidelines. A subset of isolates underwent whole-genome sequencing (Illumina) to determine genomic resistance markers. Results A total of 159 patients were included (median age = 54 years; 66.7% male); 72.3% had confirmed clinical infections, and 66% were admitted to the ICU. The most frequent infection types were pneumonia, urinary tract infection and bacteraemia. Overall, 97.5% of isolates were classified as XDR. Carbapenem resistance approached 100% (imipenem 99.4%, meropenem 98.7%). Whole-genome data revealed clonal diversity among Klebsiella pneumoniae (ST13/ST15) carrying blaNDM-1; Acinetobacter baumannii uniformly harboured blaOXA-23; and Pseudomonas aeruginosa included high-risk clones ST357 (blaIMP-93) and ST111 (blaIMP-18, blaVIM-2). Conclusions These findings demonstrate a critical burden of XDR-GNB and the presence of multiple carbapenemases (NDM, IMP, KPC and VIM) associated with clinically relevant high-risk lineages. Strengthening molecular surveillance, optimizing antimicrobial stewardship and reinforcing infection-control measures are urgently needed to contain CR-GNB in critical-care settings in Peru.