Prevalence of Carbapenem-Resistant Gram-Negative Bacteria in Shouf-Aley Area

Abstract

Background: Antimicrobial resistance (AMR) poses a significant global health threat, rendering standard treatments ineffective and leading to persistent infections, increased transmission, and elevated mortality rates. In 2019, AMR was directly responsible for at least 1.27 million deaths worldwide and associated with nearly 5 million deaths, underscoring its severe impact on public health. Carbapenems are a class of β-lactam antibiotics considered last-resort treatments for severe bacterial infections. They are particularly effective against multidrug-resistant Gram-negative bacteria due to their broad-spectrum activity and resistance to most β-lactamases. However, the emergence of carbapenem-resistant Gram-negative bacteria (CR-GNB) has compromised the efficacy of these critical antibiotics. CR-GNB, including species such as Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa, have developed mechanisms to evade the bactericidal action of carbapenems. These mechanisms include the production of carbapenemase enzymes that hydrolyze the antibiotic, alterations in membrane permeability reducing drug uptake, and efflux pumps expelling the antibiotic from bacterial cells. Infections caused by CR-GNB are associated with limited treatment options, leading to higher morbidity and mortality rates. In this study, we utilize next generation sequencing (NGS)

Objectives: This study aimed to determine the prevalence, antimicrobial susceptibility, and molecular resistance mechanisms of CR-GNB in Lebanese hospitals using phenotypic testing and whole-genome sequencing (WGS) while highlighting the discrepancy between hospital-based identification and sequencing results.

Methods: A total of 521 Gram-negative clinical isolates were collected from three hospitals in Lebanon between August 2024 and March 2025. Antimicrobial susceptibility to meropenem was assessed using disc diffusion. Forty-one meropenem-resistant isolates were further analyzed using WGS via Illumina and Oxford Nanopore platforms. Resistance genes, sequence types (STs), and plasmid content were identified using the Comprehensive Antibiotic Resistance Database (CARD) and MLST tools.

Results: Of the 521 isolates, 7.9% exhibited meropenem resistance, with the highest rate observed in Intensive Care Unit (ICU) patients and at Ain Wzain Medical Village (21.89%). Resistant isolates included Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, and Enterobacter hormaechei. WGS revealed the presence of key beta-lactamase genes (blaOXA-23, blaOXA-1, blaNDM-1, blaNDM-5, blaVIM-2) and efflux pump-related genes (adeK, adeJ, Mex, MarA, TolC). Many isolates harbored mobile genetic elements such as IncFⅡ and IncX3 plasmids, enhancing horizontal gene transfer potential.

Conclusion: This study highlights a concerning prevalence of CR-GNB in Lebanese healthcare settings, with high genomic diversity and multiple resistance mechanisms. The findings emphasize the need for nationwide genomic surveillance, improved diagnostic accuracy, and stricter antimicrobial stewardship. Integration of WGS into clinical microbiology workflows could significantly enhance AMR monitoring and outbreak control in Lebanon.