Genomic characterization of gram-negative bacteria isolated from conflict-trauma patients in a southern Lebanese hospital

INTRODUCTION Conflict-related injuries create a unique environment for the emergence of antimicrobial-resistant pathogens.METHODS To clarify the burden and dynamics of resistance in this high-risk population, we investigated the genomic and clinical profiles of 63 Gram-negative bacterial isolates recovered exclusively from conflict-trauma cases in Southern Lebanon during the 2024 war.RESULTS Whole-genome sequencing revealed Acinetobacter baumannii (31.7%) and Escherichia coli (20.6%) as the predominant species, marking a significant epidemiological shift toward A. baumannii compared to pre-conflict baselines. Acquired antimicrobial resistance genes were detected in 66.7% of isolates, with a high prevalence of determinants and mutations targeting aminoglycosides (87%), fluoroquinolones (74.6%), and carbapenems (54%). Carbapenem resistance was primarily driven by acquired blaOXA carbapenemases and blaNDM variants; notably, we report the first detection of blaNDM-40 in Lebanon, alongside blaNDM-1 and blaNDM-5. Clinically, the admitted cases (n = 23) experienced intensive broad-spectrum antibiotic exposure, high rates of major surgery (74%), and documented hospital-acquired infections (48%), culminating in a 17.4% mortality rate among admitted cases. Minimum spanning tree analysis highlighted clonal, healthcare-associated transmission for A. baumannii and Klebsiella pneumoniae, contrasted by polyclonal distributions for E. coli and Pseudomonas aeruginosa.CONCLUSION Extensive broad-spectrum antibiotic exposure and acute trauma care within compromised healthcare infrastructures accelerate the selection of multidrug-resistant (MDR) genotypes. Mitigating this dissemination in conflict settings requires integrating genomic surveillance with targeted antimicrobial stewardship and infection control.