Mutation-driven alterations in the AcrB efflux pump modulate antibiotic resistance in Klebsiella pneumoniae

To investigate the global prevalence of the acrB efflux transporter among antibiotic resistance genes (ARGs) in Klebsiella pneumoniae and to determine how mutations within AcrB drug-binding pockets influence structural stability and antibiotic interactions.

A global genomic analysis of 42 ARGs reported in K. pneumoniae isolates worldwide was performed to identify the prominence of acrB. A total of 92 AcrB protein sequences were assessed for drug-binding pocket mutations relative to the wild-type strain NCTC9637. De novo protein structures were generated using AlphaFold2 and evaluated through molecular dynamics (MD) simulations. MD analyses were conducted with multiple antibiotics to assess the impact of pocket mutations on drug-binding affinities.

acrB emerged as the most widely distributed ARG, conferring resistance to at least 12 antibiotic classes. Three isolates, NCTC9617, NCTC9645, and NCTC13635, displayed multiple drug-binding pocket mutations when compared with the wild type. MD simulations revealed marked structural instability in NCTC9645, while NCTC13635 showed convergence towards a wild-type-like conformation. Docking analyses demonstrated that binding pocket mutations altered antibiotic-binding affinities, suggesting possible alterations in substrate recognition and transport.

AcrB is a key driver of multidrug resistance in K. pneumoniae, and mutations within its drug-binding pockets can significantly impact protein stability and antibiotic-binding behaviour. Monitoring these structural variations may help predict emerging resistance patterns and guide therapeutic decision-making.

Multidrug-resistant Klebsiella pneumoniae infections are a growing clinical threat with limited therapeutic options. By integrating global resistance gene surveillance with structural modelling of AcrB efflux pump variants, this study identifies drug-binding pocket mutations that modulate antibiotic affinity and efflux pump stability. These insights provide a molecular basis for predicting treatment failure, guiding precision antibiotic therapy, and advancing the development of efflux pump inhibitors as adjunctive treatments for drug-resistant Gram-negative infections.