Analysis of AcrB in Klebsiella pneumoniae reveals natural variants promoting enhanced multidrug resistance

Infections caused by Klebsiella pneumoniae are often difficult to manage due to the high frequency of multidrug resistance, often conferred by efflux pumps. In this study, we analyzed sequence variations of the major RND family multidrug efflux pump AcrB from 387 assembled K. pneumoniae genomes. We confirm that AcrB is a highly-conserved efflux pump in K. pneumoniae, and identified several variants that were prevalent in clinical isolates. Molecular dynamics analyses on two of these variants (L118M and S966A) suggested conformational changes that may correlate with increased drug efflux capabilities. The L118M change resulted in enhanced protein rigidity while the flexibility of drug binding pockets was stable or increased, and the interactions between the proximal pockets and water molecules were stronger. For S966A, the significantly enlarged proximal pocket suggested higher drug accommodation ability. Consistent with these predictions, the L118M and S966A variants conferred a slightly increased ability to grow in the presence of tetracycline and to survive cefoxitin exposure when overexpressed. In summary, our results suggest that the emergence of enhanced-function AcrB variants may be a potential risk for increased antibiotic resistance in clinical K. pneumoniae isolates. (c) 2021 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Automated summary

Infections caused by Klebsiella pneumoniae are difficult to manage due to high rates of multidrug resistance, often caused by efflux pumps. This study analyzed the sequence variations of the AcrB efflux pump from K. pneumoniae genomes and found prevalent variants in clinical isolates. Molecular dynamics analysis revealed conformational changes in two variants that may enhance drug efflux capabilities. Experimental results showed that these variants had slightly increased growth and survival abilities in the presence of specific antibiotics. The emergence of these enhanced-function AcrB variants may pose a potential risk for increased antibiotic resistance in clinical K. pneumoniae isolates.