Vitamin B12 promotes cefiderocol resistance and small-colony variants in carbapenem-resistant Acinetobacter baumannii

Abstract

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a global health threat with few effective treatment options remaining. Cefiderocol, a last-resort siderophore-cephalosporin antibiotic, exploits bacterial iron transport systems via TonB-dependent receptors (TBDRs) to gain cellular entry. However, treatment failures and the emergence of resistance highlight concerns with in vivo efficacy. In this study, we report an unanticipated cefiderocol resistance mechanism where vitamin B12, a micronutrient supplement, modulates cefiderocol susceptibility. Our work revealed that vitamin B12 (methylcobalamin) affects and interacts with TBDRs and other metabolic and adaptation processes that contribute to increased cefiderocol MIC levels and the emergence of persistence phenotypes. We demonstrate that vitamin B12 supplementation elicits strain-specific transcriptomic responses in the AB5075 and AMA17 CRAB strains, characterized by the downregulation of genes encoding siderophore-mediated iron acquisition functions, stress responses, metabolic reprogramming, and biofilmbiofilmbiogenesis. Structural modeling and molecular docking reveal overlapping binding sites for vitamin B12 and cefiderocol within TBDRs such as CirA and PirA, suggesting competitive inhibition. Additionally, vitamin B12 exposure increases cefiderocol MICs across a panel of A. baumannii clinical and reference strains, enhances survival in time-kill assays, and promotes the emergence of small-colony variants displaying persistent phenotypes. Notably, this effect is stable, dose dependent, and further enhanced in the presence of host-derived fluids. These findings describe a previously unrecognized host–pathogen–drug interaction with potential clinical implications, suggesting that vitamin B12 exposure could contribute to cefiderocol treatment failure. Our results underscore the urgent need to consider the potential contribution of vitamin supplements to antimicrobial therapy and management strategies for CRAB infections.