In vitro selection of cefiderocol-resistant mutants in Acinetobacter baumannii harboring the most common carbapenemase genes

Carbapenem-resistant Acinetobacter baumannii represents a critical global health threat due to its high mortality rates of related infections, limited treatment options, and resistance to any last-resort antibiotics. Cefiderocol (FDC), a novel siderophore-conjugated cephalosporin, has emerged as a promising therapeutic agent. However, resistance to this antibiotic has already been reported. This study was aimed to investigate whether the expression of common carbapenemases influences FDC resistance in A. baumannii and to identify the genetic mechanisms underlying resistance development. Using isogenic recombinant A. baumannii CIP 7010 strains carrying the carbapenemase genes blaNDM-1, blaOXA-23, blaOXA-40, or blaOXA-58, mutants were selected under increasing FDC pressure. Whole-genome sequencing of resistant isolates identified recurrent mutations in the global regulators BfmS and OxyR, rather than in genes directly related to iron uptake or PBPs. Complementation assays with wildtype bfmRS or oxyR, resulted in a reversion to the parental strain FDC MICs. RT-qPCR revealed that those global regulators were responsible for decreasing the expression piuA and pirA genes, hence being associated with resistance to FDC. This study provides novel insight into the adaptive pathways of A. baumannii under FDC pressure and highlights previously unrecognized genetic targets that could be involved in resistance. Understanding these alternative resistance mechanisms is crucial for guiding the development of future antimicrobial strategies against this highly adaptable pathogen.