IS903B-mediated cirA inactivation confers cefiderocol resistance and adaptive fitness in carbapenem-resistant Klebsiella pneumoniae.

Cefiderocol (FDC) is a last-resort antimicrobial for the treatment of carbapenem-resistant Klebsiella pneumoniae (CRKP). Although cirA inactivation is a recognized mechanism of FDC resistance, whether different forms of cirA disruption influence bacterial adaptation and persistence remains unclear. By analyzing 1,965 publicly available long-read genomes and 480 clinical isolates, we found that cirA loss-of-function mutations were rare (1.1%) but accumulated over time among isolates from China, with four independently emerged cirA-inactivated ST11 isolates identified across distinct phylogenetic branches. Functional characterization of a representative ST11-KL64 clinical isolate showed that IS903B-mediated cirA inactivation conferred high-level FDC resistance (minimum inhibitory concentration, 128 μg/mL), which was reversed by cirA complementation. Functional assays further demonstrated that, unlike complete cirA deletion, IS903B-mediated cirA inactivation enhanced bacterial adaptation under iron-limited conditions, including competitive fitness, plasmid stability, and host-associated survival. Transcriptomic, enzymatic, and genetic analyses supported distinct Fe-S-associated metabolic remodelling in cirA::IS903B, while deletion of sufS attenuated these adaptive phenotypes. Construction of cirA::IS903B derivatives in multiple independent ST11 clinical isolates reproduced these adaptive phenotypes across diverse genetic backgrounds. Together, these findings demonstrate that IS903B-mediated cirA inactivation not only confers high-level FDC resistance but also promotes bacterial adaptation through mechanisms distinct from complete cirA deletion. The combination of resistance, enhanced adaptation, and increased plasmid stability suggests that specific resistance-associated cirA mutations may facilitate the persistence and dissemination of high-risk CRKP clones. Monitoring cirA integrity and IS insertion status may help identify FDC-resistant lineages with increased dissemination potential.