Genomic analysis reveals multi-level resistance network linking oxidative stress pathway mutations to cefiderocol resistance and clonal evolution in Klebsiella pneumoniae from the United Arab Emirates.

INTRODUCTION: Resistance to cefiderocol (CFDC), a novel siderophore-cephalosporin, remains poorly understood. We aimed to explore mutations in oxidative stress (OS) pathways in Klebsiella pneumoniae (KPN) and investigate their potential association with reduced susceptibility to CFDC.

METHODS: A total of 282 KPN strains from the United Arab Emirates were tested for susceptibility to various antibiotics, including CFDC. Afterward, 96 representative strains were subjected to whole-genome sequencing and bioinformatic analyses to examine 51 genes across six functional categories (OxyR, SoxRS, iron regulation, efflux pumps, DNA repair, and penicillin-binding proteins). Genotypic and phenotypic results were correlated to explore significant associations with CFDC susceptibility.

RESULTS: CFDC demonstrated high in vitro activity (96.9%), with eight isolates showing non-susceptibility. All the CFDC-resistant isolates carried bla NDM carbapenemases and belonged to high-risk clones (primarily ST14 and ST147), with enrichment of OS pathway mutations. Mutations in iron uptake genes, especially cirA frameshift insertion, were enriched in resistant isolates. Mutations in OS detoxification (mainly the OxyR regulon), efflux pump, and DNA repair pathways further contributed to altered susceptibility profiles. The negative correlations between the MICs of CFDC and mutations in detoxification and repair genes suggested that impaired stress responses increase CFDC activity. Network analysis revealed that resistance emerged through coordinated multi-pathway interactions, with iron regulation genes serving as the central hub. High-risk clones exhibited dense co-mutation networks spanning genes involved in iron uptake, OS response, and efflux systems, indicating a multifactorial adaptive strategy.

CONCLUSIONS: Coordinated interactions across iron regulation, OS, and efflux pathways are associated with reduced susceptibility to CFDC. The negative correlation between OxyR/DNA repair mutations and CFDC MICs suggests that intact OS defenses paradoxically reduce CFDC efficacy. OS pathway integrity may modulate CFDC susceptibility, informing future strategies to preserve CFDC efficacy. The identification of specific mutations linked to CFDC resistance provides potential biomarkers for surveillance and therapeutic targeting, underscoring the interplay between OS responses and antimicrobial resistance.