Spontaneous Emergence of Cefiderocol Resistance in KPC-163: Genomic and Transcriptomic Insights.

Carbapenem-resistant (CRKP) is an urgent public health threat due to its rapid dissemination and resistance to last-line antibiotics. Cefiderocol (FDC), a novel siderophore cephalosporin, targets resistant Gram-negative pathogens by exploiting bacterial iron uptake mechanisms. However, resistance to FDC is emerging among carbapenemase (KPC)-producing strains. This study characterizes a spontaneous FDC-resistant subpopulation (IHC216) derived from a KPC-producing strain (KPNMA216) using comprehensive genomic, transcriptional, and phenotypic analyses. : Given the whole-genome sequencing results, where mutations were identified in genes involved in transcriptional regulation and membrane permeability () among others, in the present work we further explore their potential implications and conduct a more detailed analysis of the IHC216 genome. A qRT-PCR analysis highlighted significant downregulation of classical siderophore-mediated iron acquisition systems (, , ) and upregulation of alternative iron uptake pathways (, ), reflecting a switch in iron acquisition strategies. : A notable downregulation of correlated with restored susceptibility to carbapenems, indicating collateral susceptibility. Altered expressions of and implicated adaptive changes in cell wall synthesis, potentially affecting FDC resistance mechanisms. Furthermore, enhanced oxidative stress responses via upregulated expression and increased capsule production were observed. : These findings underscore the complex interplay of genetic and transcriptional adaptations underlying FDC resistance, highlighting potential therapeutic vulnerabilities.