Characterization of KPC-160, a novel Ω-loop-deleted KPC variant on a dual-copy plasmid that confers cefiderocol...

The evolution of KPC-type carbapenemase variants is a major driver of resistance in Klebsiella pneumoniae. Cefiderocol (FDC), a next-generation siderophore cephalosporin, demonstrates potent activity against many KPC producers; however, emerging variants are compromising its efficacy. Here, we report the identification and functional characterization of a novel KPC variant, KPC-160, which confers resistance to FDC. This variant, harboring a unique two-amino acid deletion (ΔGlu167-Leu168) within the Ω-loop, was discovered in a clinical ST15-KL19 Klebsiella pneumoniae isolate. Antimicrobial susceptibility testing, whole-genome sequencing, and conjugation assays defined the resistance profile and genetic context, while carbapenemase activity assays, enzyme kinetics, and molecular modeling elucidated the functional mechanism. Strain K1661 exhibited FDC resistance (MIC = 8 µg/mL) alongside multidrug resistance. Genomic analysis identified the novel bla_KPC-160 variant carried on an IncFIB(K) plasmid in dual IS26-flanked copies, displaying efficient transfer frequencies (3.73 × 10⁻³-4.55 × 10⁻⁵). Compared with bla_KPC-2, bla_KPC-160 featured a ΔGlu167-Leu168 deletion, which markedly increased FDC MICs (16-fold higher than KPC-2) and increased its affinity for FDC. Molecular docking and dynamics simulations indicated that this deletion stabilized FDC binding within the active site, thereby facilitating resistance. Conventional carbapenemase detection assays (mCIM, GeneXpert Carba-R, and NG-Test Carba 5) successfully identified KPC-160. These findings describe bla_KPC-160, a deletion variant conferring clinically relevant FDC resistance via enhanced interaction and compromised inhibition. Its localization on a highly transmissible plasmid with a dual-copy architecture underscores its potential for rapid dissemination. Continuous genomic surveillance of emerging KPC variants is critical to preserving the clinical utility of FDC.