In vivo emergence of cross-resistance to ceftazidime/avibactam and cefiderocol through selection of KPC variants in Klebsiella pneumoniae clinical isolates

Objectives To investigate the clinical and molecular drivers of in-vivo cross-resistance to ceftazidime/avibactam (CZA) and cefiderocol (FDC) in infections caused by KPC-producing Klebsiella pneumoniae (KPC-Kp). Material and Methods We conducted a retrospective case series of patients initially infected or colonized by CZA- and FDC-susceptible KPC-Kp who subsequently developed infections due to strains co-resistant to both agents. Whole-genome sequencing (WGS) and cloning of bla KPC alleles into E. coli were performed to elucidate resistance mechanisms. Results Three patients developed bloodstream infections with KPC-Kp resistant to both CZA and FDC following CZA exposure. WGS identified bla KPC variants featuring substitutions within or adjacent to the Ω-loop: KPC-31 (D179Y), KPC-49 (R164S), and KPC-167 (D179Y with a DDKYSE 270-loop duplication). All resistant isolates belonged to ST512 and exhibited porin alterations (OmpK35 truncation and OmpK36 GD insertion). Cloning experiments demonstrated that these KPC variants markedly increased CZA MICs and modestly elevated FDC MICs, confirming their functional contribution to the resistance phenotype. Conclusions These findings demonstrate the in-vivo emergence of cross-resistance to CZA and FDC driven by stepwise selection of KPC Ω-loop and 270-loop variants combined with permeability defects.