cirA promoter disruption and SHV-12 production contribute to cefiderocol resistance in carbapenem-resistant Klebsiella pneumoniae.

BACKGROUND

Cefiderocol (CFDC) is a novel and potent antimicrobial agent; however, the emergence of CFDC resistance is increasingly concerning. This study investigated the mechanisms underlying CFDC resistance in ST11 carbapenem-resistant Klebsiella pneumoniae (CRKP) and explored potential therapeutic strategies against CFDC-resistant strains.

METHODS

Two isogenic ST11 CRKP isolates, KP399 (CFDC-susceptible) and KP400 (CFDC-resistant), were obtained from a single patient. Whole-genome sequencing, genetic knockout, plasmid curing, complementation assays, real-time quantitative PCR, and antimicrobial susceptibility testing (AST) were performed to elucidate the resistance mechanisms. AST of CFDC in combination with β-lactamase inhibitors (BLIs), along with computational structural modeling, was conducted to evaluate BLI activity against SHV-12.

RESULTS

An ISKpn74 insertion sequence in the cirA promoter significantly reduced cirA transcription and was associated with decreased CFDC susceptibility. SHV-12 was identified as the predominant β-lactamase conferring CFDC resistance. High-level resistance required the combined effects of reduced cirA expression (<0.5 relative units) and SHV-12 production. In silico analyses predicted that relebactam exhibits the strongest binding affinity to SHV-12, attributable to its bulky C2-linked piperidine ring that enables additional interactions with the Asp104 residue, together with its slow deacylation kinetics. Consistently, AST showed that combining CFDC with relebactam markedly enhanced antimicrobial activity against SHV-12-producing CRKP compared with other BLIs.

CONCLUSIONS

This study identifies a novel CFDC resistance mechanism and underscores the importance of assessing regulatory regions when evaluating resistance determinants. It also supports the potential use of relebactam as an effective adjunct to CFDC against SHV-12-producing, CFDC-resistant CRKP.