Caerin 1.1/1.9 Inhibits Growth and Biofilm Formation of Carbapenem-Resistant Klebsiella pneumoniae and Induces Coordinated Transcriptomic Stress Responses.

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major cause of healthcare-associated infections and a World Health Organization critical-priority pathogen due to extensive antimicrobial resistance and limited treatment options. Host-defense peptides represent promising alternatives to conventional antibiotics because of their broad-spectrum activity and low propensity for resistance development. Here, we evaluated the antibacterial activity of a fixed 1:1 combination of the frog-derived peptides caerin 1.1 and caerin 1.9 (F1/F3) against a reference K. pneumoniae strain and four clinical CRKP isolates. Individually, F1 and F3 exhibited MICs of 12 µM against the reference strain, whereas the F1/F3 combination reduced the MIC to 5 µM and showed an additive antibacterial interaction. F1/F3 retained activity against clinical CRKP isolates with strain-dependent susceptibility and inhibited biofilm formation and reduced pre-established biofilm biomass in a concentration-dependent manner. Scanning electron microscopy revealed pronounced morphological and surface alterations following peptide treatment. Transcriptomic analysis demonstrated broad bacterial responses to F1/F3 exposure, including downregulation of genes associated with ribosomal function, protein synthesis, metabolism, and oxidative phosphorylation, together with activation of stress-response pathways and differential expression of predicted small regulatory RNAs. SNP analysis revealed no evidence of increased mutation burden following peptide exposure. These findings demonstrate the antibacterial potential of F1/F3 against CRKP and provide insights into bacterial responses associated with caerin peptide treatment.