Caerin 1.1/1.9 disrupts growth and biofilms of carbapenem-resistant Klebsiella pneumoniae with a transcriptomic signature of translational and metabolic stress

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical multidrug-resistant pathogen associated with limited therapeutic options and high mortality. The development of alternative antimicrobial strategies with novel mechanisms of action is urgently needed. In this study, we evaluated the antibacterial efficacy and mechanistic impact of a fixed 1:1 combination of caerin 1.1 and caerin 1.9 (designated F1/F3), naturally derived antimicrobial peptides, against a reference K. pneumoniae strain and multiple clinical CRKP isolates. F1 and F3 individually exhibited minimum inhibitory concentrations (MICs) of 12 µM against the reference strain, whereas the combined formulation reduced the MIC to 5 µM, demonstrating enhanced antibacterial potency. F1/F3 retained inhibitory activity across diverse clinical CRKP isolates. In addition to suppressing planktonic growth, F1/F3 significantly inhibited biofilm formation and reduced established biofilm biomass in a concentration-dependent manner. Scanning electron microscopy revealed pronounced morphological abnormalities, including cell surface disruption and structural collapse, consistent with membrane damage. Transcriptomic analysis suggested coordinated repression of ribosomal and translational machinery, suppression of central carbon metabolism and oxidative phosphorylation pathways, and activation of stress-response and adaptive regulatory networks. Protein–protein interaction analysis supported disruption of translational and metabolic hubs. No treatment-associated increase in mutation burden was detected, suggesting that the observed response is unlikely to be driven by detectable mutation-based adaptation under the tested conditions. Collectively, these findings suggest that the antibacterial activity of F1/F3 may involve membrane perturbation–induced metabolic disruption and global translational shutdown. The combined phenotypic and transcriptomic evidence supports the further investigation of F1/F3 as a potential candidate against multidrug-resistant CRKP infections.