Genomic Surveillance-Guided Phage Repository Construction and Rational Cocktail Design for Carbapenem-Resistant Klebsiella pneumoniae

OBJECTIVES: Given the treatment delays inherent in reactive phage matching, we aimed to develop a preparedness-oriented strategy linking genomic surveillance of carbapenem-resistant Klebsiella pneumoniae (CRKP)to targeted phage-resource development and rational cocktail design. METHODS: We analysed >64,000K. pneumoniae genomes to characterize the geographical and temporal representation of KL types within the genomic dataset. Phages were isolated and prioritized according to host-range profiles, genomic nonredundancy, receptor-binding protein diversity and morphology. Quantitative inhibition profiling and principal component analysis guided the selection of candidate combinations targeting KL64 isolates, followed by in vitro, in vivo, and resistance analyses. RESULTS: A limited number of KL types were frequently represented among the analysed CRKP genomes and showed regional variation. From a nonredundant repository of 33 phages, 10 were selected to target 10 frequently represented KL types. In a KL64 clinical isolate panel, selected combinations broadened and prolonged bacterial suppression., The phage cocktail significantly prolonged survival in mice under lethal CRKP challenge and phage-resistant derivatives showed restored susceptibility to multiple antibiotics. CONCLUSIONS: This study presents a framework for using genomic data to prioritize phage-resource development and guide cocktail design for KL-defined CRKP groups.