Phenotypic heterogeneity and genetic mechanisms of phage resistance in hypervirulent carbapenem-resistant Klebsiella pneumoniae

Abstract

ABSTRACT Phage resistance represents a major obstacle to the clinical application of phage therapy for multidrug-resistant bacterial pathogens. A comprehensive understanding of the phenotypic heterogeneity and molecular mechanisms underlying phage resistance is critical for deciphering bacterium-phage interactions and optimizing therapeutic strategies. In this study, we identified four distinct resistance phenotypes in K2-serotype hypervirulent carbapenem-resistant Klebsiella pneumoniae (CR-hvKP) under the selective pressure of phage Kpph1. These resistant strains exhibited either complete or partial resistance, variable fitness costs, and diverse genetic mutations, suggesting multifaceted resistance strategies, including receptor masking, growth inhibition, and community-level resistance. Among these, wcaJ mutations were identified as the predominant resistance mechanism, arising from base insertions and integrations of mobile genetic elements, which serve as an efficient pre-adaptive strategy enabling CR-hvKP to evade phage infection. To circumvent this resistance, we isolated a secondary phage, K2V3, which specifically targets wcaJ-mutant strains. The rationally designed phage cocktail comprising Kpph1 and K2V3 effectively suppressed all resistant variants and prevented the emergence of further resistance. Collectively, these findings deepen the understanding of phage-bacteria interaction dynamics and provide a crucial theoretical foundation for optimizing clinical phage therapy against multidrug-resistant pathogens.