Comparative Proteomic Profiling of Clinical Klebsiella pneumoniae Strains and the Corresponding Outer Membrane Vesicles

ABSTRACT Klebsiella pneumoniae (K. pneumoniae) has become a global threat due to the convergence of carbapenem resistance and hypervirulence. Outer membrane vesicles (OMVs) play important roles in bacterial pathogenicity, yet their functional coordination with strains remains unclear. Here, we performed comparative proteomic profiling of six representative groups of K. pneumoniae , covering four major phenotypes, including carbapenem‐resistant hypervirulent (CR‐hvKP), represented by ST11‐K47 and ST11‐K64, carbapenem‐susceptible hypervirulent (CS‐hvKP), represented by ST23‐K1 and ST65‐K2, carbapenem‐resistant classical (CR‐cKP), and carbapenem‐susceptible classical (CS‐cKP). Integration of weighted co‐expression network analysis, pathway enrichment, and protein‐protein interaction analysis revealed distinct proteomic organisation and functional profiles between strains and OMVs. CR‐hvKP strains exhibited high cellular expression of resistance and DNA repair proteins. CS‐hvKP (ST23‐K1) showed elevated capsule biosynthesis proteins in strains and biofilm‐associated proteins in OMVs, whereas CS‐hvKP (ST65‐K2) strains packaged two‐component system proteins into OMVs. Module preservation and correlation analyses demonstrated limited preservation and weak correlation between cellular and OMV proteomes, suggesting that OMV protein organisation is largely distinct from the cellular proteome. Our findings highlight the specialised roles of OMVs, providing new insights into the pathogenic mechanisms of K. pneumoniae and potential therapeutic targets.