Decoding hypervirulence in carbapenem-resistant Klebsiella pneumoniae : genomic and phenotypic profiling reveals capsular polysaccharide as a key driver of pathogenicity

Background The global dissemination of hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) poses escalating threats to public health. Substantial controversy persists regarding its true virulence potential, highlighting the need for reliable biomarkers to enable early diagnosis and targeted therapy. Methods Using a mouse subcutaneous challenge model, we characterized 59 carbapenem-resistant K. pneumoniae (CRKP) isolates, identifying 37.29% (22/59) as convergent hv-CRKP. Phenotypic and genotypic characterization, integrated with genome-wide association study (GWAS) and transcriptomic analysis, was performed, and reliable biomarkers for accurate hv-CRKP detection were identified. Results Patients infected with hv-CRKP exhibited significantly higher sepsis incidence (P = 0.028) and increased mortality. Capsule production and hypermucoviscosity robustly discriminated hv-CRKP from CRKP. GWAS identified a significant association between an SNP in the rbtT locus and the hypervirulent phenotype, whereas virulence plasmid-associated genes showed no significant association. These findings suggest chromosomally encoded factors—independent of plasmid-borne elements—contribute critically to hypervirulence. Transcriptomics revealed rcsA-mediated capsule upregulation enhances macrophage phagocytosis resistance and bacterial survival, revealing a pivotal pathogenic mechanism. Both multivariable logistic regression and LASSO regression confirmed capsule production and rcsA expression as independent and robust diagnostic biomarkers to accurately assess virulence potential in carbapenem-resistant strains. Conclusions We conclude that clinical application of the term “hv-CRKP” requires prudent validation and emphasize the urgency of developing biomarkers to precisely identify truly hypervirulent CRKP strains.