Comparative Genomic Analysis of Hypervirulent and Classical Klebsiella pneumoniae Isolates from Respiratory Samples: A Computational Assessment of Virulence Genes

Hypervirulent Klebsiella pneumoniae (hvKp) has emerged as a major cause of severe respiratory infections worldwide; however, its genomic distinction from classical K. pneumoniae (cKp), particularly within respiratory isolates, remains incompletely understood. In this study, we conducted a large-scale comparative genomic analysis of 1,293 respiratory Kp genomes retrieved from the BV-BRC database, of which 538 were classified as hvKp and 755 as cKp based on established marker genes. Comprehensive profiling of 127 virulence-associated genes revealed that hvKp isolates exhibited a more specialized virulence architecture, with significantly higher prevalence of key iron acquisition systems and capsule-associated loci compared with cKp isolates (p < 0.001). In contrast, cKp isolates demonstrated greater virulence gene diversity, as reflected by higher Shannon diversity indices, despite lower prevalence of individual virulence markers. Notably, classical high-virulence risk lineages, particularly ST11-K64, displayed hybrid virulence profiles with partial acquisition of hvKp-associated determinants, suggesting an evolutionary continuum between classical and hypervirulent pathotypes. Presence–absence–based phylogenetic analysis revealed clustering driven by virulence gene repertoires rather than strict core-genome lineage, indicating functional convergence among genetically distinct isolates. Importantly, virulence gene prevalence did not directly correlate with genetic diversity, underscoring the limitations of single-marker approaches for hypervirulence prediction. Collectively, these findings provide quantitative insights into the pathotype-dependent organization and evolution of virulence determinants in respiratory Kp and highlight the value of integrated genomic frameworks for surveillance and virulence risk assessment of emerging hypervirulent lineages.