Comparative genomic analysis of the core virulence factor in Klebsiella pneumoniae ST11, based on a global genomic database

database[Title] 2025-04-20

Microb Pathog. 2025 Apr 11;204:107575. doi: 10.1016/j.micpath.2025.107575. Online ahead of print.

ABSTRACT

BACKGROUND: The global dissemination of carbapenem-resistant Klebsiella pneumoniae (CRKP) ST11 poses a major public health challenge due to its high transmissibility, multidrug resistance, and virulence. However, detailed insights into the core virulence factors (VFs) contributing to its pathogenicity and adaptability remain limited.

OBJECTIVE: To characterize the virulence profiles of global K. pneumoniae ST11 strains and explore associations between major VFs, serotypes and carbapenemase encoding genes.

MATERIALS AND METHODS: Sixty-two K. pneumoniae strains were collected from 15 hospitals in Jiangsu, and their genomes were sequenced. Additional K. pneumoniae genome sequences were retrieved from GenBank. Multi-locus sequence typing (MLST) was used to identify sequence types (STs). Comparative analyses between ST11 and non-ST11 strains were performed to identify key VFs. Phylogenetic trees were constructed to explore genetic relationships, and the distribution of serotypes and carbapenemase genes was analyzed.

RESULTS: Among the 62 clinical isolates, ST11 was the most prevalent (n = 46). A broader review of 11,429 global strains confirmed ST11 (n = 1571) as a dominant clone, followed by ST258 (n = 1240), ST15 (n = 545), ST512 (n = 451). Virulence analysis revealed that the yersiniabactin (Ybt) gene cluster-including ybtT, ybtX, fyuA, ybtP, ybtU, ybtS, ybtA, ybtQ, ybtE, irp1 and irp2 -was highly enriched in ST11 strains, particularly those belonging to serotypes K64 and K47. Given that Ybt is a siderophore system linked to iron acquisition, immune evasion, and enhanced colonization, its presence in ST11 may contribute to both its virulence and environmental adaptability. Phylogenetic analysis indicated that global ST11 strains exhibit diverse genetic backgrounds with regional epidemic trends. The predominant carbapenemase genes were bla_KPC-2 (30.8 %), bla_NDM-1 (5.3 %), and bla_OXA-48 (2.9 %), while the most common serotypes were K64 (38.0 %), K47 (19.5 %), and K24 (1.8 %).

CONCLUSION: Our findings highlight ST11-specific enrichment of the Ybt cluster and fyuA, which may facilitate colonization and immune evasion, while dominant serotypes K64 and K47 harbor more Ybt- and carbapenemase genes, notably blaKPC-2. These results reveal region-specific dissemination patterns and underscore the need for strengthened surveillance and targeted control measures against CRKP-ST11.