Emergence of a dual-threat ST1322 clinical Isolate: Hypervirulent and carbapenem-resistant Klebsiella pneumoniae revealed by genomic and virulence analysis.

The emergence of carbapenemase-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) poses a significant threat to public health. However, the pathogenesis of CR-hvKP has not been fully elucidated, calling for more genomic data to clarify. In our previous work, we identified a K. pneumoniae strain of novel sequence type 1322 (ST1322) isolated from an ICU patient with persistent infection and poor prognosis. Antibiotic susceptibility testing confirmed that ST1322 KPX was carbapenemase-resistant. The serum killing assay and Galleria mellonella lethality assay demonstrated virulence comparable to the hypervirulent reference strain NTUH-K2044. However, KPX's string test was negative. To date, no genome sequences for K. pneumoniae isolates of capsular serotype K372 and ST1322 are publicly available. Whole-genome sequencing (WGS) analysis was performed on ST1322 KPX. Phylogenetic analyses revealed a close genetic relationship between ST1322 KPX and other sequenced CR-hvKPs. ST1322 KPX has multiple resistance genes, including four β-lactamase genes blaLAP-2, blaNDM-4, blaCTX-M-14 and blaOXA-9. Additionally, KPX carries numerous virulence genes, among which the genes encoding the T6SS effectors were primarily responsible for the its hypervirulence. Given the dual threat of carbapenemase-resistant and hypervirulence in ST1322 KPX, and the lack of genomic resources, this study elucidates its pathogenic mechanisms by integrating clinical data, virulence phenotyping, and genomic analysis. We provide the first complete genome sequence of ST1322 CR-hvKP, enabling future comparative genomic studies. These findings highlight the clinical vigilance required against persistent CRKP strains lacking hypermucoviscosity.