Genomic Characterization of a Rare K30-ST198 Hypervirulent Klebsiella pneumoniae Clone with Distinctive Virulence Features

TL;DR

This paper characterizes a rare and highly virulent strain of Klebsiella pneumoniae, highlighting its unique genomic and phenotypic traits.

Contribution

The study provides the first detailed genomic and structural analysis of the K30-ST198 hypervirulent Klebsiella pneumoniae sublineage.

Findings

The K30-ST198 sublineage showed strong virulence and biofilm production in some isolates.

Genomic analysis revealed multiple virulence genes but limited antibiotic resistance.

AlphaFold and ColabFold predicted protein structures, offering insights into gene function.

Abstract

Hypervirulent Klebsiella pneumoniae (hvKp) has emerged as a significant public health concern, yet rare sublineages remain poorly characterized. Here, we described a K30-ST198 hvKp sublineage identified in four isolates from two patients, including three sequential strains (K30B1, K30B2, K30B3) recovered over eight months from recurrent liver abscesses and one strain (K30-HUMV1) from a urinary tract infection. All isolates exhibited a yYpermucoviscous phenotype and resistance restricted to ampicillin and amoxicillin. Screening with the eazyplex hvKp assay detected ybt and rmpA in all strains, yielding a virulence score of 1. Biofilm production was strong in K30B1, K30B2, moderate in K30-HUMV1, but weak in K30B3. In the Galleria mellonella infection model, K30B1 showed higher virulence than the other isolates. Whole-genome sequencing identified the ICEKp1 carrying hypervirulence-associated genes (ybt, pagO, rmpAC, iroBCDN) together with additional virulence factors (fim, mrkD, uge, ureA, wabG, wcaJ, mliC), while antibiotic resistance genes were limited to fosA and blaSHV-77. Protein structures and their functional domains were predicted using AlphaFold v3.0.1 and ColabFold v1.5.5, based on pLDDT scores, providing further insights into gene functionality. This work represents one of the first detailed characterizations of K30-ST198 hvKp, underscoring the need for integrated genomic, phenotypic, and structural approaches in hvKp surveillance.

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