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Genomic Characterization of a Rare K30-ST198 Hypervirulent Klebsiella pneumoniae Clone with Distinctive Virulence
Domingo Fernández Vecilla1, Jorge Rodríguez Grande2,3, Nuria Fraile Valcárcel2
1Microbiology Service, University Hospital Marqués de Valdecilla, Av. Valdecilla s/n, 39008 Santander, Spain.
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.
Insights
This study characterizes a rare K30-ST198 hypervirulent Klebsiella pneumoniae (hvKp) sublineage from liver abscesses and UTIs. Findings highlight the need for integrated genomic and structural analyses for hvKp surveillance.
Area of Science:
- Microbiology
- Genomics
- Infectious Diseases
Background:
- Hypervirulent Klebsiella pneumoniae (hvKp) poses a significant public health threat.
- Rare hvKp sublineages remain poorly understood, hindering effective surveillance and treatment.
Purpose of the Study:
- To characterize a novel K30-ST198 hvKp sublineage.
- To investigate its genomic, phenotypic, and structural features.
- To assess its virulence in a model organism.
Main Methods:
- Whole-genome sequencing and comparative genomics.
- Phenotypic characterization including biofilm formation and antimicrobial resistance profiling.
- Virulence assessment using the Galleria mellonella infection model.
- Protein structure prediction using AlphaFold and ColabFold.
Main Results:
- A K30-ST198 hvKp sublineage was identified from recurrent liver abscesses and a urinary tract infection.
- Isolates exhibited a hypermucoviscous phenotype and resistance to ampicillin and amoxicillin.
- Whole-genome sequencing revealed ICEKp1 with key hypervirulence genes and limited antibiotic resistance genes.
- K30B1 demonstrated higher virulence in the Galleria mellonella model.
Conclusions:
- This study provides one of the first detailed characterizations of the K30-ST198 hvKp sublineage.
- Integrated genomic, phenotypic, and structural analyses are crucial for comprehensive hvKp surveillance.
- Understanding rare hvKp sublineages is essential for public health preparedness.
