Tracing the Genomic Landscape of ST23/K1/ESBL Klebsiella pneumoniae: Regional Diversity, Resistance, and Virulence

Tracing the Genomic Landscape of ST23/K1/ESBL Klebsiella pneumoniae: Regional Diversity, Resistance, and Virulence

Abstrakt

ST23 K1 serotype extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ST23/K1/ESBL KP) strains pose a significant public health threat. The convergence of hypervirulence and extended antimicrobial resistance enhances their potential as successful nosocomial pathogens. This study comprehensively characterizes the genomic background of the ST23/K1/ESBL KP population at the University Hospital Brno (UHB), second-largest hospital in the Czech Republic. The aim is to confirm/exclude a long-term nosocomial spread and enable comparison of the UHB population with isolates from world-wide sources. We sequenced 53 ST23/K1/ESBL KP isolates using the short and long read sequencing. Additionally, we included 68 genomes with accessible raw sequencing data from the NCBI database in our comparison. Ridom SeqSphere+ (v9.0) facilitated genome comparisons, while Resfinder (v4.1) and Institute Pasteur database analysed antimicrobial resistance and virulence genes. We established a whole-genome MLST scheme consisting of 2,055 core and 2,968 accessory genes. Single nucleotide variants (SNVs) analysis revealed 8,235 SNVs positions, ranging 0-1,308 (median 245) between individual isolates (Figure 1). Phylogenetic analysis revealed 19 clusters, with 58 isolates grouping into these clusters. A total of 56 resistance gene profiles and 72 virulence gene profiles were identified. Using long-reads data, two different plasmids were identified in UHB isolates, one determined hypervirulent phenotype (including iuc, rpmA, and iro genes) identified as pKPN8 presented in all 53 UHB isolates, while the second plasmid carrying resistance genes identified as pKDO1 was missing in 5 isolates. Our findings demonstrate significant genetic diversity among ST23/K1/ESBL KP isolates, observed both regionally and globally. While resistance gene profiles exhibited greater diversity, virulence gene profiles showed less variation. Notably, all UHB isolates carried the same plasmid encoding the hypervirulent serotype K1. This high genetic diversity within the UHB ST23/K1/ESBL KP population likely reflects natural population variability rather than a sustained nosocomial outbreak within the hospital.

ST23 K1 serotype extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ST23/K1/ESBL KP) strains pose a significant public health threat. The convergence of hypervirulence and extended antimicrobial resistance enhances their potential as successful nosocomial pathogens. This study comprehensively characterizes the genomic background of the ST23/K1/ESBL KP population at the University Hospital Brno (UHB), second-largest hospital in the Czech Republic. The aim is to confirm/exclude a long-term nosocomial spread and enable comparison of the UHB population with isolates from world-wide sources. We sequenced 53 ST23/K1/ESBL KP isolates using the short and long read sequencing. Additionally, we included 68 genomes with accessible raw sequencing data from the NCBI database in our comparison. Ridom SeqSphere+ (v9.0) facilitated genome comparisons, while Resfinder (v4.1) and Institute Pasteur database analysed antimicrobial resistance and virulence genes. We established a whole-genome MLST scheme consisting of 2,055 core and 2,968 accessory genes. Single nucleotide variants (SNVs) analysis revealed 8,235 SNVs positions, ranging 0-1,308 (median 245) between individual isolates (Figure 1). Phylogenetic analysis revealed 19 clusters, with 58 isolates grouping into these clusters. A total of 56 resistance gene profiles and 72 virulence gene profiles were identified. Using long-reads data, two different plasmids were identified in UHB isolates, one determined hypervirulent phenotype (including iuc, rpmA, and iro genes) identified as pKPN8 presented in all 53 UHB isolates, while the second plasmid carrying resistance genes identified as pKDO1 was missing in 5 isolates. Our findings demonstrate significant genetic diversity among ST23/K1/ESBL KP isolates, observed both regionally and globally. While resistance gene profiles exhibited greater diversity, virulence gene profiles showed less variation. Notably, all UHB isolates carried the same plasmid encoding the hypervirulent serotype K1. This high genetic diversity within the UHB ST23/K1/ESBL KP population likely reflects natural population variability rather than a sustained nosocomial outbreak within the hospital.

Klebsiella pneumoniae; molecular typing; hypervirulent

Klebsiella pneumoniae; molecular typing; hypervirulent

BEZDÍČEK, M.; BITUŠÍKOVÁ, V.; HOLUBOVÁ, E.; JAKUBÍČKOVÁ, M.; KOCMANOVÁ, I.; LENGEROVÁ, M.

19.06.2025

ASM Microbe 2025, Los Angeles, USA