Global genomic landscape of the Klebsiella oxytoca complex: diversity, resistome and plasmidome (1974-2025)
Abstract
Background: Klebsiella oxytoca species complex (KoSC) is an opportunistic pathogen causing various infections. However, our understanding of their population structure and the co-occurrence of specific plasmid replicons with ARGs remains limited.
Methods: 3097 high-quality genomes of KoSC between 1974 and 2025 were included. The population structure was determined by phylogenetic analysis and ANI identity, while ARGs and VAGs were predicted based on genomic data.
Results: All genomes belonged to six species, with K. michiganensis (44.2%) and K. oxytoca (41.1%) being the most common. The genomes were sourced from 63 countries, with the majority originating from the USA (25.3%). 460 STs were identified within the KoSC, suggesting a high level of genetic diversity within the KoSC. The number of ARGs (median of 5 per genome) varied significantly among species, with K. michiganensis harboring the highest number. Forty-four different types of carbapenemase-encoding genes were detected across 37 countries, with bla NDM-1 (19.4%) and bla KPC-2 (19.3%) being the most prevalent. A significantly higher number of VAGs were found within K. oxytoca and K. grimontii isolates compared to the other four species. Notably, 22 plasmid replicons and 76 ISs showed significant correlations with ARGs, suggesting their potential role in ARG dissemination.
Conclusions: This study provides a comprehensive genomic framework for understanding the global population structure and antimicrobial resistance…
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