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<p>Genomic surveillance can clarify the population structure and antimicrobial resistance burden of the <i>Klebsiella pneumoniae</i> species complex (KpSC); however, African genomes remain unevenly represented in public repositories. This study reanalysed ENA/EBI assemblies annotated as <i>K. pneumoniae</i> and explicitly linked to African countries. Of the 88,183 global assemblies retrieved on 13 September 2025, 3,796 were African-linked. Quality filtering retained 3,680 assemblies, of which 3,590 were confirmed as KpSC. After removing one unassigned sequence type, 3,589 genomes were used for most downstream analyses. The dataset was geographically imbalanced, with Malawi and South Africa contributing to more than half of the African-linked assemblies. Population structure was dominated by CG39, CG17, CG307 and CG2621, with additional high-risk lineages including CG15, CG147 and CG258 and 21 newly assigned sequence types (ST9512–ST9532) carried novel MLST alleles. Genotypic resistance was common, with bla<sub>CTX−M−15</sub> detected in 82.8% of genomes and carbapenemase genes in 24.1%. The virulence marker burden was generally low, although a small subset carried high virulence scores. IncF-family replicons frequently co-occurred with ESBL and multidrug-resistance determinants. These findings define major biases and genomic signals in public African KpSC data and support broader, metadata-rich, and plasmid-resolved surveillance.</p>

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Public genomic surveillance of African Klebsiella pneumoniae species complex reveals uneven sampling and high ESBL gene carriage

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月8日

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  • Mutshiene Deogratias Ekwanzala

摘要

Genomic surveillance can clarify the population structure and antimicrobial resistance burden of the Klebsiella pneumoniae species complex (KpSC); however, African genomes remain unevenly represented in public repositories. This study reanalysed ENA/EBI assemblies annotated as K. pneumoniae and explicitly linked to African countries. Of the 88,183 global assemblies retrieved on 13 September 2025, 3,796 were African-linked. Quality filtering retained 3,680 assemblies, of which 3,590 were confirmed as KpSC. After removing one unassigned sequence type, 3,589 genomes were used for most downstream analyses. The dataset was geographically imbalanced, with Malawi and South Africa contributing to more than half of the African-linked assemblies. Population structure was dominated by CG39, CG17, CG307 and CG2621, with additional high-risk lineages including CG15, CG147 and CG258 and 21 newly assigned sequence types (ST9512–ST9532) carried novel MLST alleles. Genotypic resistance was common, with blaCTX−M−15 detected in 82.8% of genomes and carbapenemase genes in 24.1%. The virulence marker burden was generally low, although a small subset carried high virulence scores. IncF-family replicons frequently co-occurred with ESBL and multidrug-resistance determinants. These findings define major biases and genomic signals in public African KpSC data and support broader, metadata-rich, and plasmid-resolved surveillance.