Genomic investigation of a suspected Klebsiella pneumoniae outbreak in a neonatal care unit in sub-Saharan Africa

Jennifer Cornick*, Patrick Musicha, Chikondi Peno, Ezgi Seager, Pui-Ying Iroh Tam, Sithembile Bilima, Aisleen Bennett, Neil Kennedy, Nicholas Feasey, Eva Heinz, Amy K. Cain*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    6 Citations (Scopus)
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    A special-care neonatal unit from a large public hospital in Malawi was noted as having more frequent, difficult-to-treat infec-tions, and a suspected outbreak of multi-drug-resistant Klebsiella pneumoniae was investigated using genomic characterisa-tion. All K. pneumoniae bloodstream infections (BSIs) from patients in the neonatal ward (n=62), and a subset of K. pneumoniae BSI isolates (n=38) from other paediatric wards in the hospital, collected over a 4 year period were studied. After whole genome sequencing, the strain sequence types (STs), plasmid types, virulence and resistance genes were identified. One ST340 clone, part of clonal complex 258 (CC258) and an ST that drives hospital outbreaks worldwide, harbouring numerous resistance genes and plasmids, was implicated as the likely cause of the outbreak. This study contributes molecular information necessary for tracking and characterizing this important hospital pathogen in sub-Saharan Africa.

    Original languageEnglish
    Article number000703
    Pages (from-to)1-6
    Number of pages6
    JournalMicrobial Genomics
    Issue number11
    Early online date18 Nov 2021
    Publication statusPublished - 2021

    Bibliographical note

    Copyright the Author(s) 2021. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.


    • Antimicrobial resistance
    • Genome sequencing
    • Hospital outbreak
    • Klebsiella pneumoniae
    • Neonatal infection
    • Sub-Saharan Africa


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