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Microbial Genomics logo Microbial Genomics

Volume 12, Issue 4

Temporal genomic dynamics of sequence type 39 in a neonatal unit in Blantyre, Malawi Open Access

Abstract

() is an important cause of healthcare-associated infections (HAIs). In low- and middle-income countries, HAI due to disproportionately affects neonates. In this study, we investigated the genomic changes that occurred during long-term circulation of a sequence type (ST) 39 clone, causing a disproportionate number of infections on the neonatal ward at a tertiary healthcare facility in Malawi in 2017.

We analysed whole-genome sequences of ST39 collected from Queen Elizabeth Central Hospital over a 20-year period, including the generation of several high-quality hybrid genomes. We compared virulence markers, antibiotic resistance determinants and mobile genetic elements, focusing on variable regions between strains from the outbreak clone in 2017 and genomes from other co-occurring ST39 lineages.

We identified eight variable genomic regions that demonstrate the plasticity of within ST, including the role of bacteriophages in shaping the genome of ST39.

The analysed ST39 lineages have a highly variable genome capable of incorporating large genomic regions during prolonged hospital circulation, which may offer a selective advantage in hospital environments and provide resistance to antimicrobial agents.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): extended-spectrum beta-lactamase (ESBL) , hospital-acquired infection (HAI) and Sub-Saharan Africa
Funding
This study was supported by the:
  • Biotechnology and Biological Sciences Research Council (Award BB/V011278/1)
    • Principal Award Recipient: EvaHeinz
  • Biotechnology and Biological Sciences Research Council (Award BB/V011278/2)
    • Principal Award Recipient: EvaHeinz
  • Wellcome Trust (Award 217303/Z/19/Z)
    • Principal Award Recipient: EvaHeinz
  • Bill and Melinda Gates Foundation (Award INV-005180)
    • Principal Award Recipient: NicholasA Feasey
© 2026 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2026-04-01
2026-04-22

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Temporal genomic dynamics of sequence type 39 Klebsiella pneumoniae in a neonatal unit in Blantyre, Malawi
M Gen 12, 001673 (2026); https://doi.org/10.1099/mgen.0.001673
/content/journal/mgen/10.1099/mgen.0.001673
/content/journal/mgen/10.1099/mgen.0.001673
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