Temporal genomic dynamics of sequence type 39 Klebsiella pneumoniae in a neonatal unit in Blantyre, Malawi

Allan M. Zuza; Oliver Pearse; Daryl B. Domman; Zoe A. Dyson; Kondwani Kawaza; Patrick Musicha; Nicholas A. Feasey; Eva Heinz

doi:10.1099/mgen.0.001673

Temporal genomic dynamics of sequence type 39 Klebsiella pneumoniae in a neonatal unit in Blantyre, Malawi

Allan M. Zuza, Oliver Pearse, Daryl B. Domman, Zoe A. Dyson, Kondwani Kawaza, Patrick Musicha, Nicholas A. Feasey, Eva Heinz^*

^*Corresponding author for this work

Strathclyde Institute Of Pharmacy And Biomedical Sciences

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Abstract

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

Methods: We analysed whole-genome sequences of Kpn 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.

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

Conclusions: The analysed Kpn 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.

Original language	English
Article number	001673
Number of pages	12
Journal	Microbial Genomics
Volume	12
Issue number	4
DOIs	https://doi.org/10.1099/mgen.0.001673
Publication status	Published - 1 Apr 2026

Funding

EH acknowledges funding from BBSRC (BB/V011278/1, BB/V011278/2) and Wellcome (217303/Z/19/Z). NAF and EH acknowledge funding from the BMGF (INV-005180).

Keywords

neonatal sepsis
hospital-acquired infection
sub-saharan Africa
phage insertion
antimicrobial resistance islands

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10.1099/mgen.0.001673Licence: CC BY 4.0

Zuza-etal-MG-2026-Temporal-genomic-dynamics-of-sequence-type-39-Klebsiella-pneumoniae-in-a-neonatal-unitFinal published version, 4.38 MBLicence: CC BY 4.0

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@article{6572cc36d0f74419a614a2a09b0e8174,

title = "Temporal genomic dynamics of sequence type 39 Klebsiella pneumoniae in a neonatal unit in Blantyre, Malawi",

abstract = "Background: Klebsiella pneumoniae (Kpn) is an important cause of healthcare-associated infections (HAIs). In low- and middle-income countries, HAI due to Kpn disproportionately affects neonates. In this study, we investigated the genomic changes that occurred during long-term circulation of a Kpn sequence type (ST) 39 clone, causing a disproportionate number of infections on the neonatal ward at a tertiary healthcare facility in Malawi in 2017. Methods: We analysed whole-genome sequences of Kpn 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. Results: We identified eight variable genomic regions that demonstrate the plasticity of Kpn within ST, including the role of bacteriophages in shaping the genome of ST39. Conclusions: The analysed Kpn 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.",

keywords = "neonatal sepsis, hospital-acquired infection, sub-saharan Africa, phage insertion, antimicrobial resistance islands",

author = "Zuza, \{Allan M.\} and Oliver Pearse and Domman, \{Daryl B.\} and Dyson, \{Zoe A.\} and Kondwani Kawaza and Patrick Musicha and Feasey, \{Nicholas A.\} and Eva Heinz",

year = "2026",

month = apr,

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doi = "10.1099/mgen.0.001673",

language = "English",

volume = "12",

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T1 - Temporal genomic dynamics of sequence type 39 Klebsiella pneumoniae in a neonatal unit in Blantyre, Malawi

AU - Zuza, Allan M.

AU - Pearse, Oliver

AU - Domman, Daryl B.

AU - Dyson, Zoe A.

AU - Kawaza, Kondwani

AU - Musicha, Patrick

AU - Feasey, Nicholas A.

AU - Heinz, Eva

PY - 2026/4/1

Y1 - 2026/4/1

N2 - Background: Klebsiella pneumoniae (Kpn) is an important cause of healthcare-associated infections (HAIs). In low- and middle-income countries, HAI due to Kpn disproportionately affects neonates. In this study, we investigated the genomic changes that occurred during long-term circulation of a Kpn sequence type (ST) 39 clone, causing a disproportionate number of infections on the neonatal ward at a tertiary healthcare facility in Malawi in 2017. Methods: We analysed whole-genome sequences of Kpn 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. Results: We identified eight variable genomic regions that demonstrate the plasticity of Kpn within ST, including the role of bacteriophages in shaping the genome of ST39. Conclusions: The analysed Kpn 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.

AB - Background: Klebsiella pneumoniae (Kpn) is an important cause of healthcare-associated infections (HAIs). In low- and middle-income countries, HAI due to Kpn disproportionately affects neonates. In this study, we investigated the genomic changes that occurred during long-term circulation of a Kpn sequence type (ST) 39 clone, causing a disproportionate number of infections on the neonatal ward at a tertiary healthcare facility in Malawi in 2017. Methods: We analysed whole-genome sequences of Kpn 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. Results: We identified eight variable genomic regions that demonstrate the plasticity of Kpn within ST, including the role of bacteriophages in shaping the genome of ST39. Conclusions: The analysed Kpn 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.

KW - neonatal sepsis

KW - hospital-acquired infection

KW - sub-saharan Africa

KW - phage insertion

KW - antimicrobial resistance islands

U2 - 10.1099/mgen.0.001673

DO - 10.1099/mgen.0.001673

M3 - Article

SN - 2057-5858

VL - 12

JO - Microbial Genomics

JF - Microbial Genomics

IS - 4

M1 - 001673

ER -

Temporal genomic dynamics of sequence type 39 Klebsiella pneumoniae in a neonatal unit in Blantyre, Malawi

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