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

doi:10.1099/mgen.0.000703

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 journal › Article › peer-review

6 Citations (Scopus)

Abstract

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 language	English
Article number	000703
Journal	Microbial Genomics
Volume	7
Issue number	11
DOIs	https://doi.org/10.1099/mgen.0.000703
Publication status	Published - 18 Nov 2021
Externally published	Yes

Keywords

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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Cite this

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

abstract = "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.",

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AU - Musicha, Patrick

AU - Peno, Chikondi

AU - Seager, Ezgi

AU - Tam, Pui Ying Iroh

AU - Bilima, Sithembile

AU - Bennett, Aisleen

AU - Kennedy, Neil

AU - Feasey, Nicholas

AU - Heinz, Eva

AU - Cain, Amy K.

PY - 2021/11/18

Y1 - 2021/11/18

N2 - 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.

AB - 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.

KW - Antimicrobial resistance

KW - Genome sequencing

KW - Hospital outbreak

KW - Klebsiella pneumoniae

KW - Neonatal infection

KW - Sub-Saharan Africa

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ER -

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

Abstract

Keywords

UN SDGs

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