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Volume 9, Issue 6

Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing colonising adults in Blantyre, Malawi reveals previously undescribed diversity Open Access

Abstract

is one of the most prevalent Gram-negative species associated with drug resistant infections. Strains that produce extended-spectrum beta-lactamases (ESBLs) or carbapenemases are both particularly problematic and disproportionately impact resource limited healthcare settings where last-line antimicrobials may not be available. A large number of genomes are now available and have allowed insights into pathogenesis and epidemiology of ESBL but genomes from sub-Saharan Africa (sSA) are significantly underrepresented. To reduce this gap, we investigated ESBL-producing colonising adults in Blantyre, Malawi to assess bacterial diversity and AMR determinants and to place these isolates in the context of the wider population structure. We performed short-read whole-genome sequencing of 473 colonising ESBL isolated from human stool and contextualised the genomes with a previously curated multi-country collection of 10 146 genomes and sequence type (ST)-specific collections for our three most commonly identified STs. These were the globally successful ST131, ST410 and ST167, and the dominant ESBL genes were , mirroring global trends. However, 37 % of Malawian isolates did not cluster with any isolates in the curated multicountry collection and phylogenies were consistent with locally spreading monophyletic clades, including within the globally distributed, carbapenemase-associated B4/H24RxC ST410 lineage. A single ST2083 isolate in this collection harboured a carbapenemase gene. Long read sequencing demonstrated the presence of a globally distributed ST410-associated carbapenemase carrying plasmid in this isolate, which was absent from the ST410 strains in our collection. We conclude there is a risk that carbapenem resistance in could proliferate rapidly in Malawi under increasing selection pressure, and that both ongoing antimicrobial stewardship and genomic surveillance are critical as local carbapenem use increases.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Drug resistance, microbial , Africa south of the Sahara , Extended-spectrum beta-lactamase and Whole-genome sequencing
Funding
This study was supported by the:
  • Wellcome Trust (Award 109105z/15/a)
    • Principle Award Recipient: JosephLewis
© 2023 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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2023-06-14
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Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli colonising adults in Blantyre, Malawi reveals previously undescribed diversity
M Gen 9, 001035 (2023); https://doi.org/10.1099/mgen.0.001035
/content/journal/mgen/10.1099/mgen.0.001035
/content/journal/mgen/10.1099/mgen.0.001035
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