TY - JOUR
T1 - Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli colonising adults in Blantyre, Malawi reveals previously undescribed diversity
AU - Lewis, Joseph M.
AU - Mphasa, Madalitso
AU - Banda, Rachel
AU - Beale, Mathew A.
AU - Mallewa, Jane
AU - Anscome, Catherine
AU - Zuza, Allan
AU - Roberts, Adam P.
AU - Heinz, Eva
AU - Thomson, Nicholas R.
AU - Feasey, Nicholas A.
PY - 2023/6/14
Y1 - 2023/6/14
N2 - Escherichia coli 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 E. coli genomes are now available and have allowed insights into pathogenesis and epidemiology of ESBL E. coli but genomes from sub-Saharan Africa (sSA) are significantly underrepresented. To reduce this gap, we investigated ESBL-producing E. coli 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 E. coli isolated from human stool and contextualised the genomes with a previously curated multi-country collection of 10 146 E. coli 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 blaCTX-M, 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 E. coli 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.
AB - Escherichia coli 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 E. coli genomes are now available and have allowed insights into pathogenesis and epidemiology of ESBL E. coli but genomes from sub-Saharan Africa (sSA) are significantly underrepresented. To reduce this gap, we investigated ESBL-producing E. coli 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 E. coli isolated from human stool and contextualised the genomes with a previously curated multi-country collection of 10 146 E. coli 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 blaCTX-M, 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 E. coli 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.
KW - Africa south of the Sahara
KW - Drug resistance, microbial
KW - Extended-spectrum beta-lactamase
KW - Whole-genome sequencing
UR - http://www.scopus.com/inward/record.url?scp=85162863143&partnerID=8YFLogxK
UR - https://doi.org/10.5281/zenodo.5554081
UR - https://doi.org/ 10.6084/m9.figshare.22561738.v1
U2 - 10.1099/mgen.0.001035
DO - 10.1099/mgen.0.001035
M3 - Article
C2 - 37314322
AN - SCOPUS:85162863143
SN - 2057-5858
VL - 9
JO - Microbial Genomics
JF - Microbial Genomics
IS - 6
M1 - 001035
ER -