{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,5]],"date-time":"2026-09-05T23:30:40Z","timestamp":1788651040019,"version":"build-2803163510"},"reference-count":55,"publisher":"Microbiology Society","issue":"6","license":[{"start":{"date-parts":[[2023,6,14]],"date-time":"2023-06-14T00:00:00Z","timestamp":1686700800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"crossref","award":["109105z\/15\/a"],"award-info":[{"award-number":["109105z\/15\/a"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,6,14]]},"abstract":"\n \n \n Escherichia coli<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n 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\n \n \n E. coli<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n genomes are now available and have allowed insights into pathogenesis and epidemiology of ESBL\n \n \n E. coli<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n but genomes from sub-Saharan Africa (sSA) are significantly underrepresented. To reduce this gap, we investigated ESBL-producing\n \n \n E. coli<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n 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\n \n \n E. coli<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n isolated from human stool and contextualised the genomes with a previously curated multi-country collection of 10\u200a146\n \n \n E. coli<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n 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\n bla<\/jats:italic>\n CTX-M<\/jats:sub>\n , mirroring global trends. However, 37\u200a% 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\n \n \n E. coli<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>\n 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.\n <\/jats:p>","DOI":"10.1099\/mgen.0.001035","type":"journal-article","created":{"date-parts":[[2023,6,14]],"date-time":"2023-06-14T09:17:31Z","timestamp":1686734251000},"source":"Crossref","is-referenced-by-count":9,"title":["Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli colonising adults in Blantyre, Malawi reveals previously undescribed diversity"],"prefix":"10.1099","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3837-5188","authenticated-orcid":false,"given":"Joseph M.","family":"Lewis","sequence":"first","affiliation":[{"name":"Department of Clinical Sciences, Liverpool School of Tropical Medicine, 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