{
  "abstract": "Infection with extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) is a global health concern that disproportionately affects sub-Saharan Africa. Gut mucosal colonisation is thought to precede invasive infection. Understanding ESBL-Ec colonisation and transmission across communities is therefore essential. Here, we investigate the genomic epidemiology and spatial structure of 159 gut-colonising ESBL-Ec isolates from the faeces of 211 people in two rural Malawian villages using longitudinal sampling (2023–24), whole-genome sequencing and household mapping. Colonisation prevalence rose from 34.1% (95% CI: 27.8–41.0) to 54.2% (95% CI: 46.0–62.3) over one year. Isolates belonged to 33 sequence types (STs), most commonly ST38 and ST131, harbouring 46 distinct antimicrobial resistance gene types. Fifteen strains were identified in ≥3 households that were typically separated by short geographic distances ( < 400 m). Of 190 pairwise comparisons between same-strain isolates from different households sampled concurrently within villages, 88.9% differed by ≤10 single nucleotide polymorphisms, consistent with multi-household involvement in community transmission networks. Lineage-specific ST38 and ST131 network analyses linked rural isolates to urban Malawian isolates collected within the last decade. Our findings provide a transferable framework for inferring ESBL-Ec flow in community settings and highlight the need for One Health surveillance and improved sanitation infrastructure to limit transmission.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": null,
  "author_total": 15,
  "authors": [
    {
      "name": "Angus M. O’Ferrall",
      "orcid": "0000-0003-1077-968X"
    },
    {
      "name": "David Lally"
    },
    {
      "name": "Peter Makaula"
    },
    {
      "name": "Gladys Namacha"
    },
    {
      "name": "Joseph M. Lewis",
      "orcid": "0000-0002-3837-5188"
    },
    {
      "name": "Patrick Musicha"
    },
    {
      "name": "Richard N. Goodman",
      "orcid": "0009-0008-0578-789X"
    },
    {
      "name": "Ellie Allman"
    },
    {
      "name": "Sabrina J. Moyo"
    },
    {
      "name": "Claire S. Waddington"
    },
    {
      "name": "Sekeleghe A. Kayuni"
    },
    {
      "name": "Nicholas A. Feasey",
      "orcid": "0000-0003-4041-1405"
    },
    {
      "name": "Janelisa Musaya"
    },
    {
      "name": "J. Russell Stothard",
      "orcid": "0000-0002-9370-3420"
    },
    {
      "name": "Adam P. Roberts",
      "orcid": "0000-0002-0760-3088"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/cr1m61aks82mb.bib",
  "cited_by": 0,
  "doi": "10.1038/s41467-026-78449-1",
  "fulltext_url": null,
  "id": "cr1m61aks82mb",
  "issns": [
    "2041-1723"
  ],
  "landing_url": "https://www.nature.com/articles/s41467-026-78449-1",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1313|Antibiotic Resistance in Bacteria"
    ]
  ],
  "openalex": "W7221807985",
  "pdf_url": "https://www.nature.com/articles/s41467-026-78449-1_reference.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-14",
  "publisher": "Springer Science and Business Media LLC",
  "ris": "https://research.draconitic.com/paper/cr1m61aks82mb.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:38Z",
      "native_id": "10.1038/s41467-026-78449-1",
      "source": "crossref",
      "url": "https://www.nature.com/articles/s41467-026-78449-1"
    }
  ],
  "subjects": [
    {
      "field": "medicine",
      "origin": "openalex:1313|Antibiotic Resistance in Bacteria",
      "subfield": "general"
    }
  ],
  "title": "Whole-genome sequencing reveals inter-household networks of gut-colonising ESBL-producing Escherichia coli in two rural Malawian districts",
  "title_text": "Whole-genome sequencing reveals inter-household networks of gut-colonising ESBL-producing Escherichia coli in two rural Malawian districts",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:38Z",
  "url": "https://research.draconitic.com/paper/cr1m61aks82mb",
  "venue": "Nature Communications",
  "versions": []
}