{
  "abstract": "The global CTX-M pandemic is considered a plasmid-driven phenomenon, yet chromosomal integration of blaCTX-M has been reported in various settings. Screening 451,174 publicly available E. coli genomes and retaining 2,269 CTX-M-E. coli long-read or hybrid assemblies, we found that 33.5% carried at least one chromosomally integrated blaCTX-M. Chromosomal integration was strongly structured by E. coli lineage and CTX-M variant, reaching 68.5% in ST38 and 43.9% in ST131. In the latter, integration rates varied between subclades with modelling, suggesting recent acceleration within the ST131-C2 subclade. Additional resistance genes were frequently co-integrated with blaCTX-M (33%), with architectures largely inherited from plasmid-borne structures. Integrations were mainly ISEcp1- or IS26-mediated (77.3% and 18.9%, respectively) and occurred across the entire E. coli chromosome without spared zones. blaCTX-M chromosomal integration is a widespread, lineage-structured component of the CTX-M pandemic, providing stable vertical inheritance that complements or may supplant plasmid-mediated dissemination in successful ESBL-E. coli clones.",
  "abstract_shown": true,
  "affiliations": [
    "Assistance Publique - Hopitaux de Paris"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 15,
  "authors": [
    {
      "name": "M. Danjean"
    },
    {
      "name": "T. Morel-Journel"
    },
    {
      "name": "V. Berti"
    },
    {
      "name": "Y. Benhadid-Brahmi"
    },
    {
      "name": "S. Gueye"
    },
    {
      "name": "H. C. Lougbegnon"
    },
    {
      "name": "H. Jacquier"
    },
    {
      "name": "E. Denamur"
    },
    {
      "name": "S. Bonacorsi"
    },
    {
      "name": "P. Siguier"
    },
    {
      "name": "F. Cornet"
    },
    {
      "name": "M. Campos"
    },
    {
      "name": "M. Petitjean"
    },
    {
      "name": "A. Birgy"
    },
    {
      "affs": [
        0
      ],
      "name": "L. Armand-Lefevre"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/bb9dt093je9qs.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.07.757360",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.07.757360v1.full",
  "id": "bb9dt093je9qs",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.07.757360v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "microbiology"
    ],
    [
      "openalex",
      "1313|Antibiotic Resistance in Bacteria"
    ]
  ],
  "openalex": "W7221000951",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.07.757360v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-07",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/bb9dt093je9qs.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:26:41Z",
      "native_id": "10.64898/2026.10.07.757360",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.07.757360v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:microbiology",
      "subfield": "microbiology"
    }
  ],
  "title": "Chromosomal integration of blaCTX-M redefines the evolutionary trajectory of antibiotic resistance in E. coli through lineage-structured expansion",
  "title_text": "Chromosomal integration of blaCTX-M redefines the evolutionary trajectory of antibiotic resistance in E. coli through lineage-structured expansion",
  "type": "preprint",
  "updated_at": "2026-10-30T12:26:41Z",
  "url": "https://research.draconitic.com/paper/bb9dt093je9qs",
  "venue": "bioRxiv",
  "versions": []
}