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PreprintCC BYbioRxiv

Chromosomal integration of blaCTX-M redefines the evolutionary trajectory of antibiotic resistance in E. coli through lineage-structured expansion

  • M. Danjean
  • T. Morel-Journel
  • V. Berti
  • Y. Benhadid-Brahmi
  • S. Gueye
  • H. C. Lougbegnon
  • H. Jacquier
  • E. Denamur
  • S. Bonacorsi
  • P. Siguier
  • F. Cornet
  • M. Campos
3 more authors
  • M. Petitjean
  • A. Birgy
  • L. Armand-Lefevre1
  1. 1Assistance Publique - Hopitaux de Paris
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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.

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Cite

BibTeXRIS
BibTeX
@misc{danjean2026chromosomal,
  title = {{Chromosomal integration of blaCTX-M redefines the evolutionary trajectory of antibiotic resistance in E. coli through lineage-structured expansion}},
  author = {M. Danjean and T. Morel-Journel and V. Berti and Y. Benhadid-Brahmi and S. Gueye and H. C. Lougbegnon and H. Jacquier and E. Denamur and S. Bonacorsi and P. Siguier and F. Cornet and M. Campos and M. Petitjean and A. Birgy and L. Armand-Lefevre},
  howpublished = {bioRxiv},
  year = {2026},
  month = oct,
  doi = {10.64898/2026.10.07.757360},
  url = {https://www.biorxiv.org/content/10.64898/2026.10.07.757360v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - Chromosomal integration of blaCTX-M redefines the evolutionary trajectory of antibiotic resistance in E. coli through lineage-structured expansion
AU  - M. Danjean
AU  - T. Morel-Journel
AU  - V. Berti
AU  - Y. Benhadid-Brahmi
AU  - S. Gueye
AU  - H. C. Lougbegnon
AU  - H. Jacquier
AU  - E. Denamur
AU  - S. Bonacorsi
AU  - P. Siguier
AU  - F. Cornet
AU  - M. Campos
AU  - M. Petitjean
AU  - A. Birgy
AU  - L. Armand-Lefevre
PY  - 2026
DA  - 2026/10/07
PB  - bioRxiv
DO  - 10.64898/2026.10.07.757360
UR  - https://www.biorxiv.org/content/10.64898/2026.10.07.757360v1
AB  - 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.
ER  -