Plasmid-driven strategies for clone success in Escherichia coli

Sergio Arredondo-Alonso, Anna K. Pöntinen, João A. Gama, Rebecca A. Gladstone, Klaus Harms, Gerry Tonkin-Hill, Harry A. Thorpe, Gunnar S. Simonsen, Ørjan Samuelsen, Pål J. Johnsen and Jukka Corander ()
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Sergio Arredondo-Alonso: University of Oslo
Anna K. Pöntinen: University of Oslo
João A. Gama: UiT The Arctic University of Norway
Rebecca A. Gladstone: University of Oslo
Klaus Harms: UiT The Arctic University of Norway
Gerry Tonkin-Hill: University of Oslo
Harry A. Thorpe: University of Oslo
Gunnar S. Simonsen: University Hospital of North Norway
Ørjan Samuelsen: University Hospital of North Norway
Pål J. Johnsen: UiT The Arctic University of Norway
Jukka Corander: University of Oslo

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract Escherichia coli is the most widely studied microbe in history, but the population structure and evolutionary trends of its extrachromosomal elements known as plasmids remain poorly delineated. Here we used long-read technology to high-resolution sequence the entire plasmidome and the corresponding host chromosomes from an unbiased longitudinal survey covering two decades and over 2000 E. coli isolates. We find that some plasmids have persisted in lineages even for centuries, demonstrating strong plasmid-lineage associations. Our analysis provides a detailed map of recent vertical and horizontal evolutionary events involving plasmids with key antibiotic resistance, competition and virulence determinants. We present genomic evidence of both chromosomal and plasmid-driven success strategies adopted by distant lineages by independently inheriting the same genomic elements. Further, we use in vitro experiments to verify the importance of key bacteriocin-producing plasmids for clone success. Our study has general implications for understanding plasmid biology and bacterial evolutionary strategies.

Date: 2025
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DOI: 10.1038/s41467-025-57940-1

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