Escherichia coli plasmidome maps the game of clones

Escherichia coli is a major human pathogen and the most widely studied microbe in history, but 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 a longitudinal survey covering two decades and over 2,000 E. coli isolates. Separation of chromosomal and extrachromosomal DNA enabled us to reconstruct co-evolutionary trajectories of host lineages and their plasmids on a population-wide scale, demonstrating that plasmid evolution is markedly constrained contrary to the established dogma. We find that some plasmids have persisted in lineages for centuries, and provide a high-resolution map of recent vertical and horizontal evolutionary events in plasmids with key antibiotic resistance, competition and virulence determinants. We present genomic evidence of both chromosomal and plasmid-driven success strategies that represent convergent phenotypic evolution in distant lineages, and use in vitro experiments to verify the importance of bacteriocin-producing plasmids for clone success. Our study has general implications for understanding plasmid biology and bacterial evolutionary strategies, and informing development of future interventions against pathogens. ### Competing Interest Statement The authors have declared no competing interest.