Plasmid-driven strategies for clone success in Escherichia coli
Sergio Arredondo-Alonso, Anna K. Pöntinen, João Alves Gama, Rebecca A. Gladstone, Klaus Harms, Gerry Tonkin‐Hill, Harry A. Thorpe, Gunnar Skov Simonsen, Ørjan Samuelsen, Pål J. Johnsen, Jukka Corander, Norwegian E. coli BSI Study Group, Nina Handal, Nils Olav Hermansen, Anita Kanestrøm, Hege Elisabeth Larsen, Paul Christoffer Lindemann, Iren Høyland Löhr, Åshild Marvik, Einar Nilsen, Marcela Zamudio, Elisabeth Sirnes, Ståle Tofteland, Kyriakos Zaragkoulias
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. Plasmids can encode multiple traits that contribute to the emergence and dissemination of their bacterial hosts. Here the authors use Nanopore long-read technology to sequence the complete genomes of <2,000 bloodstream infection E. coli isolates, highlighting the contribution of chromosomal and plasmid-encoded traits in the success of different lineages.