Escherichia coli ST58 has recently emerged as a globally disseminated uropathogen that often progresses to sepsis. Unlike most pandemic extra-intestinal pathogenic E. coli (ExPEC), which belong to pathogenic phylogroup B2, ST58 belongs to the environmental/commensal phylogroup B1. Here, we present a pan-genomic analysis of a global collection of 752 ST58 isolates from diverse sources. We identify a large ST58 sub-lineage characterized by near ubiquitous carriage of ColV plasmids, which carry genes encoding virulence factors, and by a distinct accessory genome including genes typical of the Yersiniabactin High Pathogenicity Island. This sub-lineage includes three-quarters of all ExPEC sequences in our study and has a broad host range, although poultry and porcine sources predominate. By contrast, strains isolated from cattle often lack ColV plasmids. Our data indicate that ColV plasmid acquisition contributed to the divergence of the major ST58 sub-lineage, and different sub-lineages inhabit poultry, swine and cattle.

Biomedical Center Charles University Charles Czech Republic

CEITEC VETUNI University of Veterinary Sciences Brno Brno Czech Republic

Department of Animal Health and Antimicrobial Strategies National Veterinary Institute 75189 Uppsala Sweden

Department of Bacteria Parasites and Fungi Statens Serum Institut Copenhagen S Denmark

Department of Biology and Wildlife Disease Faculty of Veterinary Hygiene and Ecology University of Veterinary Sciences Brno Brno Czech Republic

Department of Microbiology Public Health Agency of Sweden 17182 Solna Sweden

Institute of Hydrobiology Technische Universität Dresden Dresden Germany

Institute of Microbiology and Epizootics Centre for Infection Medicine Department of Veterinary Medicine Freie Universität Berlin Berlin Germany

Institute of Microbiology Technische Universität Dresden Dresden Germany

iThree Institute University of Technology Sydney Ultimo NSW 2007 Australia

Université de Lyon ANSES Unité Antibiorésistance et Virulence Bactériennes Lyon France

Veterinary Centre for Resistance Research Freie Universität Berlin 14163 Berlin Germany

Wageningen Bioveterinary Research Lelystad Netherlands

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