The pathogenic extended-spectrum-beta-lactamase (ESBL)-producing Escherichia coli lineage ST648 is increasingly reported from multiple origins. Our study of a large and global ST648 collection from various hosts (87 whole-genome sequences) combining core and accessory genomics with functional analyses and in vivo experiments suggests that ST648 is a nascent and generalist lineage, lacking clear phylogeographic and host association signals. By including large numbers of ST131 (n = 107) and ST10 (n = 96) strains for comparative genomics and phenotypic analysis, we demonstrate that the combination of multidrug resistance and high-level virulence are the hallmarks of ST648, similar to international high-risk clonal lineage ST131. Specifically, our in silico, in vitro, and in vivo results demonstrate that ST648 is well equipped with biofilm-associated features, while ST131 shows sophisticated signatures indicative of adaption to urinary tract infection, potentially conveying individual ecological niche adaptation. In addition, we used a recently developed NFDS (negative frequency-dependent selection) population model suggesting that ST648 will increase significantly in frequency as a cause of bacteremia within the next few years. Also, ESBL plasmids impacting biofilm formation aided in shaping and maintaining ST648 strains to successfully emerge worldwide across different ecologies. Our study contributes to understanding what factors drive the evolution and spread of emerging international high-risk clonal lineages.

Australian Centre for Antimicrobial Resistance Ecology School of Animal and Veterinary Sciences The University of Adelaide Roseworthy Australia

Calgary Laboratory Services Diagnostic and Scientific Centre Calgary Alberta Canada

CEITEC VFU University of Veterinary and Pharmaceutical Sciences Brno Brno Czech Republic

Department of Biology and Wildlife Diseases Faculty of Veterinary Hygiene and Ecology University of Veterinary and Pharmaceutical Sciences Brno Brno Královo Pole Czech Republic

Department of Biostatistics University of Oslo Oslo Norway

Department of Infectious Diseases Kalmar County Council Kalmar Sweden

Department of Mathematics and Statistics University of Helsinki University of Helsinki Finland

Department of Pathology and Laboratory Medicine University of Calgary Calgary Alberta Canada

Division 13 Nosocomial Pathogens and Antibiotic Resistances Department of Infectious Diseases Robert Koch Institute Wernigerode Germany

Faculty of Medicine School of Public Health Imperial College London United Kingdom

Institute of Hygiene and Infectious Diseases of Animals Justus Liebig University Giessen Giessen Germany

Institute of Microbiology and Epizootics Free University Berlin Berlin Germany

Institute of Microbiology and Infection University of Birmingham Birmingham United Kingdom

International Center for Diarrheal Disease Research Bangladesh Dhaka Bangladesh

Kalmar County Council Department of Clinical and Experimental Medicine Linköping University Linköping Sweden

NG 1 Microbial Genomics Robert Koch Institute Berlin Germany

Pharmaceutical Biology Institute of Pharmacy University of Greifswald Greifswald Germany

Pharmaceutical Microbiology Institute of Pharmacy University of Greifswald Greifswald Germany

Robert Koch Institute Berlin Germany

The Wellcome Trust Sanger Institute Cambridge United Kingdom

Unit Epidemiology Zoonoses and Antimicrobial Resistance Department Biological Safety German Federal Institute for Risk Assessment Berlin Germany

Universidad de La Rioja Area de Bioquímica y Biología Molecular Logroño Spain

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