Extraintestinal pathogenic Escherichia coli (ExPEC) sequence type (ST) 38 is one of the top 10 human pandemic lineages. Although a major cause of urinary tract and blood stream infections, ST38 has been poorly characterized from a global phylogenomic perspective. A comprehensive genome-scale analysis of 925 ST38 isolate genomes identified two broad ancestral clades and linkage of discrete ST38 clusters with specific bla CTX-M variants. In addition, the clades and clusters carry important virulence genes, with diverse but poorly characterized plasmids. Numerous putative interhost and environment transmission events were identified here by the presence of ST38 clones (defined as isolates with ≤35 SNPs) within humans, companion animals, food sources, urban birds, wildlife, and the environment. A small cluster of international ST38 clones from diverse sources, likely representing progenitors of a hospital outbreak that occurred in Brisbane, Australia, in 2017, was also identified. Our study emphasizes the importance of characterizing isolate genomes derived from nonhuman sources and geographical locations, without any selection bias.

Asia Pacific Centre for Animal Health Melbourne Veterinary School University of Melbourne Parkville Melbourne Victoria Australia

Australian Institute for Microbiology and Infection University of Technology Sydney Ultimo Sydney New South Wales Australia

Biomedical Center Charles University Brno Czech Republic

Central European Institute of Technology University of Veterinary and Pharmaceutical Sciences Brno Czech Republic

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

Department of Clinical Microbiology and Immunology Institute of Laboratory Medicine The University Hospital Brno Czech Republic

Department of Microbiology and Infectious Diseases Concord Hospital and NSW Health Pathology Hospital Road Concord New South Wales Australia

Faculty of Medicine University of Sydney Sydney New South Wales Australia

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