High-Risk ExPEC from Commensal Phylogroup A: Genomic Characterization of a Bovine Meningoencephalitis Isolate, BN01

Extraintestinal pathogenic Escherichia coli (ExPEC) causes severe infections in humans and animals, yet bovine isolates remain poorly characterized. Here, we report the first complete genome of a bovine ExPEC strain, BN01 (serotype O101:H9-ST10-phylogroup A), isolated from calf meningoencephalitis. Unlike classical ExPEC that typically belong to B2/D phylogroups and O1/O2/O18 serotypes, BN01 represents the A-ST10-O101 sublineage that has emerged as predominant among bovine ExPEC populations. The genome comprises a chromosome encoding 197 virulence factors, with cdiA uniquely identified in BN01 compared to six other representative ExPEC genomes—a contact-dependent growth inhibition system, and three distinct plasmids: a conjugative ESBL carrier (blaCTX-M-164, IncI1), a bovine-associated multidrug resistance island (IncY), and a mobilization-ready vector (IncFII). Animal virulence assays demonstrated that intraperitoneal challenge with E. coli BN01 caused 80% mortality (8/10 mice) within the observation period and yielded an LD50 of 106.3 CFU/mouse. These findings demonstrate that high-risk ExPEC can occur in phylogroups typically associated with commensal strains, expanding the conventional understanding of phylogroup–virulence associations. They highlight the need to assess the zoonotic potential of livestock-associated atypical lineages and support integrated genomic surveillance under the One Health framework.