| Summary: | Many Shiga toxin-producing <i>Escherichia coli</i> (STEC) strains, including the serogroups of O157 and most of the top six non-O157 serotypes, are frequently associated with foodborne outbreaks. Therefore, they have been extensively studied using next-generation sequencing technology. However, related information regarding STEC O45 strains is scarce. In this study, three environmental <i>E. coli</i> O45:H16 strains (RM11911, RM13745, and RM13752) and one clinical <i>E. coli</i> O45:H2 strain (SJ7) were sequenced and used to characterize virulence factors using two reference <i>E. coli</i> O45:H2 strains of clinical origin. Subsequently, whole-genome-based phylogenetic analysis was conducted for the six STEC O45 strains and nine other reference STEC genomes, in order to evaluate their evolutionary relationship. The results show that one locus of enterocyte effacement pathogenicity island was found in all three STEC O45:H2 strains, but not in the STEC O45:H16 strains. Additionally, <i>E. coli</i> O45:H2 strains were evolutionarily close to <i>E. coli</i> O103:H2 strains, sharing high homology in terms of virulence factors, such as Stx prophages, but were distinct from <i>E. coli</i> O45:H16 strains. The findings show that <i>E. coli</i> O45:H2 may be as virulent as <i>E. coli</i> O103:H2, which is frequently associated with severe illness and can provide genomic evidence to facilitate STEC surveillance.
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