Genomic features and pathogenicity of atypical diarrheagenic Escherichia coli from a large foodborne outbreak

Abstract

An outbreak of diarrheal illness related to milk cartons served in school lunches, occurred in June 2021, involving more than 1800 cases from 25 schools. A strain of Escherichia coli OUT (OgGp9):H18 was implicated in the outbreak. This strain does not possess virulence factors typical of other E. coli pathotypes. In this study, we examined the pathogenicity of the E. coli OUT (OgGp9):H18 strain using genomic analysis and animal models. A core genome-based phylogenetic analysis revealed that this strain belongs to a clade comprising ST1380 strains and is distinct from enteroaggregative E. coli 042 and uropathogenic E. coli UMN026, which were previously considered to be phylogenetically related to this strain. In addition, the strain harbors a plasmid similar to that of atypical enterotoxigenic E. coli, encoding Coli Surface antigen CS8 and a type VI secretion system (T6SS). The strain caused mortality in mice following intraperitoneal inoculation. Marmosets inoculated orally, experienced diarrhea and long-term shedding. Curing the strain of the 103 Kbp plasmid it carries reduced mortality rates and colonization in the experimental animals, indicating that the plasmid encodes virulence factors. However, the mortality of mice treated with the plasmid-cured strain was higher than that of those treated with nonvirulent E. coli K-12, indicating that the chromosome also encodes virulence factors. Identified chromosomal virulence factors include a T6SS, the second type III secretion system in E. coli, ETT2, and the capsule gene cluster kps. These findings suggest that atypical diarrheagenic E. coli, such as the strain investigated in this study, may be the cause of foodborne illness in patients with diarrhea with an unknown cause.