ABSTRACT In August 2023, 74 symptomatic patients developed Shiga toxin-producing Escherichia coli (STEC) O157 infection after consuming raw horse meat processed at a meat shop in Yamagata, Japan. To investigate the outbreak, we conducted multilocus variable-number tandem-repeat analysis (MLVA), whole-genome sequencing (WGS), and a nationwide retrospective epidemiological survey. MLVA and WGS identified 165 genetically similar strains collected across Japan during 2022–2023. Epidemiological investigations revealed that 6/89 (6.9%) cases in 2022 and 49/76 (64.5%) cases in 2023 were linked to raw horse meat consumption from the shop. WGS of 147 strains revealed a central genomic cluster of 76 strains, while others differed by 1–8 single-nucleotide variants from this cluster. The central genomic cluster contained strains from 2022 and 2023 obtained from patients who consumed raw horse meat. Epidemiological links and clonality of O157 strains suggested continuous contamination at the shop since 2022. Indeed, the shop lacked proper hygiene management based on hazard analysis and critical control point principles and exhibited poor sanitary conditions; however, direct evidence of the causative facility was not obtained because the suspected contaminated raw horse meat could not be sampled. This preliminary investigation highlights the importance of strict hygiene management in facilities producing meat for raw consumption and demonstrates the value of combining nationwide molecular epidemiology with field investigations to identify STEC outbreak sources. IMPORTANCE Investigations of Shiga toxin-producing Escherichia coli (STEC) foodborne outbreaks incorporating whole-genome sequencing (WGS) have not been widely conducted to date. This study demonstrated that the combination of multilocus variable-number tandem-repeat analysis, WGS, and nationwide surveillance allowed for the detection of a dispersed STEC O157 outbreak linked to raw horse meat. Simultaneously, the investigation suggested persistent and low-diversity contamination at a single meat shop over a 1-year period. This study highlights (i) how combining genomic analysis with epidemiological investigation can identify geographically widespread STEC cases, (ii) the risk posed by inadequate hygiene management in facilities producing meat for raw consumption, and (iii) the potential for STEC strains to persist with minimal genomic mutations in food or processing environments. These insights support targeted control measures such as improved sanitation, the implementation of hazard analysis and critical control point principles, and ongoing genomic surveillance to prevent similar outbreaks.
Seto et al. (Tue,) studied this question.