Core-genome single-nucleotide polymorphism (SNP) analysis of two foodborne outbreaks caused by the Bacillus cereus group in Japan

Foodborne outbreaks caused by the Bacillus cereus group remain a public health concern, yet genome-based outbreak investigations in Japan remain limited. Whole-genome sequencing (WGS) and core-genome single-nucleotide polymorphism (cgSNP) analyses were used to characterize two foodborne outbreaks that occurred in Okinawa Prefecture, Japan, in 2021 (OB1) and 2022 (OB2). From the two outbreaks, 30 cereulide synthetase gene-positive isolates from patients, implicated foods (OB1 only), and food preparation environments were analyzed. All isolates were classified as B. paranthracis and were assigned to sequence type 26 (ST26) and panC group III. Although the two outbreaks involved B. paranthracis ST26 isolates and appeared similar by conventional typing, cgSNP analysis revealed low within-outbreak diversity (0–2 SNPs in OB1; 0–3 SNPs in OB2), while clearly separating the two outbreaks (353–356 SNPs), indicating that genetically distinct strains caused two outbreaks occurring one year apart in the same prefecture. In OB1, cgSNP clustering supported source attribution by linking the isolates from patients, foods, and the environment to the implicated catering facility. Overall, WGS-based SNP analysis enabled high-resolution discrimination and strengthened the epidemiological interpretation of the B. cereus group outbreak investigations.