Bacillus cereus group in sufu: Traceability, potential pathogenicity and antibiotic resistance based on 175 strains whole-genome sequencing

This study investigated species composition, contamination sources, pathogenic potential, and antibiotic resistance of 175 Bacillus cereus group strains isolated from sufu samples, raw and auxiliary materials, production line, and processing environments using whole-genome sequencing and phenotypic analysis. Six species were identified, primarily B . cereus , Bacillus pacificus , and Bacillus paranthracis . Multilocus sequence typing identified 66 sequence types (STs), including 19 novel STs. Traceability analysis demonstrated that the production environment is a likely reservoir for B . pacificus ST90 contamination, while ST2567 in the production environment may cause B . paranthracis contamination. All strains harbored diarrheal virulence genes, whereas no emetic toxin genes were found. Moreover, B . pacificus and B . paranthracis almost lack hblCDA compared to B . cereus . Twelve antibiotic resistance genes were identified, mainly fosB , followed by BcII . Notably, 77.71% contained 3 or more distinct resistance gene classes. Thirty-seven isolates exhibited phenotypic resistance, primarily to tetracycline and chloramphenicol (CHL), including 3 multidrug-resistant isolates and 1 CHL-resistant B . pacificus from sufu. Genome-wide association studies and functional protein annotation indicated associations between resistance phenotypes and genotypes. This study provides the first systematic genomic analysis of the B . cereus group throughout sufu production, supporting risk assessment and targeted control of fermented soybean products.