Population structure of Bacillus cereus sensu lato associated with foodborne outbreaks in France between 2004 and 2023

Bacillus cereus sensu lato (Bcsl) is a group of closely related bacterial species known for their resistant spores, enabling them to persist in a dormant state and thereby colonize and adapt across diverse environments. Bcsl is known for its harmful impact on human health, producing toxins that cause emetic and diarrheal syndromes or provoking extradigestive infections. Importantly, Bcsl is the most frequent confirmed or presumptive causative agent associated with foodborne outbreaks (FBOs) in France. In our study, we assessed the population structure of a large collection of Bcsl isolated during FBOs investigation in France between 2004 and 2023, focusing on the association between distinct populations and food categories. Using 294 genomes from 183 FBOs, we applied genomic clustering and phylogenomic analysis and then identified three predominant Bcsl populations. B. cereus sensu stricto (17.0 %) prevailed in composite dishes, B. paranthracis (16.1 %) was positively associated with cereals, and B. thuringiensis subsp. kurstaki (7.6 %) was predominantly found in vegetable-based salads. Some strains were phylogenetically closely related to clinical isolates, highlighting the need to assess the antibiotic susceptibility of Bcsl. Notably, one Bcsl clade, B. cytotoxicus, lacking beta-lactamase-encoding genes showed a greatly increased sensitivity to ampicillin than other Bcsl considered to be naturally resistant to beta-lactams. Additionally, various strains from distinct populations showed reduced susceptibility to macrolides and cyclins. Finally, accurately differentiated populations will be used in further epidemiological studies and in dose-response modeling.