Firmesse, O. | Search bioRxiv

bioRxiv2025

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 opportunistic infections in hospitals. 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 to accurately identify predominant Bcsl populations: B. cereus sensu stricto (17.0%), B. paranthracis (16.1%), and B. thuringiensis subsp. kurstaki (7.6%), which were positively associated with composite dishes, cereals, and vegetable-based salads, respectively. 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, some strains showed reduced susceptibility to macrolides and cyclins. Finally, we identified several signatures of recombination and horizontal transfer, suggesting the ability of Bcsl to share fitness-enhancing alleles and acquire virulence and antibiotic resistance genes by non-pathogenic strains. These findings would be valuable for improving the surveillance of Bcsl. HIGHLIGHTSBcsl associated with French food poisonings consist of 14 clusters. Bcss, the most frequent clade, is mainly found in composite dishes. Bcsl toxin genes are present in various clades, suggesting horizontal gene transfer. Some Bcsl linked to food poisonings or septicemia belong to the same populations. B. cytotoxicus, lacking bla genes, showed increased sensitivity to ampicillin.

microbiology↗

bioRxiv2022

Identification of genetic markers for the discrimination of Bacillus thuringiensis within the Bacillus cereus group, in the context of foodborne outbreaks

Bacillus thuringiensis (Bt), belonging to the Bacillus cereus (Bc) group, is commonly used as a biopesticide worldwide, due to its ability to produce insecticidal protein crystals during sporulation. The use of Bt, especially subspecies aizawai and kurstaki, to control pests such as Lepidoptera generally involves spraying mixtures containing spores and crystals on crops intended for human consumption. Recent studies have suggested that the consumption of commercial Bt strains may be responsible for foodborne outbreaks (FBOs). However, its genetic proximity to Bc strains has hindered the development of routine tests to discriminate Bt from other Bc, especially Bacillus cereus sensu stricto (Bc ss), also responsible for FBOs. Here, to develop tools for the detection and the discrimination of Bt in food, we carried out a genome-wide association study (GWAS) on 286 complete genomes of Bc group strains to identify and validate in silico new molecular markers specific to different Bt subtypes. The analyses led to the determination and the validation in silico of 128 molecular markers specific to Bt, its subspecies aizawai, kurstaki and four previously described proximity clusters associated with these subspecies. We developed a command line tool (https://github.com/afelten-Anses/Bt_typing) based on a 14-marker workflow for in silico Bt identification of a putative Bc genome with the aim of facilitating the discrimination of Bt from other Bc and between Bt subspecies, especially in the context of FBOs. Collectively, these data provide key elements for investigating Bc/Bt-associated FBOs and for monitoring Bt in food.

bioinformatics↗