Biopesticide-associated Bacillus thuringiensis on retail fresh produce: occurrence, typing and implications for food-safety surveillance

Bacillus thuringiensis is one of the most widely used microbial biopesticides and is likely to gain further relevance in the transformation of agrifood systems. However, as a member of B. cereus sensu lato ( B. cereus s.l. ), B. thuringiensis may harbor enterotoxin genes associated with diarrheal illness, raising food-safety concerns about its presence on minimally processed fresh produce. This study aimed to generate a surveillance-oriented retail dataset on the prevalence and genetic diversity of B. thuringiensis on retail fresh produce. A total of 280 fresh produce samples, including leafy greens, vegetables, and fruits, were collected from a retail distribution center in Switzerland, and presumptive B. cereus s.l. was enumerated according to ISO 7932:2004 (limit of detection, 5 CFU/g). Presumptive B. cereus s.l. isolates were subjected to PCR-based profiling of enterotoxin genes, and B. thuringiensis -associated insecticidal toxin genes ( cry genes). Selected isolates were further characterized by Fourier transform infrared (FTIR) spectroscopy for clustering, and a subset was analyzed by whole-genome sequencing for high-resolution comparison with commercially used biopesticide strains. B. thuringiensis was detected in 22% of produce samples and occurred at comparable frequencies across produce categories. Isolates predominantly showed biopesticide-associated profiles, and 20 out of 22 sequenced B. thuringiensis isolates showed close genomic relatedness to commercially used biopesticide strains. These findings provide a surveillance-relevant retail baseline for biopesticide-associated B. thuringiensis on fresh produce. The observed profiles are consistent with residues from B. thuringiensis -based biopesticides contributing to its occurrence at retail. Together, the results support improved interpretation of B. cereus s.l. findings in fresh-produce monitoring.