From Genome Inspection to Clinical Significance: Source Attribution of a Foodborne Botulism Outbreak

Background Foodborne botulism is a neuro-paralytic disease caused by the ingestion of botulinum neurotoxins (BoNTs). Given its high fatality rates and economic consequences, prompt management of human cases requires collaboration among public health authorities, supporting hospitals in rapid diagnosis, food inspections, and formal analysis. This study aims to investigate the food source responsible for a botulism outbreak in Northern Italy, which resulted in the hospitalization of a person. Methods Faecal specimen from the patient, and suspected food were collected (industrial-made asparagus cream, both packages consumed and still closed). BoNT presence and identification was performed by mouse-test. After the enrichment in TPGY broth, samples were plated on CMM medium to observe the proteolysis, and on EYA medium for colonies isolation. DNA was extracted and genome was sequenced by Illumina MiSeq. Typing was performed by MLST. SNP-based phylogenetic analysis was conducted, including isolated strains from outbreaks occurred in the same year and geographic area. Results The strains were identified as group I proteolytic Clostridium botulinum, with BoNTB responsible for the outbreak. Faeces and the ingested food exhibited the same Sequence Type (ST178), differing by only one SNP. Notably, the closed package had a distinct ST (ST29), and a significant divergence from the outbreak strains (7282 SNPs). Conversely, the other strains displayed SNP differences ranging from 11116 to 46536. Conclusions Genome characterization enabled the identification of the outbreak source as the ingestion of BoNTB present in asparagus cream, suggesting also the circulation of several different strains of Cl. botulinum causing foodborne outbreaks. These findings highlight the ongoing public health concern of foodborne botulism, even in industrial-processed foods. Our study underscores the importance of source attribution and effective outbreak management in preventing hazardous botulism outbreaks. Key messages • Genome sequencing enabled the source identification of a foodborne outbreak caused by Cl. botulinum toxin B. • Our study emphasizes the current significance of foodborne botulism as a public health issue.