Genomic characterisation and traceability analysis of a Clostridium botulinum strain involved in a food poisoning incident.

Objective: To identify the source of Clostridium botulinum (C. botulinum) involved in a food poisoning case in Kunming and analyze its molecular characteristics.

Results: This study examined samples from a clustered food poisoning incident, including pickled pig liver consumed by three patients, hospital vomit from a deceased patient, and household waste mixed with vomit. Enrichment culture, microscopic examination, and real-time quantitative PCR confirmed the presence of C. botulinum (designated KM001) with type E botulinum toxin. The full-length genomic sequence of this strain was obtained through second and third-generation sequencing, revealing a genome size of 3,713,470 bp. KEGG annotation indicated that 1,840 single genes were assigned to 44 KEGG pathways. Whole-genome sequencing revealed genetic diversity among toxin gene clusters, with 94.76% homology to C. botulinum E3 strain (Alaska E43) and 93.65% homology to C. botulinum B strain (Eklund 17B, NRP). Evolutionary analysis, incorporating complete genomes of foodborne and environmental C. botulinum strains worldwide along with KM001, showed stronger phylogenetic affinity of KM001 to other type E strains.

Conclusion: Overall, this study identified KM001 as the causative agent in a food poisoning incident, marking the first report of type E botulinum toxin poisoning in the region. Genomic analysis revealed the serotype and genetic diversity among toxin gene clusters, providing insights into its gene function, virulence, and evolutionary relationships. Understanding the genetic relationships and evolutionary pathways of different C. botulinum strains is crucial for predicting infection risks and implementing effective control measures.The findings contribute to the documentation of botulinum toxin incidents in Yunnan, China, but do not examine the antimicrobial resistance of C. botulinum or its interactions with other microorganisms; further research is needed to address these aspects.