Whole-genome sequencing-based typing methods for <i>Clostridium butyricum</i> strains from clinical, animal, plant, and environmental sources

<i>Clostridium butyricum</i> has been identified in fecal samples from both asymptomatic neonates and cases of necrotizing enterocolitis (NEC). Using a large collection of strains from different origins and spatiotemporal contexts, we developed and established a cgMLST scheme for the molecular typing of <i>C. butyricum</i>. Our results show that most <i>C. butyricum</i> strains cluster independently of origin and spatiotemporal context factors. However, specific cgMLST clades of <i>C. butyricum</i> were found for plant and botulinum neurotoxin type E strains. Clonal strains were also identified. No specific cgMLST clade was found to be genetically associated with NEC. cgSNP showed higher discriminatory power compared to cgMLST. Importantly, cgSNP provided better discriminatory power for strain relatedness with respect to strains isolated from NEC patients.