Multi-spacer typing as an effective method to distinguish the clonal lineage of Clostridium butyricum strains isolated from stool samples during a series of necrotizing enterocolitis cases

SummaryBackgroundNecrotizing enterocolitis (NEC) is a devastating gastrointestinal disease with high morbidity and mortality that predominantly affects preterm neonates during outbreaks. In a previous study, the present authors identified 15 Clostridium butyricum isolates from stool samples during a series of NEC cases involving four neonatal intensive care units. A clonal lineage of these strains was observed by in-silico multi-locus sequence typing.AimTo confirm the previous findings by sequencing a larger number of C. butyricum genomes and using other genotyping approaches.MethodsThe previously isolated 15 C. butyricum strains were characterized and compared with 17 other commensal and environmental C. butyricum strains using whole-genome sequencing (WGS). In addition, the clustering was analysed using multi-spacer sequence typing (MST).FindingsThe core genome of C. butyricum was composed of 1251 genes, and its pan-genome consisted of 12,628 genes with high variability between strains. It was possible to distinguish the clonal lineage of strains from a series of NEC cases, forming three clades with geographical clustering. The results obtained using WGS and MST approaches were congruent.ConclusionMST is a fast, cheap and effective genotyping method for investigating NEC outbreaks associated with C. butyricum.