title: 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.
abstract: BACKGROUND
  Necrotizing 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.
  
  
  OBJECTIVE
  To confirm the previous findings by sequencing a larger number of C. butyricum genomes and using other genotyping approaches.
  
  
  METHODS
  The 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).
  
  
  RESULTS
  The 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.
  
  
  CONCLUSIONS
  MST is a fast, cheap and effective genotyping method for investigating NEC outbreaks associated with C. butyricum.
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, France.
authors.forename: S
authors.initials: S
authors.lastname: Benamar
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, France.
authors.forename: N
authors.initials: N
authors.lastname: Cassir
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, France.
authors.forename: V
authors.initials: V
authors.lastname: Merhej
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, France.
authors.forename: P
authors.initials: P
authors.lastname: Jardot
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, France.
authors.forename: C
authors.initials: C
authors.lastname: Robert
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, France.
authors.forename: D
authors.initials: D
authors.lastname: Raoult
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, France. Electronic address: bernard.la-scola@univ-amu.fr.
authors.forename: B
authors.initials: B
authors.lastname: La Scola
mesh_terms: D000328:Adult; D000368:Aged; D002648:Child; D002675:Child, Preschool; D003015:Clostridium Infections / Q000453:epidemiology / Q000382:microbiology*; D046972:Clostridium butyricum / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D016000:Cluster Analysis; D020345:Enterocolitis, Necrotizing / Q000453:epidemiology / Q000382:microbiology*; D005243:Feces / Q000382:microbiology; D005838:Genotype; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D017720:Molecular Epidemiology; D058889:Molecular Typing / Q000379:methods*
keywords: Clostridium butyricum; In-silico multi-locus sequence typing; Multi-spacer sequence typing; Necrotizing enterocolitis; Outbreak; Whole-genome sequencing