S Benamar1, N Cassir1, V Merhej1, P Jardot1, C Robert1, D Raoult1, B La Scola2. 1. 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. 2. 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.
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. AIM: 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). FINDINGS: 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. CONCLUSION: MST is a fast, cheap and effective genotyping method for investigating NEC outbreaks associated with C. butyricum.
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. AIM: 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). FINDINGS: 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. CONCLUSION: MST is a fast, cheap and effective genotyping method for investigating NEC outbreaks associated with C. butyricum.
Authors: Sarah Benabdelkader; Julien Andreani; Alexis Gillet; Elodie Terrer; Marion Pignoly; Herve Chaudet; Gerard Aboudharam; Bernard La Scola Journal: PLoS One Date: 2019-03-11 Impact factor: 3.240
Authors: Michel Hosny; Jacques Yaacoub Bou Khalil; Aurelia Caputo; Rita Abou Abdallah; Anthony Levasseur; Philippe Colson; Nadim Cassir; Bernard La Scola Journal: Sci Rep Date: 2019-02-14 Impact factor: 4.379