title: New Insights into the Genetic Diversity of Clostridium botulinum Group III through Extensive Genome Exploration.
abstract: Animal botulism is caused by group III Clostridium botulinum strains producing type C and D toxins, or their chimeric forms C/D and D/C. Animal botulism is considered an emerging disease in Europe, notably in poultry production. Before our study, 14 genomes from different countries were available in the public database, but none were from France. In order to investigate the genetic relationship of French strains with different geographical areas and find new potential typing targets, 17 strains of C. botulinum group III were sequenced (16 from France and one from New Caledonia). Fourteen were type C/D strains isolated from chickens, ducks, guinea fowl and turkeys and three were type D/C strains isolated from cattle. The New Caledonian strain was a type D/C strain. Whole genome sequence analysis showed the French strains to be closely related to European strains from C. botulinum group III lineages Ia and Ib. The investigation of CRISPR sequences as genetic targets for differentiating strains in group III proved to be irrelevant for type C/D due to a deficient CRISPR/Cas mechanism, but not for type D/C. Conversely, the extrachromosomal elements of type C/D strains could be used to generate a genetic ID card. The highest level of discrimination was achieved with SNP core phylogeny, which allowed differentiation up to strain level and provide the most relevant information for genetic epidemiology studies and discrimination.
authors.affiliation: Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety - Université Paris-Est Maisons-Alfort, France.
authors.forename: Cédric
authors.initials: C
authors.lastname: Woudstra
authors.affiliation: Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan-Plouzané Laboratory, UEB, French Agency for Food, Environmental and Occupational Health & SafetyPloufragan, France; l'UBL Université Bretagne LoireRennes, France.
authors.forename: Caroline
authors.initials: C
authors.lastname: Le Maréchal
authors.affiliation: l'UBL Université Bretagne LoireRennes, France; Avian and Rabbit Epidemiology and Welfare Unit, Ploufragan-Plouzané Laboratory, UEB, French Agency for Food, Environmental and Occupational Health & SafetyPloufragan, France.
authors.forename: Rozenn
authors.initials: R
authors.lastname: Souillard
authors.affiliation: Laboratoire Public Conseil, Expertise et Analyse en Bretagne Ploufragan, France.
authors.forename: Marie-Hélène
authors.initials: MH
authors.lastname: Bayon-Auboyer
authors.affiliation: Veterinary Diagnostic Laboratory, Laboratoires Officiels Vétérinaires, Agroalimentaires et Phytosanitaires, La Direction des Affaires Vétérinaires Païta, New Caledonia.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Mermoud
authors.affiliation: Veterinary Diagnostic Laboratory, Laboratoires Officiels Vétérinaires, Agroalimentaires et Phytosanitaires, La Direction des Affaires Vétérinaires Païta, New Caledonia.
authors.forename: Denise
authors.initials: D
authors.lastname: Desoutter
authors.affiliation: Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety - Université Paris-Est Maisons-Alfort, France.
authors.forename: Patrick
authors.initials: P
authors.lastname: Fach
keywords: CRISPR; Clostridium botulinum group III; animal botulism; phage; whole genome sequencing