title: Clostridium botulinum Group II Isolate Phylogenomic Profiling Using Whole-Genome Sequence Data.
abstract: Clostridium botulinum group II isolates (n = 163) from different geographic regions, outbreaks, and neurotoxin types and subtypes were characterized in silico using whole-genome sequence data. Two clusters representing a variety of botulinum neurotoxin (BoNT) types and subtypes were identified by multilocus sequence typing (MLST) and core single nucleotide polymorphism (SNP) analysis. While one cluster included BoNT/B4/F6/E9 and nontoxigenic members, the other comprised a wide variety of different BoNT/E subtype isolates and a nontoxigenic strain. In silico MLST and core SNP methods were consistent in terms of clade-level isolate classification; however, core SNP analysis showed higher resolution capability. Furthermore, core SNP analysis correctly distinguished isolates by outbreak and location. This study illustrated the utility of next-generation sequence-based typing approaches for isolate characterization and source attribution and identified discrete SNP loci and MLST alleles for isolate comparison.
authors.affiliation: National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
authors.forename: K A
authors.initials: KA
authors.lastname: Weedmark
authors.affiliation: National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
authors.forename: P
authors.initials: P
authors.lastname: Mabon
authors.affiliation: National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
authors.forename: K L
authors.initials: KL
authors.lastname: Hayden
authors.affiliation: Bureau of Microbial Hazards, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada.
authors.forename: D
authors.initials: D
authors.lastname: Lambert
authors.affiliation: National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
authors.forename: G
authors.initials: G
authors.lastname: Van Domselaar
authors.affiliation: Bureau of Microbial Hazards, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada.
authors.forename: J W
authors.initials: JW
authors.lastname: Austin
authors.affiliation: National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada cindi.corbett@phac-aspc.gc.ca.
authors.forename: C R
authors.initials: CR
authors.lastname: Corbett
mesh_terms: D000818:Animals; D001483:Base Sequence; D001715:Bird Diseases / Q000382:microbiology; D001717:Birds; D001906:Botulism / Q000382:microbiology* / Q000662:veterinary*; D003014:Clostridium botulinum / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D004783:Environmental Microbiology; D005516:Food Microbiology; D016680:Genome, Bacterial; D006801:Humans; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D010802:Phylogeny