Clostridium botulinum Group II Isolate Phylogenomic Profiling Using Whole-Genome Sequence Data

• DOI: 10.1128/aem.01155-15
• Publication Date: 2015-06-27T12:26:52Z
• Authors: K. A. Weedmark; P. Mabon; K. L. Hayden; D. Lambert; G. Van Domselaar; J. W. Austin; C. R. Corbett
• Keywords: 0303 health sciences; Base Sequence; Bird Diseases; Molecular Sequence Data; Botulism; Birds; 03 medical and health sciences; Clostridium botulinum; Environmental Microbiology; Food Microbiology; Animals; Humans; Genome, Bacterial; Phylogeny; Multilocus Sequence Typing

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.