Large Numbers of Single Nucleotide Polymorphisms Facilitate Fine Scale Phylogenetic Analysis of the Genetically Diverse Organism, Clostridium botulinum

Gillece J. D., Smith T. J., Hill K. K., Contente T., Schupp J. M., Engelthaler D. M.

Author address: 

TGen North, Flagstaff, AZ, 2USAMRIID, Fort Detrick, MD, Los Alamos Natl. Lab., Los Alamos, NM.

Abstract: 

Botulinum, a powerful and potentially fatal neuroparalytic toxin, is produced by Clostridium botulinum, an anaerobic, spore-forming, gram-positive microorganism that poses both a public health and national defense threat. Significant genetic diversity within C. botulinum makes meaningful phylogenetic analysis within this organism a challenge. Isolates are commonly grouped based on the serotype of botulinum toxin that they express, of which there are 7 types (from A-G) and at least 26 subtypes therein. The use of a large number of phylogenetically stable genetic markers, such as Single Nucleotide Polymorphisms (SNPs) may facilitate more accurate and meaningful fine scale phylogenetic analysis of this organism. Publicly available whole genome sequences of diverse C. botulinum isolates were used to identify SNP’s for phylogenetic analysis. 1260 SNPs were included on an Affymetrix Molecular Inversion Probe (MIP) GeneChip and used to analyze samples from multiple serotypes. Phylogenetic analysis of the resulting genotypes revealed several serotype-associated groupings strongly supported by bootstrapping analysis. In addition, the use of large numbers of SNPs provided for resolution among isolates within these serotype-associated clades. Finally, this analysis was able to resolve a number of European serotype A1 isolates from US serotype A1 isolates. These SNP data are consistent with a recent analysis of C. botulinum using VNTR loci, resulting in nearly the same level of strain differentiation, but provide an alternative analytical tool that is less susceptible to homoplasy. As described above, large numbers of SNPs has provided for fine scale serotype and phylogeographic grouping and resolution within these groups. The continued development of tools that can utilize large SNP data sets, such as MIP analysis, as well as whole genome sequencing, promise to facilitate improved epidemiological and, if needed, forensic analysis of C. botulinum.
2010

abstract No: 

Y-957

Full conference title: 

110th General Meeting American Society for Microbiology
    • ASM 110th (2010)