Whole-genome typing of Bacillus anthracis isolates by next-generation sequencing accurately and rapidly identifies strain-specific diagnostic polymorphisms

Craig A. Cummings, Christina A. Bormann Chung, Rixun Fang, Melissa Barker, Pius M. Brzoska, Phillip Williamson, Jodi A. Beaudry, Molly Matthews, James M. Schupp, David M. Wagner, Manohar R. Furtado, Paul Keim, Bruce Budowle

Research output: Contribution to journalArticle

10 Scopus citations

Abstract

In the event of bioterrorism, infectious disease outbreaks in the food supply chain, or hospital acquired infections, rapid, high-resolution genetic characterization is critical for determining the identity of the agent and attributing it to a specific source. Four Bacillus anthracis strains were sequenced to demonstrate the utility of next-generation sequencing technology, specifically the SOLiD™ system (Applied Biosystems™, Foster City, CA), for microbial forensics investigations. Reads from the B. anthracis Ames ancestor strain detected only a single false positive SNP. Of the 148 SNPs that distinguish the Ames and Sterne strains, 126 (85%) were identified with 19 of the 22 uncalled SNPs in two dense clusters that precluded mapping of reads. Three previously unsequenced, geographically distinct B. anthracis strains from the A branch lineage were found to have between 352 and 471 SNPs each, relative to the Ames ancestor reference genome. The high throughput, multiplexing capability, and accuracy of the SOLiD™ system make it suitable for rapid whole-genome typing of microbial pathogens during a forensic or epidemiological investigation.

Original languageEnglish (US)
Pages (from-to)300-301
Number of pages2
JournalForensic Science International: Genetics Supplement Series
Volume2
Issue number1
DOIs
StatePublished - Jan 1 2009

Keywords

  • Bacillus anthracis
  • Microbial forensics
  • SOLiD system
  • Sequencing

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Genetics

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    Cummings, C. A., Bormann Chung, C. A., Fang, R., Barker, M., Brzoska, P. M., Williamson, P., Beaudry, J. A., Matthews, M., Schupp, J. M., Wagner, D. M., Furtado, M. R., Keim, P., & Budowle, B. (2009). Whole-genome typing of Bacillus anthracis isolates by next-generation sequencing accurately and rapidly identifies strain-specific diagnostic polymorphisms. Forensic Science International: Genetics Supplement Series, 2(1), 300-301. https://doi.org/10.1016/j.fsigss.2009.08.097