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

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.