Rapid, high-throughput identification of anthrax-causing and emetic Bacillus cereus group genome assemblies using BTyper, a computational tool for virulence-based classification of Bacillus cereus group isolates using nucleotide sequencing data.

The Bacillus cereus group comprises nine species, several of which are pathogenic. Differentiating between isolates that may cause disease and those that do not is a matter of public health and economic importance, but can be particularly challenging due to the high genomic similarity of the group. To this end, we have developed BTyper, a computational tool that employs a combination of (i) virulence gene-based typing, (ii) multi-locus sequence typing (MLST), (iii) panC clade typing, and (iv) rpoB allelic typing to rapidly classify B. cereus group isolates using nucleotide sequencing data. BTyper was applied to a set of 662 B. cereus group genome assemblies to (i) identify anthrax-associated genes in non-B. anthracis members of the B. cereus group, and (iI) identify assemblies from B. cereus group strains with emetic potential. With BTyper, anthrax toxin genes cya, lef and pagA were detected in 8 genomes classified in NCBI as B. cereus that clustered into two distinct groups using k-medoids clustering, while B. anthracis poly-γ-D-glutamate capsule biosynthesis genes capABCDE or hyaluronic acid capsule gene hasA were detected in an additional 16 assemblies classified as either B. cereus or B. thuringiensis isolated from clinical, environmental, and food sources. Emetic toxin genes cesABCD were detected in 24 assemblies belonging to panC clades III and VI that had been isolated from food, clinical, and environmental settings. The command line version of BTyper is available at https://github.com/lmc297/BTyper In addition, BMiner, a companion application for analyzing multiple BTyper output files in aggregate, can be found at https://github.com/lmc297/BMinerImportanceBacillus cereus is a foodborne pathogen that is estimated to cause tens of thousands of illnesses each year in the United States alone. Even with molecular methods, it can be difficult to distinguish non-pathogenic B. cereus group isolates from their pathogenic counterparts, including the human pathogen B. anthracis, which is responsible for anthrax, as well as insect pathogen B. thuringiensis By using the variety of typing schemes employed by BTyper, users can rapidly classify, characterize, and assess the virulence potential of any isolate using its nucleotide sequencing data.