Rapid, High-Throughput Identification of Anthrax-Causing and Emetic Bacillus cereus Group Genome Assemblies via BTyper, a Computational Tool for Virulence-Based Classification of Bacillus cereus Group Isolates by Using Nucleotide Sequencing Data

The 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 it can be particularly challenging due to the high genomic similarity within the group. To this end, we have developed BTyper, a computational tool that employs a combination of (i) virulence gene-based typing, (ii) multilocus sequence typing (MLST), (iii) clade typing, and (iv) allelic typing to rapidly classify group isolates using nucleotide sequencing data. BTyper was applied to a set of 662 group genome assemblies to (i) identify anthrax-associated genes in non- members of the group, and (ii) identify assemblies from group strains with emetic potential. With BTyper, the anthrax toxin genes , , and were detected in 8 genomes classified by the NCBI as that clustered into two distinct groups using -medoids clustering, while either the poly-γ-d-glutamate capsule biosynthesis genes or the hyaluronic acid capsule gene was detected in an additional 16 assemblies classified as either or isolated from clinical, environmental, and food sources. The emetic toxin genes were detected in 24 assemblies belonging to 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/BMiner 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 nonpathogenic group isolates from their pathogenic counterparts, including the human pathogen , which is responsible for anthrax, as well as the insect pathogen 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.