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

Abstract

The <i>Bacillus cereus</i> 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) <i>panC</i> clade typing, and (iv) <i>rpoB</i> allelic typing to rapidly classify <i>B. cereus</i> group isolates using nucleotide sequencing data. BTyper was applied to a set of 662 <i>B. cereus</i> group genome assemblies to (i) identify anthrax-associated genes in non-<i>B. anthracis</i> members of the <i>B. cereus</i> group, and (ii) identify assemblies from <i>B. cereus</i> group strains with emetic potential. With BTyper, the anthrax toxin genes <i>cya</i>, <i>lef</i>, and <i>pagA</i> were detected in 8 genomes classified by the NCBI as <i>B. cereus</i> that clustered into two distinct groups using <i>k</i>-medoids clustering, while either the <i>B. anthracis</i> poly-γ-d-glutamate capsule biosynthesis genes <i>capABCDE</i> or the hyaluronic acid capsule <i>hasA</i> gene was detected in an additional 16 assemblies classified as either <i>B. cereus</i> or <i>Bacillus thuringiensis</i> isolated from clinical, environmental, and food sources. The emetic toxin genes <i>cesABCD</i> were detected in 24 assemblies belonging to <i>panC</i> 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<b>IMPORTANCE</b> <i>Bacillus cereus</i> 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 <i>B. cereus</i> group isolates from their pathogenic counterparts, including the human pathogen <i>Bacillus anthracis</i>, which is responsible for anthrax, as well as the insect pathogen <i>B. thuringiensis</i> 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.