Characterization of Emetic and Diarrheal Bacillus cereus Strains From a 2016 Foodborne Outbreak Using Whole-Genome Sequencing: Addressing the Microbiological, Epidemiological, and Bioinformatic Challenges

Abstract

The Bacillus cereus group comprises multiple species capable of causing emetic or diarrheal foodborne illness. Despite being responsible for tens of thousands of illnesses each year in the U.S. alone, whole-genome sequencing (WGS) is not yet routinely employed to characterize <i>B. cereus</i> group isolates from foodborne outbreaks. Here, we describe the first WGS-based characterization of isolates linked to an outbreak caused by members of the <i>B. cereus</i> group. In conjunction with a 2016 outbreak traced to a supplier of refried beans served by a fast food restaurant chain in upstate New York, a total of 33 <i>B. cereus</i> group isolates were obtained from human cases (<i>n</i> = 7) and food samples (<i>n</i> = 26). Emetic (<i>n</i> = 30) and diarrheal (<i>n</i> = 3) isolates were most closely related to <i>B. paranthracis</i> (group III) and <i>B. cereus sensu stricto</i> (group IV), respectively. WGS indicated that the 30 emetic isolates (24 and 6 from food and humans, respectively) were closely related and formed a well-supported clade distinct from publicly available emetic group III genomes with an identical sequence type (ST 26). The 30 emetic group III isolates from this outbreak differed from each other by a mean of 8.3 to 11.9 core single nucleotide polymorphisms (SNPs), while differing from publicly available emetic group III ST 26 <i>B. cereus</i> group genomes by a mean of 301.7-528.0 core SNPs, depending on the SNP calling methodology used. Using a WST-1 cell proliferation assay, the strains isolated from this outbreak had only mild detrimental effects on HeLa cell metabolic activity compared to reference diarrheal strain <i>B. cereus</i> ATCC 14579. We hypothesize that the outbreak was a single source outbreak caused by emetic group III <i>B. cereus</i> belonging to the <i>B. paranthracis</i> species, although food samples were not tested for presence of the emetic toxin cereulide. In addition to showcasing how WGS can be used to characterize <i>B. cereus</i> group strains linked to a foodborne outbreak, we also discuss potential microbiological and epidemiological challenges presented by <i>B. cereus</i> group outbreaks, and we offer recommendations for analyzing WGS data from the isolates associated with them.