Table 2.
Reference genomes used for reference-based variant calling in this study.
| Reference genome | Phylogenetic groupa | Data set(s)b | ANI rangec | NCBI accession number | Assembly level | Rationale for selection |
|---|---|---|---|---|---|---|
| B. cereus strain ATCC 14579 chromosome | IV | All 33 isolates from two groups (groups III and IV) | 98.8–98.9 (group IV) 91.8–92.3 (group III) |
NC_004722.1 | Complete Genome | B. cereus s.s. type strain; RefSeq reference genome; member of panC group IV, the same group as the three non-emetic outbreak-associated isolates sequenced in this study |
| B. cereus strain AH187 chromosome | III | All 33 isolates from two groups (groups III and IV); 30 emetic group III isolates | 92.0–92.2 (group IV) 99.8–99.9 (group III) |
NC_011658.1 | Complete Genome | Human clinical isolate associated with an emetic outbreak in 1972 (cooked rice, United Kingdom); identical virulotype, MLST sequence type, rpoB allelic type, and panC group as 30 emetic outbreak isolates sequenced in this study |
| B. cytotoxicus strain NVH 391-98 chromosome | VII | All 33 isolates from two groups (groups III and IV) | 82.6–82.7 (group IV) 82.5–82.9 (group III) |
NC_009674.1 | Complete Genome | Type strain of B. cytotoxicus, the most distant member of the B. cereus group as currently defined; shares a common ancestor with all isolates sequenced in this study |
| FOOD_10_19_16_RSNT1_2H_R9-6393 | III | 30 emetic group III isolates | 92.0–92.2 (group IV) 100d-100 (group III) |
SRR6825038 | Contigs | Emetic isolate from the outbreak reported here; assembly had high per-base coverage, as well as the fewest number of contigs of all genome assemblies from isolates in this outbreak |
a
Phylogenetic group determined via panC group assignment function in BTyper version 2.2.0.
b
Data set(s) in this study for which given genome was used as a reference genome for reference-based SNP calling.
c
Minimum and maximum average nucleotide identity (ANI) values of reference strain relative to group IV and group III genomes sequenced in this outbreak (n = 3 and 30, respectively) calculated using FastANI.
d
Minimum ANI value was <100 prior to rounding.