cgMLST and Accessory Genome Target Definitions for Investigating Bacillus cereus Bloodstream Infection Outbreaks

This dataset provides a comprehensive core genome MultiLocus Sequence Typing (cgMLST) and accessory genome scheme, generated using Ridom SeqSphere+ cgMLST Target Definer version 1.5, specifically designed for the high-resolution analysis of Bacillus cereus bloodstream infection outbreaks in hospital settings.

The scheme utilizes the Bacillus anthracis strain PR02 chromosome (NZ_CP012721) as the seed genome, complemented by eight additional related Bacillus genome sequences (GCF_000160915.1, GCF_000239195.1, GCF_002021355.1, GCF_002021695.1, GCF_013267235.1, GCF_013267775.1, GCF_016757895.1, GCF_016758415.1) for  target definition.

Taxonomic Clarification:

The nomenclature Bacillus mosaicus reflects the proposed taxonomic framework for the Bacillus cereus group, as proposed by Carroll and colleagues (2020). This classification acknowledges the extensive genomic diversity within the group, consolidating several previously recognized species, including B. anthracis, B. wiedmannii, and emetic B. cereus strains, under the B. mosaicus genomospecies. This unified approach enhances the clinical relevance of genomic data by aligning bacterial classification with observed phenotypes.   

Key Features:

cgMLST Targets: 3741 core genome targets (3,141,072 bases)

Accessory Targets: 1270 accessory genome targets (985,956 bases)

Seed Genome: Bacillus anthracis strain PR02 (NZ_CP012721)

Query Genomes: Eight additional related Bacillus genomes used for penetration and filtering.

Filtering: Targets were filtered based on length, start/stop codons, homology, gene overlap, BLAST hit criteria (100% overlap, >=90% identity), and stop codon percentage in query genomes.

Software: Generated using Ridom SeqSphere+ cgMLST Target Definer v1.5 with BLAST v2.2.12.

Genome Coverage: The cgMLST targets cover approximately 60.1% of the seed genome and between 51.8% to 59.4% of the query genomes.

Discarded Targets: 341 targets were discarded due to filtering.

References:

Carroll LM, Wiedmann M, Kovac J. Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes. mBio. 2020 Feb 25;11(1):e00034-20. doi: 10.1128/mBio.00034-20.