BTyper3

BTyper3 performs taxonomic classification of Bacillus cereus group genomes, assigning isolates to genomospecies, subspecies, biovars, and panC groups to support a standardized nomenclature for Bacillus cereus sensu lato (B. cereus s.l.).

Key Features:

• Genomospecies-subspecies-biovar framework: Implements the proposed genomospecies-subspecies-biovar classification to standardize nomenclature within the B. cereus group.
• Average Nucleotide Identity (ANI): Leverages ANI for genomospecies and subspecies assignments.
• MLST support: Uses multi-locus sequence typing (MLST) and MLST-derived sequence types to infer genomospecies classifications when WGS is unavailable.
• panC group assignment: Implements a refined eight-group panC framework that aligns with the eight-genomospecies taxonomy and resolves prior seven-group inconsistencies.
• rpoB allelic typing: Performs rpoB allelic typing for lineage assignment within the B. cereus group.
• Virulence factor detection: Detects virulence factors to inform assessments of pathogenic potential.
• Pseudo-gene flow units: Categorizes genomes into pseudo-gene flow units within proposed genomospecies.
• Input data types: Supports whole-genome sequencing (WGS), MLST, and panC data for taxonomic assignment.

Scientific Applications:

• Species- and subspecies-level assignment: Assigns B. cereus s.l. isolates to genomospecies and subspecies using ANI and complementary typing data.
• Genomospecies inference from MLST: Enables determination of genomospecies from MLST-derived sequence types when WGS is not available.
• panC-based grouping: Resolves panC group assignments using a refined eight-group framework consistent with genomospecies designations.
• Pathogenicity assessment: Identifies virulence factors to aid inference of pathogenic potential among isolates.
• Population structure analysis: Assigns genomes to pseudo-gene flow units to delineate population subdivisions within genomospecies.

Methodology:

Uses average-nucleotide identity (ANI) for genomospecies and subspecies assignments, MLST-derived sequence types for genomospecies inference, refined eight-group panC assignment, rpoB allelic typing, virulence factor detection, and categorization into pseudo-gene flow units.