MGT

MGT assigns hierarchical multi-locus genotypes to Vibrio cholerae genomes to resolve genetic relationships and transmission patterns at global and local scales.

Key Features:

• Hierarchical levels: Eight hierarchical levels (MGT1–MGT8) provide increasing resolution from broad to fine genotype distinctions.
• Locus composition: MGT1 analyzes seven loci, while MGT8 employs a 3,759-locus core genome specific to the seventh pandemic (7P).
• Genome dataset: Built from analysis of over 5,771 V. cholerae genomes to capture genetic relationships and transmission patterns.
• Resolution mapping: Lower levels (MGT1–MGT4) recapitulate large-scale 7P transmission trends across continents, and higher levels (MGT5–MGT8) differentiate subgroups within national outbreaks.
• Non-7P classification: Classifies non-7P strains by delineating continental and regional distributions using MGT2 and MGT3 within large non-7P MGT1 types.
• Genotype grouping: Groups isolates by ctxB, tcpA, and ctxB-tcpA genotypes to analyze virulence trends within the 7P over time.
• Nomenclature: Employs a stable, transferable nomenclature system for direct comparison across studies.

Scientific Applications:

• Outbreak source identification: Enabled retrospective confirmation of the Nepalese origin of the 2010 Haiti outbreak.
• Epidemiological surveillance: Supports rapid identification of genetic similarities among V. cholerae isolates to determine outbreak origins.
• Public health support: Provides a genomic classification system that aids local and global cholera control decision-making, aligning with the WHO "Ending Cholera" initiative.

Methodology:

MGT is structured into eight hierarchical levels (MGT1–MGT8); MGT1 analyzes seven loci and MGT8 uses a 3,759-locus core genome specific to the 7P. Analyses were performed on over 5,771 V. cholerae genomes. Isolates are grouped by ctxB, tcpA, and ctxB-tcpA genotypes, and non-7P strains are classified using MGT2 and MGT3 within large non-7P MGT1 types; a stable, transferable nomenclature is used for cross-study comparisons.