MGTdb

MGTdb assigns multilevel genome-typing sequence types to bacterial isolates using multiple multilocus sequence typing (MLST) schemes to enable genomic epidemiology and surveillance at multiple resolutions.

Key Features:

• Multilevel Genome Typing (MGT): Uses multiple MLST schemes (levels) to assign stable sequence types (STs) and characterize isolates at multiple resolutions.
• Input data processing: Processes sequence reads or allele data to assign MGT identifiers to isolates.
• Automated public-repository ingestion: Retrieves new sequences from the NCBI Sequence Read Archive on a daily basis and processes them to assign MGT identifiers.
• Interactive visualization and data export: Produces interactive visualizations and provides isolate assignments for external analysis.
• Pathogen-specific implementations: Includes implementations for Salmonella enterica serovars Typhimurium and Enteritidis and for Vibrio cholerae with demonstrated case studies.

Scientific Applications:

• National surveillance (S. Typhimurium): Supports long-term national surveillance analyses of Salmonella enterica serovar Typhimurium.
• Local outbreak investigation (S. Typhimurium): Enables local epidemiology and outbreak investigations of S. Typhimurium.
• Global epidemiology (V. cholerae): Supports global epidemiological analyses of Vibrio cholerae.
• Evolutionary and outbreak tracking: Assignment and analysis of MGT STs enable tracking pathogen evolution and detecting outbreaks across spatial and temporal scales.

Methodology:

Uses multiple MLST schemes to define typing levels; processes sequence reads or allele data to assign MGT identifiers; regularly retrieves new sequences from the NCBI Sequence Read Archive (daily) for automated processing; and generates interactive visualizations and exports of isolate assignments for external analysis.