TyphiNET

TyphiNET enables exploration of Salmonella Typhi genotype and antimicrobial resistance distributions derived from publicly available pathogen genome sequences to inform typhoid control and intervention strategies.

Key Features:

• Country-level summaries: Displays frequency of pathogen lineages and temporal trends in resistance to clinically relevant antimicrobials.
• AMR mechanism resolution: Identifies specific variants and mechanisms underlying emergent antimicrobial resistance trends.
• Data curation: Populated by high-quality genome data curated by the Global Typhoid Pathogen Genomics Consortium and analysed using the Pathogenwatch platform.
• Sampling frame filtering: Includes only genomes from non-targeted sampling frames suitable for estimating AMR prevalence amongst Typhi infections.

Scientific Applications:

• Typhoid epidemiology: Supports exploration of pathogen lineage frequencies and geographic distribution patterns.
• Antimicrobial resistance surveillance: Tracks temporal trends in resistance to guide empirical therapy guidance.
• Vaccine implementation support: Informs national immunisation program planning where antimicrobial resistance prevalence is high.
• Public health policy: Provides genome-derived insights for typhoid control and intervention strategies to researchers and policy-makers.

Methodology:

Genome data are curated by the Global Typhoid Pathogen Genomics Consortium and analysed using the Pathogenwatch platform.