ArticleGenome medicine2025
The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health.
Article in Genome medicine, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Presence of globally prominent multidrug-resistant genotypes ofMicrobial genomics · 2026Article
- Integrated genomic analysis of Salmonella Typhi from Pakistan: Antimicrobial resistance determinants, pangenome structure, and reverse vaccinology-driven vaccine target discovery.Functional & integrative genomics · 2026Article
- The Potential of Bioinformatics in Revolutionizing Disease Diagnosis in Sub-Saharan Africa: A Narrative Review.Health science reports · 2026Article
- AMRnet: a data visualization platform to interactively explore pathogen variants and antimicrobial resistance.Nucleic acids research · 2026Article
- Observational
- Laboratory epidemiology ofOne health (Amsterdam, Netherlands) · 2025Article
- Conference report of the 2024 Antimicrobial Resistance Meeting.npj antimicrobials and resistance · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundSalmonella enterica subspecies enterica serovar Typhi (abbreviated as 'Typhi') is the bacterial agent of typhoid fever. Effective antimicrobial therapy reduces complications and mortality; however, antimicrobial resistance (AMR) is a major problem in many endemic countries. Prevention through vaccination is possible through recently-licensed typhoid conjugate vaccines (TCVs). National immunisation programs are currently being considered or deployed in several countries where AMR prevalence is known to be high, and the Gavi vaccine alliance has provided financial support for their introduction. Pathogen whole genome sequence data are a rich source of information on Typhi variants (genotypes or lineages), AMR prevalence, and mechanisms. However, this information is currently not readily accessible to non-genomics experts, including those driving vaccine implementation or empirical therapy guidance.
resultsWe developed TyphiNET ( https://www.typhi.net ), an interactive online dashboard for exploring Typhi genotype and AMR distributions derived from publicly available pathogen genome sequences. TyphiNET allows users to explore country-level summaries such as the frequency of pathogen lineages, temporal trends in resistance to clinically relevant antimicrobials, and the specific variants and mechanisms underlying emergent AMR trends. User-driven plots and session reports can be downloaded for ease of sharing. Importantly, TyphiNET is populated by high-quality genome data curated by the Global Typhoid Pathogen Genomics Consortium, analysed using the Pathogenwatch platform, and identified as coming from non-targeted sampling frames that are suitable for estimating AMR prevalence amongst Typhi infections (no personal data is included in the platform). As of February 2024, data from a total of n = 11,836 genomes from 101 countries are available in TyphiNET. We outline case studies illustrating how the dashboard can be used to explore these data and gain insights of relevance to both researchers and public health policy-makers.
conclusionsThe TyphiNET dashboard provides an interactive platform for accessing genome-derived data on pathogen variant frequencies to inform typhoid control and intervention strategies. The platform is extensible in terms of both data and features, and provides a model for making complex bacterial genome-derived data accessible to a wide audience.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.