This is the home of the Global Typhoid Genomics Consortium on github
- Encourage prompt sharing of typhoid genome data for public health benefit
- Facilitate the extraction and reporting of key data of public health relevance
- Promote and facilitate the dissemination and use of information derived from typhoid genomic data to monitor antimicrobial resistance and post-vaccination impact
For more info or to join the Consortium (membership is open to all) - see here for more info.
- Genotyphi scheme and typing tools: GitHub Repo - GenoTyphi
- Consortium Metadata Template: Google Sheet - bit.ly/typhiMeta
- TyphiNET dashboard for interactive exploration of genotype and AMR prevalences, estimated from the consortium data:
- Dashboard: TyphiNET
- Code: GitHub Repo - TyphiNET
- Paper: Global diversity and antimicrobial resistance of typhoid fever pathogens: insights from 13,000 Salmonella Typhi genomes
- Data, code & figures: GitHub Repo - TyphoidGenomicsConsortiumWG1
- Assemblies (13,000 genomes): Figshare - Fasta files
- Paper and analysis is in development
- Typhi Mykrobe code: GitHub Repo - GenoTyphi
- Technical report: GenoTyphi Implementation in Mykrobe
- Typhi Pathogenwatch (described in this paper) - Analyse your own Typhi genomes, and interactively explore public genomes curated by the Consortium