Global Typhoid Genomics Consortium

This is the home of the Global Typhoid Genomics Consortium on github

Consortium goals are to:

• 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.

Tools and resources

• 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

Working Group 1: 21-years of Typhoid Genomics - Epidemiology and Descriptive Stats

• 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

Working Group 2: 21-years of Typhoid Genomics - Phylodynamics

• Paper and analysis is in development

Working Group 3: Typhi Mykrobe implementation

• Typhi Mykrobe code: GitHub Repo - GenoTyphi
• Technical report: GenoTyphi Implementation in Mykrobe

Other resources

• Typhi Pathogenwatch (described in this paper) - Analyse your own Typhi genomes, and interactively explore public genomes curated by the Consortium