Global Typhoid Genomics Consortium

How We Work

The role of the Consortium is to encourage and assist the deposition of raw genome data into public databases (ENA or SRA) and to coordinate downstream integration of the data for public health benefit. Members retain full control over their data and when they choose to make it public. 

Consortium membership is open to anyone, contingent on signing up to a Memorandum of Understanding and Code of Ethics. Activities are coordinated by Working Groups, with oversight from a Steering Committee and Advisory Group. Details of how to join are outlined below.

The goals of the Consortium are as follows: 

1. Encourage prompt sharing of typhoid genome data for public health benefit

2. Facilitate the extraction and reporting of key data of public health relevance

3. Promote and facilitate the dissemination and use of information derived from typhoid genomic data to monitor antimicrobial resistance and post-vaccination impact

Resources & Publications

Code, data and resources developed / maintained by the Consortium are summarised here: https://github.com/typhoidgenomics

• We maintain the GenoTyphi genotyping scheme and associated genotyping tools.

• We use Typhi Pathogenwatch as the central analysis platform and database to generate inferred genotypes and AMR determinants from raw genomes, and to maintain a publicly available, continually updated interactive global phylogeny (described in this paper).

• We developed the TyphiNET genomic surveillance dashboard to provide interactive global and national reports on AMR, and to indicate the underlying genetic drivers based on the Pathogenwatch database. See this preprint.

• We have established a standardised metadata template to facilitate harmonization of source information across aggregated Typhi data.

Papers

1. An overview of the Consortium's activities and the TyphiNET dashboard, along with information on additional freely available genomic analysis and visualisation resources, has been published in OFID: "Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization." Read the paper here. 

2. The Consortium's first global genomics snapshot is published in eLife: "Global diversity and antimicrobial resistance of typhoid fever pathogens: insights from 13,000 Salmonella Typhi genomes". Read the paper here.

3. A paper describing the TyphiNET dashboard which allows interactive visualisation and exploration of the Consortium data, is preprinted in BioRxiv: "The TyphiNET data visualisation dashboard: Unlocking Salmonella Typhi genomics data to support public health". Read the preprint here.

4. A paper describing the Typhi Mykrobe genotyping tool, validated on Consortium data and including analysis of nanopore data and demonstration of AMR phenotype prediction accuracy, is preprinted in BioRxiv: "Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi". Read the preprint here.

Projects and Working Groups

Global Typhoid Genomics  Snapshot

Since the first Salmonella Typhi genome sequence was published in 2001, both sequencing technology and the pathogen population have changed radically. The Consortium set out to provide an updated global snapshot of typhoid genome diversity and AMR, to identify key international transmission events, and to introduce a mechanism for regular updates. We aimed to involve every lab that has sequenced a Typhi genome, and to engage them in a collective effort to ensure that these data are translated for maximal public health impact. Thanks to a broad network of international collaborators, we were able to include 13,000 Typhi genomes from 110 countries in these analyses. All data contributors were included in the Consortium, and many have contributed to one of two analysis working groups (see below) and associated manuscripts.

• Working Group 1: Descriptive Statistics & Data visualisation (Leads: Kat Holt & Megan Carey)

Working Group 1 conducted statistical analysis and data visualisation to generate an updated overview of global genetic and AMR distribution and trends over time. This overview was developed into a manuscript, which has now been published in eLife: "Global diversity and antimicrobial resistance of typhoid fever pathogens: insights from 13,000 Salmonella Typhi genomes." 

Read the paper here | Data and code are available here

• Working Group 2:  Phylodynamic analysis (Leads: Danielle Ingle & Zoe Dyson)

Working Group 2 has been focused on phylodynamic analyses with this Typhi dataset. Analyses and manuscript development are in advanced stages.

Other Active Consortium Working Groups

• Typhi Mykrobe Working Group (Leads: Zoe Dyson & Danielle Ingle)

This working group's objective is to validate GenoTyphi and AMR genotyping direct from sequence reads (including nanopore reads) using the kmer-based Mykrobe typing platform (code here). This builds on an initial technical report: GenoTyphi Implementation in Mykrobe.

Read the paper here | Manuscript data and code are available here | Typhi Mykrobe software available here

• Paratyphi A Genomics and Software Tools Working Group (Leads: Yogesh Hooda & Zoe Dyson)

This working group's objectives are:

• • • To conduct a global analysis of the genetic epidemiology of Paratyphi A populations, focusing on drug-resistance and transmission dynamics

    • To increase the accessibility of the Paratype genotyping software via existing open-source software platforms (e.g. Mykrobe, Pathogenwatch)

• GenoTyphi Genotyping Scheme Development and Curation Working Group (Leads: Zoe Dyson & Anton Spadar)

This working group's objectives are to:

• • • Develop criteria and processes for the addition of new genotypes to the GenoTyphi scheme

    • Formalise naming conventions for new genotypes

    • Establish consistent methods for defining a marker SNV for each new genotype

    • Maintain the open-source GenoTyphi scheme specification, defining genotypes and associated marker SNVs, and establish an appropriate schedule and process for regular updates

    • Support and facilitate regular updates of common genotyping tools (Mykrobe and Pathogenwatch) with the growing GenoTyphi scheme specification

How to join

If you are interested in joining the Global Typhoid Genomics Consortium, please first read the Memorandum of Understanding for consortium members and the associated Code of Ethics.

If you would like to register for membership, please complete the registration form and then email a signed copy of the MOU to typhinetinfo@gmail.com.

Contact us

For queries, please email typhinetinfo@gmail.com.

Feel free to watch a recording of our webinar for more information about consortium goals, activities, and how to get involved. 

You may also wish to follow us on twitter @TyphiNET and follow Coalition against Typhoid (CaT) and the Typhoid Vaccine Acceleration Consortium (TyVAC) @PreventTyphoid