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 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 has been focused on phylodynamic analyses with this Typhi dataset. Analyses and manuscript development are in advanced stages.
Other Active Consortium Working Groups
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.
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)
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