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As whole-genome sequencing capacity becomes increasingly decentralized, there is a growing opportunity for collaboration and the sharing of surveillance data within and between countries to inform typhoid control policies. This vision requires free, community-driven tools that facilitate access to genomic data for public health on a global scale. Here we present the Pathogenwatch scheme for Salmonella enterica serovar Typhi (S. Typhi), a web application enabling the rapid identification of genomic markers of antimicrobial resistance (AMR) and contextualization with public genomic data. We show that the clustering of S. Typhi genomes in Pathogenwatch is comparable to established bioinformatics methods, and that genomic predictions of AMR are highly concordant with phenotypic susceptibility data. We demonstrate the public health utility of Pathogenwatch with examples selected from >4,300 public genomes available in the application. Pathogenwatch provides an intuitive entry point to monitor of the emergence and spread of S. Typhi high risk clones.

Original publication





Nature communications

Publication Date





Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.


Humans, Salmonella typhi, Typhoid Fever, Bacterial Proteins, Membrane Transport Proteins, Anti-Bacterial Agents, Microbial Sensitivity Tests, Genomics, Drug Resistance, Multiple, Bacterial, Genotype, Mutation, Genome, Bacterial, Geography, Tanzania, Malawi