The TyphiNET data visualisation dashboard: Unlocking Salmonella Typhi genomics data to support public health

Background Salmonella enterica subspecies enterica serovar Typhi (abbreviated as ‘Typhi’) is the bacterial agent of typhoid fever. Effective antimicrobial therapy reduces complications and mortality; however, antimicrobial resistance (AMR) is a major problem in many endemic countries. Prevention through vaccination is possible through recently-licensed Gavi-supported typhoid conjugate vaccines (TCVs), and national immunisation programs are currently being considered or deployed in several countries where AMR prevalence is known to be high. Pathogen whole genome sequence data are a rich source of information on Typhi variants (genotypes or lineages), AMR prevalence, and mechanisms. However, this information is currently not readily accessible to non-genomics experts, including those driving vaccine implementation or empirical therapy guidance. Results We developed TyphiNET (), an interactive online dashboard for exploring Typhi genotype and AMR distributions derived from publicly available pathogen genome sequences. TyphiNET allows users to explore country-level summaries such as the frequency of pathogen lineages, temporal trends in resistance to clinically relevant antimicrobials, and the specific variants and mechanisms underlying emergent AMR trends. User-driven plots and session reports can be downloaded for ease of sharing. Importantly, TyphiNET is populated by high-quality genome data curated by the Global Typhoid Pathogen Genomics Consortium, analysed using the Pathogenwatch platform, and identified as coming from non-targeted sampling frames that are suitable for estimating AMR prevalence amongst Typhi infections (no personal data is included in the platform). As of February 2024, data from a total of n=11,836 genomes from 101 countries are available in TyphiNET. We outline case studies illustrating how the dashboard can be used to explore these data and gain insights of relevance to both researchers and public health policy-makers. Conclusions The TyphiNET dashboard provides an interactive platform for accessing genome-derived data on pathogen variant frequencies to inform typhoid control and intervention strategies. The platform is extensible in terms of both data and features, and provides a model for making complex bacterial genome-derived data accessible to a wide audience. ### Competing Interest Statement KLC has received consultancy payments from Pfizer, travel support from BD, and is a member of the Society for Infectious Disease (Singapore). Robert SH was a chair for a Phase I/II/III studies to determine efficacy, safety and immunogenicity of the candidate Coronavirus Disease (COVID-19) vaccine ChAdOx1 nCoV-19, and a chair for a Phase 1 Clinical Study to Determine the Safety and Immunogenicity of a Novel GMMA Vaccine Against Invasive Non-Typhoid Salmonella. Robert SH is also an executive board member of the International Society of Infectious Diseases, a member of the Infection & Immunity Board for the MRC/UKRI, and a member of the NIHR Global Health Research Professorships Committee. MML was a co-developer of a Trivalent Salmonella (Enteritidis/Typhimurium/Typhi Vi) conjugate vaccine with Bharat Biotech International and the Wellcome Trust. MML has also received payments from Pfizer for consultancy work. MML holds US patents for Compositions and Methods for Producing Bacterial Conjugate Vaccines. MML was a member of a NIH DSMB that oversaw US government-funded efficacy trials of COVID-19 vaccines. DSMB was disbanded after several vaccines were given Emergency Use Authorization. MML was a member of the Vaccines and Related Biological Products Advisory Committee of the FDA. CAM holds a patent for Salmonella conjugate vaccines and was an employee of Novartis Vaccines Institute for Global Health. INO has received payments from the Wellcome Trust for consultancy work (review panel member). INO receives royalties for books or book chapters published via Springer, Cornell University Press, and Oxford University Press. INO has received travel support from BMGF, ESCMID, and the American ASM. INFO has held leadership or advisory roles for Wellcome SEDRIC, the BMGF surveillance advisory group, the Thomas Bassir Biomedical Foundation, and International Centre for Antimicrobial Resistance Solutions (ICARS) Technical Advisory Forum. INO has also been the surveillance lead for the AMR Technical Work Group, Nigeria Center for Disease Control, the commissioner for The Lancet Commission for Nigeria, a scientific advisor for The Lancet Infectious Diseases, a senior editor for Microbial Genomics, and the editor in chief of the African Journal of Laboratory Medicine. AJP has been involved an Oxford University partnership with AZ for development of COVI19 vaccines. AJP has received payments for consultancy work from Shionogi. AJP is chair of DHSCs Joint Committee on Vaccination and Immunisation, and was a member of WHOs SAGE. MAC received support for travel from UKHSA, HEE and NIHR. JAC received support from BMGF, US NIH, and the WHO. NAF holds an NIHR Global Health Professorship. ARG received support from BMGF.