The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health
Year: 2025
Type: article
Abstract: 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 typhoid conjugate vaccines (TCVs). National immunisation programs are currently being considered or deployed in several countries where AMR prevalence is known to be high, and the Gavi vaccine alliance has provided financial support for their introduction. 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 ( https://www.typhi.net ), 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.
Source: Genome Medicine
Authors: Zoe A. Dyson, Louise Cerdeira, Vandana Sharma, Megan E. Carey, Kathryn E. Holt, David M. Aanensen, Ali H. Abbas, Antoine Abou Fayad, Ayorinde O. Afolayan, Niyaz Ahmed, Irshad Ahmed, Afreenish Amir, Saadia Andleeb, Silvia Argimón, Abraham Aseffa, Philip M. Ashton, Mabel K. Aworh, Ashish R. Bavdekar, Marie A. Chattaway, Ka Lip Chew, John A. Crump, Thomas C. Darton, Paula L. Diaz, Christiane Dolecek, Nicholas A. Feasey, Andrew R. Greenhill, Madhu Gupta, Mochammad Hatta, Rene S. Hendriksen, Robert S. Heyderman, Odion O. Ikhimiukor, Aamer Ikram, Danielle J. Ingle, Arti Kapil, Jacqueline A. Keane, Karen H. Keddy, Robert A. Kingsley, Myron M. Levine, Calman A. MacLennan, Mailis Maes, Jaspreet Mahindroo, Tapfumanei Mashe, Masatomo Morita, Elli Mylona, Geetha Nagaraj, Satheesh Nair, Take K. Naseri, Elisabeth Njamkepo, Sophie Octavia, Iruka N. Okeke, Michael Owusu, Maria Pardos de la Gandara, Andrew J. Pollard, Sadia I. A. Rahman, Saikt Rahman, David A. Rasko, Elrashdy M. Redwan, Assaf Rokney, Priscilla Rupali, Jean Pierre Rutanga, Jivan Shakya, Senjuti Saha, Michael J. Sikorski, Anthony M. Smith, Kaitlin A. Tagg, Neelam Taneja, Dipesh Tamrakar, Paul Turner, James E. Ussher, Sandra Van Puyvelde, Koen Vandelannoote, François-Xavier Weill, Vanessa K. Wong, Jackie Wright
Language: English
Subfield: Food Science
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $5,290
Funders: Bill and Melinda Gates Foundation, University of Otago, Wellcome Trust, National Institute for Health Research Health Protection Research Unit, National Institute for Health and Care Research, Department of Health and Social Care, University of Warwick, University of Oxford, National Institutes of Health, Centers for Disease Control and Prevention, Horizon 2020 Framework Programme, Biotechnology and Biological Sciences Research Council, National Institute of Allergy and Infectious Diseases
Awards: University of Oxford - to understand the immunological basis of susceptibility to invasive nontyphoidal Salmonella disease, and to facilitate the analysis and publication..., G1710002244, G1941985984, College of Medicine, University of Ibadan - to support the development of scientists and emerging leaders from low and middle income countries to ensure transformative solutions fully deliver..., Quadram Institute Bioscience - to generate information about Salmonella Typhi, the organism causing typhoid, in the aquatic environment of Zimbabwe, G2660568001, AMRnet, London School of Hygiene and Tropical Medicine - To harness the Fourier-Transform infrared-Attenuated total reflection (FTIR-ATR) microbiology diagnostic technology to support rapid clinical and p..., G3318240052, G3330975527, Imperial College London - To develop tools for direct detection of AMR pathogens from sewage, Thailand Africa and Asia Programme - GBP Core, Child Health Research Foundation (CHRF) - To investigate the variation in response to the pneumococcal conjugate vaccine in pre-term infants in Bangladesh using single-cell RNA sequencing, G5375049375, TyphiNET – Unlocking public health lab data on travel-associated typhoid for sentinel surveillance, G6420955438, G6425325077, University of Maryland, Baltimore - to support typhoid surveillance in Samoa during typhoid conjugate vaccine introduction, Child Health Research Foundation (CHRF) - to harness the potential of Artificial Intelligence (AI) to improve the lives of those living in low-and-middle income countries who otherwise lack..., G683092327, G7094195217, University of Maryland, Baltimore - to accelerate introduction of typhoid conjugate vaccine into Gavi-eligible countries and reduce the global burden of typhoid fever, Wellcome Trust Sanger Institute - generic account for deposition of all core- funded research papers., Child Health Research Foundation (CHRF) - to provide insight on the persistence of Salmonella Typhi, the causative organism of typhoid, in the environment in Bangladesh, Impact of a Typhoid Conjugate Vaccine Campaign on Antimicrobial Use in Harare, Zimbabwe, The Impact of Pneumococcal and Malaria Vaccines on Bacterial Resistance, Febrile Illness and Antibiotic Usage in Young Children In Malawi, G8926217196, Exploiting genetics, genomics, and immunological responses to construct novel conjugate vaccines against Salmonella Paratyphi A; an emerging global health threat, G996558070
OpenAlex ID: W4410242389