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Background <p><i>Salmonella enterica</i> subspecies <i>enterica</i> 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.</p> Results <p>We developed TyphiNET (<a href="https://www.typhi.net">https://www.typhi.net</a>), 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 <i>n</i> = 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.</p> Conclusions <p>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.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年5月9日

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  • 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

摘要

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.