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Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes.

Megan E Carey | Zoe A Dyson | Danielle J Ingle | Afreenish Amir | Mabel K Aworh | Marie Anne Chattaway | Ka Lip Chew | John A Crump | Nicholas A Feasey | Benjamin P Howden | Karen H Keddy | Mailis Maes | Christopher M Parry | Sandra Van Puyvelde | Hattie E Webb | Ayorinde Oluwatobiloba Afolayan | Anna P Alexander | Shalini Anandan | Jason R Andrews | Philip M Ashton | Buddha Basnyat | Ashish Bavdekar | Isaac I Bogoch | John D Clemens | Kesia Esther da Silva | Anuradha De | Joep de Ligt | Paula Lucia Diaz Guevara | Christiane Dolecek | Shanta Dutta | Marthie M Ehlers | Louise Francois Watkins | Denise O Garrett | Gauri Godbole | Melita A Gordon | Andrew R Greenhill | Chelsey Griffin | Madhu Gupta | Rene S Hendriksen | Robert S Heyderman | Yogesh Hooda | Juan Carlos Hormazabal | Odion O Ikhimiukor | Junaid Iqbal | Jobin John Jacob | Claire Jenkins | Dasaratha Ramaiah Jinka | Jacob John | Gagandeep Kang | Abdoulie Kanteh | Arti Kapil | Abhilasha Karkey | Samuel Kariuki | Robert A Kingsley | Roshine Mary Koshy | A C Lauer | Myron M Levine | Ravikumar Kadahalli Lingegowda | Stephen P Luby | Grant Austin Mackenzie | Tapfumanei Mashe | Chisomo Msefula | Ankur Mutreja | Geetha Nagaraj | Savitha Nagaraj | Satheesh Nair | Take K Naseri | Susana Nimarota-Brown | Elisabeth Njamkepo | Iruka N Okeke | Sulochana Putli Bai Perumal | Andrew J Pollard | Agila Kumari Pragasam | Firdausi Qadri | Farah N Qamar | Sadia Isfat Ara Rahman | Savitra Devi Rambocus | David A Rasko | Pallab Ray | Roy Robins-Browne | Temsunaro Rongsen-Chandola | Jean Pierre Rutanga | Samir K Saha | Senjuti Saha | Karnika Saigal | Mohammad Saiful Islam Sajib | Jessica C Seidman | Jivan Shakya | Varun Shamanna | Jayanthi Shastri | Rajeev Shrestha | Sonia Sia | Michael J Sikorski | Ashita Singh | Anthony M Smith | Kaitlin A Tagg | Dipesh Tamrakar | Arif Mohammed Tanmoy | Maria Thomas | Mathew S Thomas | Robert Thomsen | Nicholas R Thomson | Siaosi Tupua | Krista Vaidya | Mary Valcanis | Balaji Veeraraghavan | François-Xavier Weill | Jackie Wright | Gordon Dougan | Silvia Argimón | Jacqueline A Keane | David M Aanensen | Stephen Baker | Kathryn E Holt | Global Typhoid Genomics Consortium Group Authorship
eLife | 2023

The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000).

Pubmed ID: 37697804

Research resources used in this publication

None found

Additional research tools detected in this publication

Antibodies used in this publication

None found

Associated grants

  • Agency: NIAID NIH HHS, United States
    Id: F30 AI156973
  • Agency: Biotechnology and Biological Sciences Research Council, United Kingdom
    Id: BBS/E/F/00PR10348
  • Agency: NIAID NIH HHS, United States
    Id: U19 AI110820
  • Agency: Biotechnology and Biological Sciences Research Council, United Kingdom
    Id: BB/R012504/1
  • Agency: FIC NIH HHS, United States
    Id: R01 TW009237
  • Agency: NIAID NIH HHS, United States
    Id: U01 AI062563
  • Agency: Medical Research Council, United Kingdom
    Id: MR/TOO5033/1
  • Agency: Wellcome Trust, United Kingdom
    Id: 206545/7/17/Z
  • Agency: Wellcome Trust, United Kingdom
    Id: 106158/7/14/Z
  • Agency: NIAID NIH HHS, United States
    Id: R01 AI099525
  • Agency: World Health Organization, International
    Id: 001
  • Agency: NIAID NIH HHS, United States
    Id: R01 AI121378
  • Agency: Wellcome Trust, United Kingdom
    Id: 206194
  • Agency: Medical Research Council, United Kingdom
    Id: MR/L00464X/

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NCBI BioProject (tool)

RRID:SCR_004801

Database of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. It is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. Submissions are supported by a web-based Submission Portal. The database facilitates organization and classification of project data submitted to NCBI, EBI and DDBJ databases that captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. BioProject records link to corresponding data stored in archival repositories. The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource. The redesign adds tracking of several data elements including more precise information about a project''''s scope, material, and objectives. Genome Project identifiers are retained in the BioProject as the ID value for a record, and an Accession number has been added. Database content is exchanged with other members of the International Nucleotide Sequence Database Collaboration (INSDC). BioProject is accessible via FTP.

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PubMed (tool)

RRID:SCR_004846

Public bibliographic database that provides access to citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. PubMed citations and abstracts include fields of biomedicine and health, covering portions of life sciences, behavioral sciences, chemical sciences, and bioengineering. Provides access to additional relevant web sites and links to other NCBI molecular biology resources. Publishers of journals can submit their citations to NCBI and then provide access to full-text of articles at journal web sites using LinkOut.

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ggplot2 (tool)

RRID:SCR_014601

Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.

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