Nature Communications (May 2021)
A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch
- Silvia Argimón,
- Corin A. Yeats,
- Richard J. Goater,
- Khalil Abudahab,
- Benjamin Taylor,
- Anthony Underwood,
- Leonor Sánchez-Busó,
- Vanessa K. Wong,
- Zoe A. Dyson,
- Satheesh Nair,
- Se Eun Park,
- Florian Marks,
- Andrew J. Page,
- Jacqueline A. Keane,
- Stephen Baker,
- Kathryn E. Holt,
- Gordon Dougan,
- David M. Aanensen
Affiliations
- Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus
- Corin A. Yeats
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford
- Richard J. Goater
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus
- Khalil Abudahab
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus
- Benjamin Taylor
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford
- Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus
- Leonor Sánchez-Busó
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford
- Vanessa K. Wong
- Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus
- Zoe A. Dyson
- Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus
- Satheesh Nair
- Gastrointestinal Bacterial Reference Unit, Public Health England
- Se Eun Park
- International Vaccine Institute
- Florian Marks
- International Vaccine Institute
- Andrew J. Page
- Pathogen Informatics, Wellcome Sanger Institute, Wellcome Genome Campus
- Jacqueline A. Keane
- Pathogen Informatics, Wellcome Sanger Institute, Wellcome Genome Campus
- Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge
- Kathryn E. Holt
- London School of Hygiene and Tropical Medicine
- Gordon Dougan
- Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus
- David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus
- DOI
- https://doi.org/10.1038/s41467-021-23091-2
- Journal volume & issue
-
Vol. 12,
no. 1
pp. 1 – 12
Abstract
Whole genome sequencing data are increasingly becoming routinely available but generating actionable insights is challenging. Here, the authors describe Pathogenwatch, a web tool for genomic surveillance of S. Typhi, and demonstrate its use for antimicrobial resistance assignment and strain risk assessment.
