A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch
Por:
Argimón S, Yeats CA, Goater RJ, Abudahab K, Taylor B, Underwood A, Sánchez-Busó L, Wong VK, Dyson ZA, Nair S, Park SE, Marks F, Page AJ, Keane JA, Baker S, Holt KE, Dougan G and Aanensen DM
Publicada:
17 may 2021
Ahead of Print:
17 may 2021
Resumen:
As whole-genome sequencing capacity becomes increasingly decentralized, there is a growing opportunity for collaboration and the sharing of surveillance data within and between countries to inform typhoid control policies. This vision requires free, community-driven tools that facilitate access to genomic data for public health on a global scale. Here we present the Pathogenwatch scheme for Salmonella enterica serovar Typhi (S. Typhi), a web application enabling the rapid identification of genomic markers of antimicrobial resistance (AMR) and contextualization with public genomic data. We show that the clustering of S. Typhi genomes in Pathogenwatch is comparable to established bioinformatics methods, and that genomic predictions of AMR are highly concordant with phenotypic susceptibility data. We demonstrate the public health utility of Pathogenwatch with examples selected from >4,300 public genomes available in the application. Pathogenwatch provides an intuitive entry point to monitor of the emergence and spread of S. Typhi high risk clones. 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.
Filiaciones:
Argimón S:
Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
Yeats CA:
Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
Goater RJ:
Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
Abudahab K:
Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
Taylor B:
Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
Underwood A:
Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
:
Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain
Wong VK:
Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
Dyson ZA:
Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
London School of Hygiene and Tropical Medicine, London, UK
Department of Infectious Diseases, Monash University, Melbourne, Australia
Nair S:
Gastrointestinal Bacterial Reference Unit, Public Health England, Colindale, London, UK
Park SE:
International Vaccine Institute, Seoul, Republic of Korea
Marks F:
International Vaccine Institute, Seoul, Republic of Korea
Page AJ:
Pathogen Informatics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
Keane JA:
Pathogen Informatics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
Baker S:
Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, UK
Holt KE:
London School of Hygiene and Tropical Medicine, London, UK
Department of Infectious Diseases, Monash University, Melbourne, Australia
Dougan G:
Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
Aanensen DM:
Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK.
Green Published, Green Submitted, gold
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