CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database-Reference-Cited by-同舟云学术

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

Published:2019-10-29 Issue: Volume: Page:
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Alcock Brian P¹²³,Raphenya Amogelang R¹²³,Lau Tammy T Y²³,Tsang Kara K¹²³,Bouchard Mégane²⁴,Edalatmand Arman²³,Huynh William²³,Nguyen Anna-Lisa V²⁴,Cheng Annie A²³,Liu Sihan²³,Min Sally Y²³,Miroshnichenko Anatoly²³,Tran Hiu-Ki²³,Werfalli Rafik E²³,Nasir Jalees A²³,Oloni Martins²³,Speicher David J²³,Florescu Alexandra²⁴,Singh Bhavya⁵,Faltyn Mateusz²⁶,Hernandez-Koutoucheva Anastasia⁷,Sharma Arjun N²³,Bordeleau Emily¹²³,Pawlowski Andrew C⁸,Zubyk Haley L¹²³,Dooley Damion⁹,Griffiths Emma¹⁰,Maguire Finlay¹¹,Winsor Geoff L¹⁰^ORCID,Beiko Robert G¹¹,Brinkman Fiona S L¹⁰,Hsiao William W L⁹¹⁰¹²,Domselaar Gary V¹³¹⁴^ORCID,McArthur Andrew G¹²³

Affiliation:

1. David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada

2. M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada

3. Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada

4. Bachelor of Health Sciences Program, McMaster University, Hamilton, Ontario, L8S 4K1, Canada

5. Honours Biology Program, McMaster University, Hamilton, Ontario, L8S 4K1, Canada

6. Bachelor of Arts & Science Program, McMaster University, Hamilton, Ontario, L8S 4K1, Canada

7. Center for Genome Sciences, National Autonomous University of Mexico, Cuernavaca, Morelos 62210, Mexico

8. Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA

9. Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, V6T 2B5, British Columbia, Canada

10. Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada

11. Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, B3H 1W5, Canada

12. British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, V5Z 4R4, Canada

13. National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2, Canada

14. Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada

Abstract

Abstract The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models and bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses on providing high-quality reference data and molecular sequences within a controlled vocabulary, the Antibiotic Resistance Ontology (ARO), designed by the CARD biocuration team to integrate with software development efforts for resistome analysis and prediction, such as CARD’s Resistance Gene Identifier (RGI) software. Since 2017, CARD has expanded through extensive curation of reference sequences, revision of the ontological structure, curation of over 500 new AMR detection models, development of a new classification paradigm and expansion of analytical tools. Most notably, a new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes. By adding these resistance variants to CARD, we are able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants. Here, we describe updates and recent expansions to CARD and its biocuration process, including new resources for community biocuration of AMR molecular reference data.

Funder

Canadian Institutes of Health Research

Genome Canada

Cisco Systems

Cisco Research Chair in Bioinformatics

Ontario Graduate Scholarship

Publisher

Oxford University Press (OUP)

Subject

Genetics

Link

http://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkz935/30324790/gkz935.pdf

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