CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database.

Journal: Nucleic acids research
PMID: 36263822

Abstract

The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation and interpretation of resistomes. As of version 3.2.4, CARD encompasses 6627 ontology terms, 5010 reference sequences, 1933 mutations, 3004 publications, and 5057 AMR detection models that can be used by the accompanying Resistance Gene Identifier (RGI) software to annotate genomic or metagenomic sequences. Focused curation enhancements since 2020 include expanded β-lactamase curation, incorporation of likelihood-based AMR mutations for Mycobacterium tuberculosis, addition of disinfectants and antiseptics plus their associated ARGs, and systematic curation of resistance-modifying agents. This expanded curation includes 180 new AMR gene families, 15 new drug classes, 1 new resistance mechanism, and two new ontological relationships: evolutionary_variant_of and is_small_molecule_inhibitor. In silico prediction of resistomes and prevalence statistics of ARGs has been expanded to 377 pathogens, 21,079 chromosomes, 2,662 genomic islands, 41,828 plasmids and 155,606 whole-genome shotgun assemblies, resulting in collation of 322,710 unique ARG allele sequences. New features include the CARD:Live collection of community submitted isolate resistome data and the introduction of standardized 15 character CARD Short Names for ARGs to support machine learning efforts.

Authors

  • Brian P Alcock
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • William Huynh
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Romeo Chalil
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Keaton W Smith
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Amogelang R Raphenya
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Mateusz A Wlodarski
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Arman Edalatmand
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Aaron Petkau
    Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada.
  • Sohaib A Syed
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Kara K Tsang
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Sheridan J C Baker
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Mugdha Dave
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Madeline C McCarthy
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Karyn M Mukiri
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Jalees A Nasir
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Bahar Golbon
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Hamna Imtiaz
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Xingjian Jiang
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Komal Kaur
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Megan Kwong
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Zi Cheng Liang
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Keyu C Niu
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Prabakar Shan
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Jasmine Y J Yang
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Kristen L Gray
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
  • Gemma R Hoad
    Research Computing Group, Simon Fraser University, Burnaby, British Columbia, Canada.
  • Baofeng Jia
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
  • Timsy Bhando
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Lindsey A Carfrae
    Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada.
  • Maya A Farha
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Shawn French
    Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada.
  • Rodion Gordzevich
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Kenneth Rachwalski
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Megan M Tu
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Emily Bordeleau
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Damion Dooley
    Centre for Infectious Disease Genomics and One Health, Simon Fraser University, 8888 University Dr, Burnaby, BC V5A 1S6, Canada.
  • Emma Griffiths
    Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada.
  • Haley L Zubyk
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Eric D Brown
    Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada.
  • Finlay Maguire
    Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.
  • Robert G Beiko
    Faculty of Computer Science Dalhousie University Halifax NS Canada.
  • William W L Hsiao
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
  • Fiona S L Brinkman
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
  • Gary Van Domselaar
    National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
  • Andrew G McArthur
    David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.

Keywords

External Resources

Popular Topics
Recent Journals