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

Autor:	Alcock BP; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Huynh W; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Chalil R; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Smith KW; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Raphenya AR; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Wlodarski MA; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Edalatmand A; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Petkau A; Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada.; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada., Syed SA; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Tsang KK; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Baker SJC; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Dave M; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., McCarthy MC; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Mukiri KM; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Nasir JA; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Golbon B; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Imtiaz H; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Jiang X; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Kaur K; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Kwong M; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Liang ZC; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Niu KC; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Shan P; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Yang JYJ; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Gray KL; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada., Hoad GR; Research Computing Group, Simon Fraser University, Burnaby, British Columbia, Canada., Jia B; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada., Bhando T; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Carfrae LA; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Farha MA; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., French S; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Gordzevich R; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Rachwalski K; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Tu MM; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Bordeleau E; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Dooley D; Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada., Griffiths E; Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada., Zubyk HL; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Brown ED; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada., Maguire F; Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.; Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada.; Department of Community Health & Epidemiology, Dalhousie University, Halifax, Nova Scotia, Canada., Beiko RG; Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada.; Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada., Hsiao WWL; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.; Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada., Brinkman FSL; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada., Van Domselaar G; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada., McArthur AG; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2023 Jan 06; Vol. 51 (D1), pp. D690-D699.
DOI:	10.1093/nar/gkac920
Abstrakt:	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. (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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