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CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database.
Alcock, Brian P; Huynh, William; Chalil, Romeo; Smith, Keaton W; Raphenya, Amogelang R; Wlodarski, Mateusz A; Edalatmand, Arman; Petkau, Aaron; Syed, Sohaib A; Tsang, Kara K; Baker, Sheridan J C; Dave, Mugdha; McCarthy, Madeline C; Mukiri, Karyn M; Nasir, Jalees A; Golbon, Bahar; Imtiaz, Hamna; Jiang, Xingjian; Kaur, Komal; Kwong, Megan; Liang, Zi Cheng; Niu, Keyu C; Shan, Prabakar; Yang, Jasmine Y J; Gray, Kristen L; Hoad, Gemma R; Jia, Baofeng; Bhando, Timsy; Carfrae, Lindsey A; Farha, Maya A; French, Shawn; Gordzevich, Rodion; Rachwalski, Kenneth; Tu, Megan M; Bordeleau, Emily; Dooley, Damion; Griffiths, Emma; Zubyk, Haley L; Brown, Eric D; Maguire, Finlay; Beiko, Robert G; Hsiao, William W L; Brinkman, Fiona S L; Van Domselaar, Gary; McArthur, Andrew G.
Afiliación
  • Alcock BP; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Huynh W; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
  • Chalil R; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
  • Smith KW; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Raphenya AR; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
  • Wlodarski MA; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
  • Edalatmand A; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Petkau A; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
  • Syed SA; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
  • Tsang KK; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Baker SJC; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
  • Dave M; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
  • McCarthy MC; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Mukiri KM; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
  • Nasir JA; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
  • Golbon B; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Imtiaz H; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
  • Jiang X; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
  • Kaur K; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Kwong M; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
  • Liang ZC; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
  • Niu KC; Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada.
  • Shan P; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
  • Yang JYJ; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Gray KL; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
  • Hoad GR; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
  • Jia B; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Bhando T; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
  • Carfrae LA; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
  • Farha MA; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • French S; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
  • Gordzevich R; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
  • Rachwalski K; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Tu MM; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
  • Bordeleau E; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
  • Dooley D; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Griffiths E; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
  • Zubyk HL; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
  • Brown ED; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Maguire F; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
  • Beiko RG; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
  • Hsiao WWL; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
  • Brinkman FSL; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
  • Van Domselaar G; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
  • McArthur AG; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
Nucleic Acids Res ; 51(D1): D690-D699, 2023 01 06.
Article en En | MEDLINE | ID: mdl-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 ß-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 CARDLive collection of community submitted isolate resistome data and the introduction of standardized 15 character CARD Short Names for ARGs to support machine learning efforts.
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Texto completo: 1 Base de datos: MEDLINE Asunto principal: Farmacorresistencia Microbiana / Bases de Datos Factuales / Curaduría de Datos / Aprendizaje Automático Tipo de estudio: Prognostic_studies / Risk_factors_studies Idioma: En Revista: Nucleic Acids Res Año: 2023 Tipo del documento: Article
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Base de datos: MEDLINE Asunto principal: Farmacorresistencia Microbiana / Bases de Datos Factuales / Curaduría de Datos / Aprendizaje Automático Tipo de estudio: Prognostic_studies / Risk_factors_studies Idioma: En Revista: Nucleic Acids Res Año: 2023 Tipo del documento: Article