In Nucleic acids research ; h5-index 217.0
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.
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
2022-Oct-20
