CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database
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- Teacher spread
- 0.299 · how far apart the two teachers sit on this one work
- Validation status
score_only:v0-immature-baseline· verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it
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.
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The record
- Venue
- Nucleic Acids Research
- Topic
- Antibiotic Resistance in Bacteria
- Field
- Biochemistry, Genetics and Molecular Biology
- Canadian institutions
- Dalhousie UniversitySimon Fraser UniversityUniversity of ManitobaPublic Health Agency of CanadaMcMaster University
- Funders
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster UniversityCisco Systems CanadaSimon Fraser UniversityInstitute of Infection and ImmunityCanadian Institutes of Health ResearchGenome CanadaCanada Foundation for InnovationNatural Sciences and Engineering Research Council of CanadaMcMaster UniversityCisco Systems
- Keywords
- ResistomeBiologyDatabaseData curationGeneticsComputational biologyAntibiotic resistanceGene nomenclatureGenomeGeneAntibioticsComputer scienceMobile genetic elementsWorld Wide Web
- Has abstract in OpenAlex
- yes