15-055
G. Wright A. McArthur
https://card.mcmaster.ca/
Caryn Anthony Licensing Associate
The CARD is an ontology- and model-based framework for detection of antibiotic resistance genes. It contains an expert-curated collection of characterized, peer-reviewed resistance determinants and associated antibiotics, organized by the Antibiotic Resistance Ontology (ARO) and antimicrobial resistance (AMR) gene detection models. The software utilizes these detection models for predicting AMR genes from genome sequences.
Other associated tools include the Resistance Gene Identifier (RGI) which is a novel genome analysis tool for resistome prediction. It annotates DNA and protein sequences and detects matches to CARD reference sequences, variants of known AMR genes and emergent threats.
CARD-R: Resistomes & Variants is a computer-generated data set including genome annotation and variants data using RGI for over 400 pathogens of interest. For each of these pathogens, complete chromosome sequences, plasmid sequences, and whole genome shotgun assemblies were analyzed individually by RGI to generate prevalence data. Results are further categorized using the ARO.
References
[1] Alcock, P., Huynh, W., Chalil, R. et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res. 2023 Jan 6;51(D1):D690-D699. doi: 10.1093/nar/gkac920. PMID 36263822.
[2] Hackenberger et al. CARPDM: cost-effective antibiotic resistome profiling of metagenomic samples using targeted enrichment. Appl Environ Microbiol. 2025 Mar 19;91(3): e0187624. doi: 10.1128/aem.01876-24. PMID 40019273.
[3] Smith et al. 2023. A standardized nomenclature for resistance-modifying agents in the Comprehensive Antibiotic Resistance Database. Microbiol Spectr. 2023 Dec 12;11(6): e0274423. doi: 10.1128/spectrum.02744-23. PMID 37971258.
[4] Edalatmand & McArthur. 2023. CARD*Shark: automated prioritization of literature curation for the Comprehensive Antibiotic Resistance Database. Database (Oxford). 2023 Apr 20:2023:baad023. doi: 10.1093/database/baad023. PMID 37079891.
New Curation: First steps towards re-organization of efflux components and regulatory proteins. Extensive addition of antifungal compounds and resistance ontology terms. Re-organization of nonribosomal peptide antibiotics, peptide antibiotics, and nybomycin-like antibiotics. Additional AMM beta-lactamases, 23S rRNA methyltransferases, and Mycobacterium tuberculosis mutation data. Drug Class classification updates.
Bait Capture Platform: Probe updates to match the latest curation in CARD.
Variant Types: The Antibiotic Resistance Ontology has been expanded to include standardized variant type terminology, e.g. “disrupting variant detected”, to support resistance gene annotators or interpreters. Based on the schemes developed by hAMRonization (https://github.com/pha4ge/hAMRonization) and AMRRules (https://docs.amrrules.org), with additional terms from the NCIT ontology.
CARD-Epidemiology: Release of CARD’s natural-language-processing (NLP) module that captures literature-derived associations between antibiotic resistance genes (ARGs) in CARD’s Antibiotic Resistance Ontology (ARO) and normalized epidemiological terms drawn from external lexicons (SO, NCBI_TAXON, GAZ, IDO, UBERON, FOODON, ENV). Each association records the source lexicon, the normalized term’s accession and name, and the number of supporting PubMed publications, with individual supporting citations (PMID and sentence-level location) tracked separately. These are new data to aid interpretation of gene and mutation lists, with models, training data, and results available for download.
Pre-Prints:
Wlodarski et al. 2025. CARD k-mers: Unmasking the pathogen hosts and genomic contexts of antimicrobial resistance genes in metagenomic sequences. bioRxiv, 2025.09.15.676352.
Mukiri et al. 2025. Increasing the predictive accuracy of the Resistance Gene Identifier by evaluating antimicrobial resistance gene over- and underprediction. bioRxiv, 2025.12.11.693720.
Edalatmand & Ta et al. 2026. CARD:Epi – Contextualizing antimicrobial resistance determinants using deep learning language models. bioRxiv, 2026.08.14.744850.
New: Additional Mycobacterium tuberculosis mutations, predominantly insertions and deletions. Addition of new anti-fungal compounds, daptomycin resistance mutations, and beta-lactamases. Review of SNV alignments for many resistance genes. Assignment of official Antibiotic Resistance Ontology accessions to custom relationship terms.
Completed: Over 1500 Mycobacterium tuberculosis mutations conferring AMR have been added via curation & cross-referencing of the ReSeqTB, CRyPTIC, and WHO 2023 mutation catalogs. This includes addition of over 30 new M. tuberculosis drug targets.
Updated: The recently released FungAMR catalog including over 50,000 mutations across 184 antifungal molecules and 92 fungal species has been updated at the CARD website.
Completed: Mutation data in CARD has been updated to reflect the Human Genome Variation Society (HGVS) nomenclature, with additional rules from GARC (a Grammar for Antimicrobial Resistance Catalogues). The HGVS Nomenclature is an internationally recognized standard for the description of DNA, RNA, and protein sequence variants. It is used to convey variants in clinical reports and to share variants in publications and databases.
This major update includes several new data sets, new download files, and technical improvements: