CARD – 15-055

Comprehensive Antibiotic Resistance Database (CARD)

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.

[CARD-L] Comprehensive Antibiotic Resistance Database – Updates

May 2025

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.

December 2024

This major update includes several new data sets, new download files, and technical improvements:

• Over 1200 new beta-lactamase genes (a several new families) have been added to CARD. In addition, classification of beta-lactam molecules has been re-organized (and additional antibiotics added) to reflect functional groups: monobactams, penicillins, early (1st-2nd generation) cephalosporins, extended-spectrum (3rd-generation) cephalosporins, carbapenems, 4th generation cephalosporin cefepime, 5th generation cephalosporin ceftaroline, and updated beta-lactamase plus inhibitor combinations.
• Over 1400 new 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 29 new M. tuberculosis drug targets. A new interface has been provided for easy assessment of level of evidence for each M. tuberculosis mutation from the literature and the three catalogs. Thanks to our TB curation team: Brian Alcock, Monica Warner, Karyn Mukiri, Sidrah Shaikh, & Nilasha Mohan.
• The recently released FungAMR catalog including over 50,000 mutations across 184 antifungal molecules and 92 fungal species have been added to CARD as a searchable interface. Full incorporation of these data into CARD is ongoing. Thanks to Bédard et al. for sharing these data (see https://www.biorxiv.org/content/10.1101/2024.10.07.617009v1).
• Our chemistry curation team is currently adding SMILES, PubChem, ChEBI, ChEMBL, and CAS data for every molecule in CARD, with some of these data now available. New download files and tools will be provided once this curation is complete.
• 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.
• Additional resistomes data have been provided by the Canadian Genomics R&D Initiative on AMR One Health, via NCBI BioProject PRJNA1076250.
• For laboratory work, the CARD metagenomics Bait Capture Platform has been updated to reflect these latest curation updates and information on the Antibiotic Resistance Platform (ARP) for direct antibiotic susceptibility testing of individual resistance determinants or antibiotic & adjuvant discovery dereplication is provided.
• CARD’s search box now enables searches based on associated publications (PMID) or NCBI sequence accessions. The SNPs download file now includes source of evidence and citation. A new download file is also provided that cross-references Antibiotic Resistance Ontology (ARO) terms with citations.

February 2024

• This update includes addition of gyrA, gyrB, and folp mutations for additional Salmonella species, 23S rRNA mutations for Treponema pallidum, and gyrA mutations for Helicobacter pylori. It also includes addition of OXA beta-lactamase sub-families, with subsequent re-organization of the OXA beta-lactamase classification.

October 2023

• This update includes improved curation of 16S rRNA mutations, the addition of TEM and OXA beta-lactamase sequences, improvements in tet gene curation, additional aminoglycoside resistance genes, and improvements to antibiotic and drug class curation. In addition to the database, the Resistance Gene Identifier software has been updated to use BLAST 2.14.0, with config file, and adds HSP subject coordinates and impacted antibiotics to output. https://github.com/arpcard/rgi

June 2023

• The in silico Resistomes, Variants, & Prevalence data set has been updated to 381 pathogens, 24291 chromosomes, 2662 genomic islands, 48212 plasmids, 172216 WGS assemblies, 276270 alleles based on sequence data acquired from NCBI on May 2, 2023 and Islandviewer 4, analyzed using RGI 6.0.2 (DIAMOND homolog detection) and CARD 3.2.7. Includes pre-compiled k-mer classifier data for pathogen-of-origin prediction.

May 2023

• CARD curation updates include continued improvements for aminoglycoside modifying enzymes, curation of Mycobacterium tuberculosis mutations, and curation of additional TEM, EBR, IND, KPC, LAQ, NDM, WUS, and IMP beta-lactamases.In addition, the CARD team are happy to announce that the Resistance Gene Identifier (RGI) has been incorporated into the Chan Zuckerberg ID platform for free, cloud-based metagenomics analysis by researchers, allowing high-throughput use of RGI’s read-mapping algorithms online: https://chanzuckerberg.zendesk.com/hc/en-us/articles/15091031482644-AMR-Pipeline-Workflow