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Overview of the three databases

Pros and cons table, compare and contrast the three databases, make sure we mention that you can use their databases with other tools (abricate, srs

The following table compares and contracts the three databases. You can use the databases with their associated tools (which are also listed in the table).

  NCBI CARD ResFinder
URL to DB https://github.com/ncbi/amr/wiki/AMRFinderPlus-database https://card.mcmaster.ca/ https://github.com/cadms/resfinder/tree/master?tab=readme-ov-file#databases
Curation method Engages with domain experts and GEN-FS work groupings (genomic food safety group in the USA). Curators regularly survey the literature for new genes and mutations. Is the allele assignment authority for beta-lactamase genes. Collaborates with the CARD team Takes submissions from the public via their github issues page or via email. Collaborates with the NCBI team Expert curators working for the ResFinder team. Also takes submissions from the public
Can you download their database? yes yes yes
Includes promoter mutations yes under development yes
Database structure Consists of the Reference Gene Catalog, the Reference Gene Hierarchy and Reference HMMs Consists of a gene/mutation database, as well as the Antibiotic Resistance Ontologies (ARO) Consists of ResFinder database (for genes) and PointFinder database (for mutations in genes)
Licensing Freely available without copyright https://github.com/ncbi/amr/wiki/Licenses Available for non-commercial use https://card.mcmaster.ca/about Available for non-commercial use http://genepi.food.dtu.dk/license
Associated tool AMRFinderPlus RGI & RGI-bwt ResFinder
URL to tool https://github.com/ncbi/amr/wiki https://card.mcmaster.ca/analyze & https://github.com/arpcard/rgi http://genepi.food.dtu.dk/resfinder
How can you use it? Command line tool Web interface and command line Web interface and command line
Can take assemblies as input yes yes yes
Can take reads as input no yes, but command-line tool only (web interface available at czid.org) no
Species specific curation of results for some species No, but some pre-compiled annotations by species in the “CARD Resistomes” data set for some species
Phenotype prediction No, but provides curated suggestions of likely phenotype effects in the ‘class’ and ‘subclass’ fields of the output No, but database provides suggestions of likely phenotype effects of genes in their respective database entries Yes, for some species

You can download this table as a PDF document in the link below and use it as a reference.

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Antimicrobial Databases and Genotype Prediction: Data Sharing and Analysis

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