CARD is an external reference resource for antibiotic resistance. CARD includes the Antibiotic Resistance Ontology (ARO), a separate component of the database rather than another name for it. The corpus names ARO as a way to classify resistance genes systematically by ontology 1. It also names CARD’s bla group of β-lactamase families as a reference set for known horizontal gene transfer (HGT) 2.
Aliases: CARD; Comprehensive Antibiotic Resistance Database 1,2.
Role in the corpus
Not used for mechanism labels in the AMR pangenome atlas (caveat). The atlas built on amrfinderplus classified resistance mechanisms by keyword matching against AMRFinderPlus product descriptions, for example “beta-lactamase”, “efflux” and “acetyltransferase”. It did not use CARD ARO terms 1. Its mechanism categories therefore come from keywords, not from an ontology 1.
Proposed remedy for the unclassified fraction (caveat). The atlas’s 22.2% “Other/Unclassified” category includes genes whose product descriptions match no keyword set. Examples are ribosomal protection proteins with non-standard names and novel resistance mechanisms 1. As future work, the report proposes mapping bakta bakta_db_xrefs cross-references to CARD ARO terms. This would give a systematic, ontology-based classification and could shrink that fraction. The remedy is only a proposal and has not been tested 1.
Source of known-HGT positive controls. In the gene-function ecological agora project, the Phase 1B design for the consumer null added a set of known-HGT positive controls. AMR was the closest control then available, but a parent-phylum anchor masks intra-phylum HGT, and the new set addressed that gap 2. The added controls were specific beta lactamases families with documented cross-phylum spread, taken from the CARD bla group. The design also added class-I crispr-cas systems, defined by a pfam family, based on the cross-tree-of-life HGT documented by Metcalf et al 2014 2. The evidence describes this as a planned design addition and reports no results from the control set 2.
Related: Pan-Bacterial AMR Gene Landscape · Gene Function Ecological Agora 1,2