The Comprehensive Antibiotic Resistance Database (CARD)

The Comprehensive Antibiotic Resistance Database (CARD) provides a curated collection of reference DNA and protein sequences, detection models, and the Antibiotic Resistance Ontology (ARO) to support identification, prediction, and analysis of bacterial antimicrobial resistance (AMR).

Key Features:

• Curated reference sequences: Curated reference DNA and protein sequences representing antimicrobial resistance determinants.
• AMR detection models: A repository of detection models including over 500 AMR detection models for sequence-based identification of resistance determinants.
• Antibiotic Resistance Ontology (ARO): ARO is a controlled vocabulary developed by the CARD biocuration team that models AMR genes, mechanisms, and phenotypes.
• Resistance Gene Identifier (RGI): RGI software that uses CARD reference sequences and detection models to identify and predict AMR genes from sequence data.
• Resistomes & Variants module: Analysis and statistical summarization of in silico predicted resistance variants across 82 pathogens and more than 100,000 genomes, with incorporation of predicted variants into CARD.
• Novel classification paradigm: A revised classification paradigm for AMR determinants implemented within CARD.
• ARO integration for software development: Programmatic integration of ARO to support resistome analysis and prediction software development.
• Community biocuration: Support for community-driven biocuration of molecular reference data and AMR annotations.

Scientific Applications:

• Resistome surveillance: Surveillance of antibiotic resistomes and comparative analysis of AMR across bacterial populations.
• AMR gene identification and prediction: Sequence-based identification and prediction of AMR genes using detection models and RGI.
• Variant summarization: Statistical summarization of in silico predicted resistance variants across 82 pathogens and over 100,000 genomes.
• AMR mobility analysis: Analysis of trends in AMR mobility and distribution using aggregated variant data.
• Novel variant discovery: Detection and cataloguing of previously undescribed or novel resistance variants integrated into CARD.
• Molecular mechanism elucidation: Investigation of the molecular basis of antimicrobial resistance through curated sequences, models, and ontology annotations.

Methodology:

CARD uses curated reference DNA and protein sequences, structured detection models, the Antibiotic Resistance Ontology (ARO), and the Resistance Gene Identifier (RGI) to perform sequence-based identification and in silico prediction of resistance, with statistical summarization and incorporation of predicted variants via the Resistomes & Variants module.