Comprehensive Antibiotic Resistance Database (CARD) and CARPDM

CARPDM generates hybridization probe sets for targeted enrichment of antibiotic resistance genes from metagenomic samples, working alongside the Comprehensive Antibiotic Resistance Database (CARD) to enable cost-effective resistome profiling.

Key Features:

• Probe design automation: CARPDM is a probe design software package made to run alongside all future Comprehensive Antibiotic Resistance Database releases.
• Pre-configured probe sets: allCARD enriches all genes encoded in CARD's protein homolog models (n = 4,661), while clinicalCARD focuses on a clinically relevant subset of resistance genes (n = 323).
• Enrichment efficacy: allCARD increases the number of reads mapping to resistance genes by up to 594-fold, and clinicalCARD increases resistance-gene mapping reads by up to 598-fold when clinically relevant genes are present.
• In-house synthesis protocol: An established protocol enables synthesis of any probe set in-house, saving up to 350 dollars per reaction.

Scientific Applications:

• Metagenomic resistome profiling: Enables detection and characterization of antimicrobial resistance genes in complex samples such as wastewater and environmental samples.
• Clinical resistance gene monitoring: clinicalCARD allows focused detection of clinically relevant resistance genes in metagenomic samples.
• Antimicrobial resistance surveillance: Supports tracking of resistance genes among pathogens, environments, patients, and animals for risk assessment.

Methodology:

CARPDM uses bait-capture hybridization for targeted enrichment of antimicrobial resistance genes, with probe sets designed based on CARD's protein homolog models and synthesized through an established in-house protocol.