CARPDM: cost-effective antibiotic resistome profiling of metagenomic samples using targeted enrichment.

ABSTRACT: Better interrogation of antimicrobial resistance requires new approaches to detect the associated genes in metagenomic samples. Targeted enrichment is an ideal method for their sequencing and characterization. However, no open-source, up-to-date hybridization probe set targeting antimicrobial resistance genes exists. Here, we describe the Comprehensive Antibiotic Resistance Probe Design Machine (CARPDM), a probe design software package made to run alongside all future Comprehensive Antibiotic Resistance Database releases. To test its efficacy, we have created and tested two separate probe sets: allCARD, which enriches all genes encoded in the Comprehensive Antibiotic Resistance Database's protein homolog models (n = 4,661), and clinicalCARD, which focuses on a clinically relevant su

SUBMITTER: Hackenberger D 

PROVIDER: S-EPMC11921354 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature