NCM 2022: DART: a toolbox for the rapid detection of antibiotic resistance

Antibiotic resistance is an ongoing public health threat. The surveillance of environmental reservoirs of antibiotic resistance genes (ARGs) can both inform and enhance the way that we combat resistant pathogens. The Oxford Nanopore Technologies MinION sequencer enables streamlined library preparation that reduces the cost and time elapsed between sample collection and sequence analysis. Here, we describe the development of DART (Detection of Antibiotic Resistance Toolbox), a novel toolbox developed for the detection of antibiotic-resistant organisms in soil microbiomes. DART applies adaptive sampling technology to enrich ARG implemented with a combination of low-cost GPUs, Flongle Flow Cells, and the MinION sequencer. Despite a decrease in total sequencing output, adaptive sampling increased target composition and tended to increase the total number of hits to our ARG panel. Overall, adaptive sampling demonstrated the ability to enrich for ARGs.