Multiplexed optical DNA mapping to identify plasmids and their resistance genes in fecal samples

Abstract

Multi-drug resistant bacteria are a major health threat worldwide. Resistance is frequently horizontally transferred among bacteria via mobile genetic elements, such as plasmids. We have developed a one-step staining protocol to reveal sequence-correlated fluorescence profiles along stretched plasmids. In this report, we demonstrate an automation approach to increase the throughput of nanofluidic optical DNA mapping(ODM). Using plasmid samples derived from patients\u27 feces, the results demonstrate an improved throughput, both regarding the number of plasmids analyzed per sample as well as the number of samples analyzed. By combining the ODM with Cas9/CRISPR, plasmids containing the antibiotic resistance gene are readily identified