Potential clinical applications of adaptive sampling

Abstract

Depletion and enrichment by Oxford Nanopore’s adaptive sampling provides potential new application options for sequencing in the hospital. For instance, alterations of the vaginal microbiome are associated with adverse pregnancy outcomes but these samples deal with high amounts of host DNA and thus low microbial load. We demonstrated how selective 'human host depletion' resulted in increased sequencing depth, while the microbial composition remains consistent. We further leveraged the enrichment capabilities as a flexible antimicrobial resistance genotyping panel for routine microbiology covering 1,147 antimicrobial resistance genes. Our study examined the limitations and the relationship between database, sequence similarities, and prepared DNA.