Nanopore-based DNA sequencing in clinical microbiology: preliminary assessment of basic requirements

Abstract

AimIdentify basic requirements for a metagenomic nanopore sequencing protocol permitting frequent application in a clinical microbiology daily routine diagnostic setting.\n\nBackgroundNanopore sequencing with the Oxford Nanopore Technologies MinION device has a potential to markedly improve clinical diagnosis of infections. Reports have emerged recently that it may provide direct-from-clinical-sample information; for example, with urine samples, bronchial tuberculosis samples and orthopedic prostheses. However, the ideal protocol for clinical use remains to be determined, especially relating to detection of relevant pathogen quantities and to finding a reasonable level of economic costs.\n\nResultsMinION can provide qualitatively and quantitatively correct identification of multiple species in metagenomics samples. For detection of clinically relevant quantities of bacteria (on a nanogram DNA level) there is a need for carrier DNA. Importantly, high-purity DNA and a naive MinION flow cell seem to be critical parameters.\n\nConclusionsOur results suggest that high-purity clinical sample DNA, addition of carrier DNA and a naive flow cell are critical factors for clinical use of MinION. A relatively high error rate may limit detection of antimicrobial resistance genes, and a realistic level of costs will require availability of a price-reduced and single-use flowcell.