Rapid and reliable species-level identification from clinical samples using 16S rRNA gene nanopore sequencing analysis

The aim of this study was to develop and validate a faster and more discriminative 16S rRNA gene sequencing workflow to improve our routine diagnostic method. For this, the updated protocol replaced Illumina short-read sequencing for nanopore long-read sequencing. To validate our method, a dilution series of an equimolar synthetic microbial community (SMC) sample was processes as well as six clinical samples with no bacterial biomass (n=2), low bacterial biomass (n=2) and high bacterial biomass (n=2). The micelle PCR/nanopore sequencing results obtained were compared to the results obtained with our previously published micelle PCR/NGS method.