Comparative study of different approaches to use MinION on a routine basis of infection diagnosis. MinION routine deployment

Although 16S-rRNA is a powerful strategy for mono-bacterial infections diagnosis, it has its limitations in case of a polymicrobial infection when sequences of the multiple DNA amplicons yield a mixed chromatogram and hamper the identification of each bacterium. While the gain of Nanopore-based 16S-rRNA metagenomic approach has been assessed in culture-positive infections, little is known about its performances on negative-culture samples when we find ourselves in a dead-end diagnosis. We here aimed to explore its suitability as a routine diagnostic tool for bacterial infections in a clinical laboratory.