Evaluation of rapid Nanopore-based 16S rRNA gene sequencing as diagnostic tool for clinical service
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Traditionally, the diagnosis of bacterial infections relies on culture based techniques considered the gold standard of pathogen identification in clinical microbiology. However, standard microbiology has limited sensitivity, specificity and slow turnaround time leading to overuse of broad spectrum antibiotics and emergence of antimicrobial resistance. Poor diagnostics also lead to poor patient outcomes, prolonged hospital stay and increased costs. Oxford Nanopore Technologies (ONT) long read sequencing holds promise of a microbiology revolution generating data analysable in real-time. We started evaluating an ONT based 16S rRNA gene assay, to investigate whether low accuracy long reads and high speed analysis can combine to a clinically useful diagnostics.