Oxford Nanopore enhanced accuracy of long-read amplicons applied to microbial whole-genome sequencing

Abstract

Recent advances in genome sequencing have greatly improved our ability to study microbes and detect infections. One such technology, Oxford Nanopore Technologies (ONT), can read long stretches of nucleic acids. ONT is also portable and can sequence in real time, making it useful in clinical settings. However, ONT accuracy is known to be lower than traditional short-read methods, limiting its widespread use. Fortunately, many strategies have emerged to overcome this limitation: better ONT chemistry, better basecaller, and hybrid approaches combining ONT with highly accurate short reads. Another promising method uses molecular barcodes or “Unique Molecular Identifiers” (UMIs) to make long reads at high accuracy, reaching accuracy levels similar to the existing short-read technologies. In our study, we optimized this UMI-based method and successfully applied it to human blood samples spiked with common infection-causing bacteria. The results showed a significant drop in ONT error rate, suggesting that this approach could make ONT a reliable tool for diagnosing infections and analyzing microbial DNA in clinical samples.