Nanopore sequencing – disruptive technology in clinical microbiology?

The diagnosis of infectious diseases by culture takes at least two days: one to grow the bacteria and then, at best, one to identify pathogens and test their antimicrobial susceptibility. Meanwhile the patient is treated empirically, which often results in inappropriate treatment. A paradigm shift in diagnostics technology is required, to allow the development of a universal diagnostic which can detect any pathogen, known or unknown. We are developing the first culture independent non-targeted NGS based methods for the routine diagnosis of clinical syndromes such as sepsis and urinary tract infections. NGS based infectious diseases diagnostics represents a disruptive advance in the field, providing rapid, comprehensive molecular diagnostics. The biggest challenges to successfully applying NGS in medical microbiology are (1) the vast quantity of host vs pathogen nucleic acid present (e.g. blood) and (2) turnaround time to results. We are combining novel pathogen DNA enrichment techniques with rapid MinION sequencing to make NGS based infectious diseases diagnostics a reality.