Pathogen DNA enrichment strategies for nanopore sequencing based infectious diseases diagnostics.

Abstract
The infectious diseases which are most important to diagnose rapidly are those which are life threatening. These include sepsis and pneumonia, which have complex aetiology and which require the recognition of pathogens within challenging sample matrices. The “gold standard” culture techniques are labour intensive, have long turn-around times and offer poor clinical sensitivity. 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. Nucleic acid amplification tests (NAATs) are a step in the right direction, providing results within hours, but are limited by the range of pathogens they can detect.
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 (i.e. no specific amplification or capture) next generation sequencing (NGS) based methods for the routine diagnosis of clinical syndromes such as sepsis and UTIs. NGS based ID diagnostics represents a disruptive advance in the field, combining the speed of NAATs with comprehensiveness beyond that of culture (capable of detecting bacteria, viruses and fungi).
One of the biggest challenges to successfully applying NGS in medical microbiology is the vast quantity of host vs pathogen nucleic acid present in clinical samples such as blood. We are combining novel pathogen DNA enrichment techniques with the latest nanopore NGS technologies (Oxford Nanopore MinION device) to make this possible.
I will describe our pathogen DNA enrichment strategies and present data from our projects on the NGS based diagnosis of blood stream and urinary tract infections. I will also discuss some of our other applications of MinION sequencing technology and present our most recent performance data.