Development of Nanopore metagenomic DNA-sequencing for bloodstream infection diagnostics

Sepsis is a large healthcare burden, with more than 11 million sepsis-related deaths p.a. worldwide. To treat sepsis it is vital to initiate effective treatment immediately, preferably within the first hour. This is not met by the diagnostic tools available to treating physicians, which have turnaround times of 1-3 days and also a poor sensitivity (50%). This leads to excess mortality and overuse of empiric broad-spectrum antibiotics. In this project, we want to develop real-time DNA sequencing methods used in a clinical setting for diagnostic microbiology to provide pathogen identification within 6 hours of patient admission. We aim to develop new molecular methods to increase sensitivity and decrease turnaround time with the Oxford Nanopore platform and explore algorithms to identify antibiotic resistance patterns. The project has already obtained an ethical committee approval for the inclusion of 350 patients in a clinical cohort.