Optimization of nanopore-based sequencing for bloodstream infection diagnostics

Principal Investigator: 
Alban Ramette, PhD, PD, Head Bioinformatics/Biostatistics Group, Institute for Infectious Diseases, University of Bern. For more information, please visit the website. 

Co-Investigator:
Yok-Ai Quei, Prof. Dr. med. Dr. phil., Department of Intensive Care Medicine, Inselspital; University Hospital, Bern
Carlo Casanova, PhD, FAMH, Institute for Infectious Diseases, University of Bern

The individualized treatment and management of patients with bloodstream infections remain one of the major challenges in intensive care units. Here we aim to use long-read sequencing technology to analyse the genomic DNA of pathogens directly from blood samples of septic patients. Although long-read-based sequencing has great potential as a microbial diagnostic tool, further protocol optimizations are needed to gain more clinically-relevant insights from blood samples. We therefore want to specifically optimize laboratory protocols to improve the detection of human pathogens and to compare the new approach to current diagnostic procedures in terms of turnaround time and costs.