Real-time identification of pathogens and antibiotic resistance profile using Oxford Nanopore sequencing

Clinical pathogen sequencing has been demonstrated to have a positive outcome on treatment of patients with unknown bacterial infection. However, widespread adoption of clinical pathogen sequencing has been impeded by the lack of real-time sequencing devices. Our recent experience with the Nanopore MinION sequencing has allowed us to overcome this hurdle. Here we demonstrate the potential of analysing clinical microbial samples in real-time using this miniature sequencing device. We have been able to accurately identify the bacterial species and strains in a sample within half an hour of loading the sample into the sequencer and to characterize the antibiotic resistance profile within few hours of sequencing time. We have developed a graphical user interface (GUI) to perform the analysis which streamlines the bioinformatics pipelines involving the sequence data analysis. Furthermore the results are exhibited in a user friendly format to output the most relevant information for clinicians. We anticipate the MinION devices will fast become indispensable tools for informing treatment options for patients with bacterial infection.