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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.

Authors: Minh Duc Cao

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