Drug resistant Mycobacterium tuberculosis is making tuberculosis disease (TB) difficult to control. Sequencing data can be used to identify drug resistance mutations and track the evolution and transmission of M. tuberculosis, thereby informing infection control and clinical decision making. Portable sequencing platforms (e.g. Oxford Nanopore MinION) can characterize genomes in real-time from sputum and culture samples, without the need for time-consuming drug phenotypic testing. Here, we propose to evaluate MinION sequencing as a diagnostic and whole genome platform for clinical samples, and explore its robustness for drug resistance profiling, identifying transmission events, and characterising genes interacting with the human host.
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