Abstract

Routine full characterization of Mycobacterium tuberculosis (TB) is culture-based, taking many weeks. Whole-genome sequencing (WGS) can generate antibiotic susceptibility profiles to inform treatment, and unlike traditional tests, also delivers strain information which can be used for local epidemiology and global surveillance; such data could be transformative if provided at or near point of care. In the first half of my talk, I will talk about our recent work developing methods for low-cost extraction of DNA direct from respiratory samples, and integration with Illumina and Oxford Nanopore sequencing technologies, with potential for application in the field. In the second half, I will address the question of how to tie point-of-care diagnostics in with global surveillance in a world where whole-genome sequencing -based diagnostics take off. I ask what challenges must computational biologists solve to enable true global surveillance of bacteria, coping with open pan-genomes, outbreaks, evolving resistance and Joe Medic as a user of our tools. I will describe and demonstrate our cloud-based solution that will scale to millions of bacteria.