Microfluidic capture of Mycobacterium tuberculosis for culture-free whole genome sequencing

Whole genome sequencing (WGS) of Mycobacterium tuberculosis (Mtb) DNA has greatly contributed to our understanding of this pathogen, particularly with drug resistance profiles, transmission of the disease, mixed infection and hetero-resistance but currently requires amounts of DNA only reached following Mtb culture. Microfluidics applications have the capability to separate bacterial cells, rather than DNA, from raw samples and play a valuable role in single-cell research but have not yet found a foothold in the field of NGS-diagnostics of infectious diseases. Here, we evaluated the use of a microfluidics platform to enrich Mtb bacilli from clinical sputum specimens for downstream DNA extraction and WGS. We compared two different sputum preparation approaches and processed both captured and uncaptured samples for WGS. Only samples that underwent capture yielded successful WGS Mtb data. This is the first study to assessing the use of microfluidics for Mtb sequencing directly from sputum and provides proof-of-principle evidence that microfluidics-based cell capture may be a promising method for culture-free sequencing.