Whole genome sequencing of sputum to identify drug resistant Mycobacterium tuberculosis compared to MGIT sequencing.

Whole genome sequencing (WGS) of Mycobacterium tuberculosis from culture is being adopted into routine diagnostic workflows. Previous attempts to sequence M. tuberculosis directly from sputa tended not provide sufficient genomic data. However, we have previously shown a successful method for capturing M. tuberculosis DNA directly from sputum samples and another recent study has shown adequate genome recovery after the removal of human DNA from the sample. Our study shows that WGS of Mycobacterium tuberculosis direct from diagnostic sputum samples using target enrichment can generate antimicrobial resistance profiles faster than MGIT culture WGS, and phenotypic testing. The success of sequencing can be predicted by semi-quantitative molecular and microscopy methods already widely used in TB laboratories. We have also shown that if only information on possible resistance mutations are required, an even faster, cheaper method can be employed to enrich only those regions of interest. As methods of sequencing M. tuberculosis directly from clinical samples are refined, it will provide a faster time to result than sequencing from culture. Direct sputum sequencing also has the potential to improve detection of minority resistance mutations and mixed infections.