Molecular capture of Mycobacterium tuberculosis genomes directly from clinical samples: a potential backup approach for epidemiological and drug susceptibility inferences

The application of whole genome sequencing of Mycobacterium tuberculosis directly on clinical samples has been investigated during the last years as a means to avoid the time-consuming need for culture isolation that can lead to a potential prolonged suboptimal antibiotic treatment. We aimed to provide a proof-of-concept regarding the application of the molecular capture of M. tuberculosis genomes directly from positive sputum samples as an approach for epidemiological and drug susceptibility predictions. Smear-positive sputum samples (n=100) were subjected to the SureSelectXT HS Target Enrichment protocol (Agilent Technologies, CA, USA) and whole-genome sequencing analysis. A higher number of reads on target were obtained for higher smear grades samples (i.e., 3+ followed by 2+). Also, 37 out of 100 samples showed ≥90% of the reference genome covered with at least 10-fold depth of coverage (27, nine and one sam-ples were 3+, 2+ and 1+, respectively). Regarding drug-resistance/susceptibility prediction, for 42 samples, ≥90% of the >9000 hits that are surveyed by TB-profiler were detected. Our results demonstrated that M. tuberculosis genome capture and sequencing directly from clinical samples constitute a potential valid backup approach for phylogenetic inferences and resistance predic-tion, essentially in settings when culture is not routinely performed or for samples that fail to grow.