Mycobacterium tuberculosis Next-Generation Whole Genome Sequencing: Opportunities and Challenges

Table 2

Summary of methods developed for DNA extraction directly from sputum samples for M. tuberculosis next-generation whole genome sequencing.

Reference	Sample	Sample preparation for sequencing	Sequencing Platform	Whole genome sequencing success rate ()	Coverage; Average Depth of coverage
Doyle et al., 2018 [24]	Sputum	SureSelectXT target enrichment system (Agilent technologies)	Illumina MiSeq or NextSeq sequencer	74.4%	>85%; 25X to 300X
Votinseva et al., 2017 [25]	Smear positive sputum	Saline wash, MolYsis Basic5 kit (Molzym, Germany) for depletion of human cells/DNA, Ethanol precipitation method.	Illumina MiSeq sequencer	62%	>90%; >12X
Doughty et al., 2014 [26]	Smear positive sputum	Differential lysis protocol followed by DNA extraction using the NucleoSpin Tissue-Kit (Machery-Nagel, Duren, Germany)	Illumina MiSeq sequencer	87%	20% to 99%; 0.002X to 0.7X
Brown et al., 2015 [27]	Smear positive sputum	SureSelectXT target enrichment system (Agilent technologies)	Illumina MiSeq sequencer	83%	90%; >20X