South Africa remains challenged with a high tuberculosis burden accompanied by an
increase in drug resistant cases. We assessed the use of the Illumina MiSeq, a next-generation
sequencing platform for whole genome sequencing, followed by bioinformatic analysis
using a commercial software package to determine resistance to selected drugs used for
Mycobacterium tuberculosis treatment in our setting. Whole genome sequencing shows
potential as a diagnostic platform for the detection of drug resistance in Mycobacterium
tuberculosis with the provision of information for several drugs simultaneously.