top of page


Performance of targeted and whole genome sequencing for routine genotypic drug resistance profiling of Mycobacterium tuberculosis

M De Diego Fuertes(1) A Dippenaar(1) E Costa Conceição(2) F Wells(2) A Paulse(2) T Tu(1) V Rennie(1) R M Warren(2) A Van Rie(1)

1:University of Antwerp; 2:Stellenbosch University

Interest in Next-Generation sequencing (NGS) to determine the comprehensive drug resistance profile of Mycobacterium tuberculosis is increasing, but it remains unclear which application is most suited for high-burden countries. We compared the performance of whole genome sequencing (WGS) and targeted deep sequencing (tNGS) in 67 consecutive patients diagnosed with rifampicin-resistant tuberculosis (RR-TB) by Xpert MTB/RIF Ultra. Patients were predominantly HIV positive (72%) and 40% had prior TB treatment. Deeplexâ Myc-TB (tNGS) was performed on DNA extracted from NALC-NaOH sputum sediments. The MAGMA pipeline was used to analyse WGS for DNA extracted from clinical primary liquid cultures (CPLCs) of the same sediment. For the 67 patients, WGS/MAGMA was successful in 52 (78%) and Deeplex in 46 (69%). For 45 patients where both methods were successful, drug resistance profiles were identical in 35 (78%) but differed for one drug in five (11%) cases, and for >1 drug in another five (11%). Discordances in resistance calling were due to a difference in ethA variant classification (n=1), presence of variants outside of Deeplex targets: upstream of inhA (n=3) and embA (n=1), large genomic deletions in katG (n=1) or pncA (n=1), and minor variants (2-4% allele frequency) detected by only one method (n=5): three detected by Deeplex but missed by WGS/MAGMA, and two identified by MAGMA but missed by Deeplex. Results of this small study suggest an increased yield for culture-based WGS, small differences in resistance profile between sputum-based tNGS and CPLC-based WGS, low prevalence of hetero-resistance, and no evidence of clinically relevant culture bias.

bottom of page