tNGS and WGS of Mtb
Challenges in tuberculosis (TB) control have fuelled interest in routine Next-Generation Sequencing (NGS). However, the comparative performance of targeted NGS (tNGS) and whole genome sequencing (WGS) for drug resistance and genetic relatedness inference remains unclear. We compared WGS (MICK-MAGMA platform) and the Deeplex® MycTB tNGS assay in 60 patients with rifampicin-resistant TB in South Africa. tNGS was conducted directly on DNA from sputum, and WGS on cultured isolates from the same samples. Drug resistance inference was highly concordant (=92%) for most drugs, but lower for isoniazid (82%) and ethionamide (78%). Mixed infections were more commonly detected in tNGS (6.7%) than WGS (1.7%), though likely due to analytical errors. tNGS detected more minor variants (allelic frequency <25%) than WGS (76 vs. 32), with minimal overlap. Most minor variants were of unknown significance; some likely stemmed from contamination or sequencing errors. Heteroresistance involving minor variants was rare (4.7% in tNGS, 0% in WGS).WGS provided lineage and sub-lineage information for all samples, while tNGS reported lineage for 67% and sub-lineage for 20%. WGS classified more samples as genetically unrelated (76%) than tNGS (40%). In this cohort, drug resistance inference was largely concordant between tNGS and WGS. WGS offered higher resolution for genetic relatedness, while tNGS showed greater sensitivity for minor variants. Further research is needed to clarify the clinical relevance of minor variants and assess the utility of WGS for transmission control.