London Calling 2023: Tuberculosis drug resistance profiling from native sputum using nanopore targeted sequencing: a field application study

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), and drug-resistant tuberculosis (DR-TB) remain global public-health threats. Drug susceptibility testing is essential for diagnosing and treating DR-TB effectively, but current molecular diagnostic assays are limited. We tested Oxford Nanopore’s targeted next-generation sequencing (tNGS) assay at two clinics in Southern Africa as part of an ongoing prospective TB cohort research study to evaluate its feasibility and performance in profiling DR-TB in a near-patient setting. Sequencing results were compared with local routine drug susceptibility testing results. Our initial findings suggest that Oxford Nanopore tNGS can detect Mtb and drug resistance  associated mutations using native sputum samples and is a promising and feasible rapid sequencing approach for comprehensive genotypic drug resistance profiling in high TB burden countries.