Evaluation of T-NGS, Xpert Ultra, and Line Probe Assay on Clinical Samples for the Diagnosis of Drug-Resistant Pulmonary Tuberculosis in Rio de Janeiro

Background The rapid detection of drug resistance in Mycobacterium tuberculosis is essential for managing drug-resistant tuberculosis (DR-TB). This study evaluated the performance of molecular assays compared to phenotypic drug susceptibility testing (pDST) and targeted next-generation sequencing (T-NGS). Methods We retrospectively analyzed 40 presumptive pulmonary DR-TB cases in Rio de Janeiro from 2018 to 2022. Xpert MTB/RIF Ultra (Xpert Ultra) and Line Probe Assay (LPA; MTBDRplus = LPA-1, MTBDRsl = LPA-2) were performed directly on clinical respiratory specimens, with pDST serving as the reference standard. T-NGS was used to identify resistance mutations and clarify discordant results. Results Most samples (92.5%) were smear-positive. Xpert Ultra and LPA-1 demonstrated high sensitivity for detecting resistance to rifampicin (91.7% and 89.3%, respectively). However, LPA-1 exhibited lower sensitivity for isoniazid (81.5%). The performance of LPA-1 decreased in samples with cycle threshold (Ct) values ≥16, indicating low bacterial load (p = 0.001). T-NGS detected resistance to fluoroquinolones (22.5%) and injectables (15-20%) that was missed by LPA-2 and MGIT. Mixed infections were identified in 17.5% of samples and accounted for 27.8% of discordant results. Isoniazid heteroresistance was detected in 32.5% of samples by LPA-1 and in 7.5% by T-NGS. Conclusions Xpert Ultra and LPA-1 are effective for the rapid detection of rifampicin resistance but have limitations for isoniazid and second-line drugs. T-NGS improved the detection of low-level resistance, heteroresistance, and mixed infections, supporting its implementation in reference laboratories for comprehensive DR-TB diagnosis.