Comparative assessment of line-probe assays and targeted next-generation sequencing in drug-resistant tuberculosis diagnosis

Background Rapid and accurate detection of drug-resistant tuberculosis
(DR-TB) is crucial for ensuring effective treatment, halting transmission
and preventing the amplification of resistance. Comparative evaluations of
molecular diagnostic assays in high-burden settings are essential for
informing clinical decision-making for DR-TB treatment. Findings Among 720
clinical samples tested, MTBDRplus LPA sensitivity for rifampicin and
isoniazid was 92.3 % (95 % CI 88.9–94.8) and 91.9 % (88.4–94.4), each
significantly lower than ≥95% achieved by both tNGS workflows (p <
0.01). For fluoroquinolones (moxifloxacin and levofloxacin), the MTBDRsl
LPA and ONT had similar sensitivities (94.3% and 92.7%, and 94.8% and
93.9%, respectively), while GenoScreen outperformed both (97.3% and
96.6%). GenoScreen also demonstrated the highest sensitivity for amikacin
resistance (94.6%) compared to LPAs (88.7%) and ONT (88.3%). Complete
assay failure rates were low for LPAs (4.9%) and ONT (5.0%) and moderately
higher for GenoScreen (8.6%), with differences in single-target failures
across all assays. Interpretation LPAs demonstrated lower sensitivity and
more limited drug resistance detection compared to tNGS workflows,
underscoring the advantages of tNGS for improving DR-TB diagnostic
algorithms. These findings provide critical evidence to guide updates in
DR-TB diagnostic programs.