Data from: Evaluating culture-free targeted next-generation sequencing for diagnosing drug-resistant tuberculosis: A multicentre clinical study of two end-to-end commercial workflows

Background: Drug-resistant tuberculosis remains a major obstacle in ending
the global tuberculosis epidemic. Deployment of molecular tools for
comprehensive drug resistance profiling is imperative for successful
detection and characterisation of tuberculosis drug resistance. We aimed
to assess the diagnostic accuracy of a new class of molecular diagnostics
for drug-resistant tuberculosis. Methods: We conducted a prospective,
cross-sectional, multicentre clinical evaluation of the performance of two
targeted next-generation sequencing (tNGS) assays for drug-resistant
tuberculosis at reference laboratories in three countries (Georgia, India,
and South Africa) to assess diagnostic accuracy and index test failure
rates. Eligible participants were aged 18 years or older, with molecularly
confirmed pulmonary tuberculosis, and at risk for rifampicin-resistant
tuberculosis. Sensitivity and specificity for both tNGS index tests
(GenoScreen Deeplex Myc-TB and Oxford Nanopore Technologies [ONT]
Tuberculosis Drug Resistance Test) were calculated for rifampicin,
isoniazid, fluoroquinolones (moxifloxacin, levofloxacin), second
line-injectables (amikacin, kanamycin, capreomycin), pyrazinamide,
bedaquiline, linezolid, clofazimine, ethambutol, and streptomycin against
a composite reference standard of phenotypic drug susceptibility testing
and whole-genome sequencing. Findings: Between April 1, 2021, and June 30,
2022, 832 individuals were invited to participate in the study, of whom
720 were included in the final analysis (212, 376, and 132 participants in
Georgia, India, and South Africa, respectively). Of 720 clinical sediment
samples evaluated, 658 (91%) and 684 (95%) produced complete or partial
results on the GenoScreen and ONT tNGS workflows, respectively, with 593
(96%) and 603 (98%) of 616 smear-positive samples producing tNGS sequence
data. Both workflows had sensitivities and specificities of more than 95%
for rifampicin and isoniazid, and high accuracy for fluoroquinolones
(sensitivity approximately ≥94%) and second line-injectables (sensitivity
80%) compared with the composite reference standard. Importantly, these
assays also detected mutations associated with resistance to critical new
and repurposed drugs (bedaquiline, linezolid) not currently detectable by
any other WHO-recommended rapid diagnostics on the market. We note that
the current format of assays have low sensitivity (≤50%) for linezolid and
more work on mutations associated with drug resistance is needed.
Interpretation: This multicentre evaluation demonstrates that culture-free
tNGS can provide accurate sequencing results for detection and
characterisation of drug resistance from Mycobacterium tuberculosis
clinical sediment samples for timely, comprehensive profiling of
drug-resistant tuberculosis.