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] Tu..., Participants meeting eligibility criteria were asked to provide at least 6 mL sputum either in one or two samples collected on day 1 and day 2. Samples were homogenized, decontaminated, re-suspended in 4mL final volume for all downstream testing. MTB/RIF, acid-fast bacilli (AFB) smear, Hain MTBDRplus and MTBDRsl, Mycobacteria Growth Indicator Tube (MGIT) and Löwenstein–Jensen medium (LJ) culture were performed on the sediment for standard of care testing. MGIT pDST was performed for all culture-positive samples for RIF, INH, FQ (MFX, LFX), PZA, AMK, CAP, KAN, BDQ, LZD, CLF, STR, and EMB at WHO endorsed critical concentrations. , , # 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

[https://doi.org/10.5061/dryad.dr7sqvb8m](https://doi.org/10.5061/dryad.dr7sqvb8m)

## Description of the data and file structure

Associated per sample clinical, genetic reference, phenotypic drug susceptibility, and tNGS results for Mycobacterium tuberculosis collected during the Seq&Treat clinical trial sponsored by FIND, the Foundation for Innovative New Diagnostics

### Files and variables

#### File: dryad.txt

**Description:** 

##### Variables

* insdc_biosample_accession: Unique BioSample Accession ID linking to publicly available sequencing data at the INSDC
* antibiotic: drug name
* dst_method: Culture Medium used to perform the phenotypic susceptibility testing
* critical_concentration: Concentration at which the antibiotic was tested
* resistance_phenotype: Susceptible or resistant result

#..., This dataset has been de-identified and is publicly available in accordance with participant consent and ethical research standards. All participants provided informed consent for their de-identified data to be shared in a public data repository for the purposes of scientific research and transparency.

De-identification was carried out by removing all direct identifiers and indirect identifiers. Additionally, all free-text fields were reviewed to ensure that no potentially identifying information was retained. The dataset was reviewed to confirm that no combination of variables could reasonably lead to re-identification of individual participants.