DOI: 10.5061/dryad.gqnk98t0f
title: Comparative assessment of line-probe assays and targeted next-generation sequencing in drug-resistant tuberculosis diagnosis

description: 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 &lt;
 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.
description: The Seq&Treat clinical study previously evaluated the
 performance of two targeted Next-Generation Sequencing (tNGS) workflows,
 Genoscreen Deeplex Myc-TB and Oxford Nanopore Technology Tuberculosis Drug
 Resistance Test, on direct sediment samples from persons at risk for
 DR-TB. Hain Line Probe Assay (LPAs – MTBDR<em>plus</em> and
 MTBDR<em>sl</em>) were run as a comparator test using an
 aliquot of the same sediment samples. Diagnostic performance of the LPAs
 and previously established tNGS performance were compared, including
 sensitivity and specificity, for rifampicin, isoniazid, fluoroquinolones
 (moxifloxacin, levofloxacin), and amikacin, using a composite reference
 standard of phenotypic drug susceptibility testing and whole-genome
 sequencing.
description: # Comparative assessment of line-probe assays and targeted next-generation
 sequencing in drug-resistant tuberculosis diagnosis ## Description of the
 data and file structure Per patient LPA results with variables for
 participant ID and NCBI Biosample ID for association with manuscript
 "Evaluating culture-free targeted next-generation sequencing for
 diagnosing drug-resistant tuberculosis: a multicentre clinical study of
 two end-to-end commercial workflows" ### Files and variables ####
 File: Seq&Treat_LPA_data.txt **Description:**  ##### Variables *
 ParticipantID: Unique Participant ID; text * BioSample ID: Unique
 BioSample Accession ID linking to publicly available sequencing data at
 the NCBI; text * PLUS_AMP_CTL: PLUS AMP CTL Presence of Hain MTBDRplus
 amplification control POSITIVE NEGATIVE; * PLUS_AMP_CTL_REP: PLUS AMP CTL
 REP Presence of Hain MTBDRplus amplification control on repeated test if
 done POSITIVE NEGATIVE NA; * PLUS_CON_CTL: PLUS CON CTL Presence of Hain
 MTBDRplus Conjugate control POSITIVE NEGATIVE; * PLUS_CON_CTL_REP: PLUS
 CON CTL REP Presence of Hain MTBDRplus Conjugate control on repeated test
 if done POSITIVE NEGATIVE NA; * PLUS_RES: PLUS RES Presence of Hain
 MTBDRplus Mtb complex specific control TUB POSITIVE NEGATIVE Invalid
 Indeterminate; * RPOB_RES: RPOB RES Hain MTBDRplus rpoB band results;
 *LPA_RIF: LPA RIF Hain MTBDRplus RIF result S susceptible R resistant NA
 not available Inv Invalid; * WHO_CALL_RIF: WHO CALL RIF Interpretation of
 MTBDRplus RIF call as per WHO guidelines R detected Resistance detected R
 inferred Resistance inferred R not detected Resistance not detected
 Invalid Indeterminate; * KATG_RES: KATG RES Hain MTBDRplus katG band
 results; * INHA_RES: INHA RES Hain MTBDRplus inhA band results; * LPA_INH:
 LPA INH Hain MTBDRplus INH result S susceptible R resistant NA not
 available Inv Invalid; * WHO_CALL_INH: WHO CALL INH Interpretation of
 MTBDRplus INH call as per WHO guidelines R detected Resistance detected R
 inferred Resistance inferred R not detected Resistance not detected
 Invalid Indeterminate; * SL_YN: SL YN Hain MTBDRsl run not done, done; *
 SL_AMP_CTL: SL AMP CTL Presence of Hain MTBDRsl amplification control
 POSITIVE NEGATIVE; * SL_AMP_CTL_REP: SL AMP CTL REP Presence of Hain
 MTBDRsl amplification control on repeated test if done POSITIVE NEGATIVE
 NA; * SL_CON_CTL: SL CON CTL Presence of Hain MTBDRsl Conjugate control
 POSITIVE NEGATIVE; * SL_CON_CTL_REP: SL CON CTL REP Presence of Hain
 MTBDRsl Conjugate control on repeated test if done POSITIVE NEGATIVE NA; *
 SL_RES: SL RES Presence of Hain MTBDRsl Mtb complex specific control TUB
 POSITIVE NEGATIVE Invalid Indeterminate; * GYRA_RES: GYRA RES Hain MTBDRsl
 gyrA band results; * GYRB_RES: GYRB RES Hain MTBDRsl gyrB band results; *
 LPA_FQ: LPA FQ Hain MTBDRsl FQ result S susceptible R resistant NA not
 available Inv Invalid; * WHO_CALL_FQ: WHO CALL FQ Interpretation of of
 MTBDRsl FQ call as per WHO guidelines R detected Resistance detected R
 inferred Resistance inferred R not detected Resistance not detected
 Invalid Indeterminate; * RRS_RES: RRS RES Hain MTBDRsl rrs band results; *
 EIS_RES: EIS RES Hain MTBDRsl eis band results; * LPA_AMK: LPA AMK Hain
 MTBDRsl AMK result S susceptible R resistant NA not available Inv Invalid;
 * WHO_CALL_AMK: WHO CALL AMK Interpretation of of MTBDRsl AMK call as per
 WHO guidelines R detected Resistance detected R inferred Resistance
 inferred R not detected Resistance not detected Invalid Indeterminate; *
 LPA_COMM: LPA COMM Laboratory notes; * LPA_sample_failure: LPA sample
 failure; indicates whether a sample failed both the MTBDRplus and MTBDRsl
 assays; "Passed" indicates a successful result, while
 "Failed" indicates a sample failure, which occurs if the TUB
 band is absent and/or the control bands for all four drug target gene loci
 are missing. * LPA_RIF_failure: LPA RIF failure; sample that failed to
 provide a result for RIF. "Passed" indicates a successful result
 for RIF, while "Target failure" indicates a failed results for
 RIF due to the absence TUB and the lack of the control bands for the RPOB
 gene locus. * LPA_INH_failure: LPA INH failure; sample that failed to
 provide a result for INH. "Passed" indicates a successful result
 for INH , while "Target failure" indicates a failed results for
 INH due to the absence TUB and the lack of the control bands for the KATG
 and INHA gene loci. * LPA_FQ_failure: LPA FQ failure; sample that failed
 to provide a result for FQ. "Passed" indicates a successful
 result for FQ , while "Target failure" indicates a failed
 results for FQ due to the absence TUB and the lack of the control bands
 for the GYRA abd GYRB gene loci. * LPA_AMK_failure: LPA AMK failure;
 sample that failed to provide a result for AMK. "Passed"
 indicates a successful result for AMK , while "Target failure"
 indicates a failed results for AMK due to the absence TUB and the lack of
 the control bands for the RRS abd EIS gene loci. ## Access information
 Other publicly accessible locations of the data: *
 [doi.org/10.5061/dryad.qjq2bvqs6](doi.org/10.5061/dryad.qjq2bvqs6) *
 [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1160005](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1160005) ## Human subjects data This publicly available metadata dataset has been de-identified to ensure the protection of human subjects in accordance with international ethical standards and applicable data protection regulations, including but not limited to the U.S. Health Insurance Portability and Accountability Act (HIPAA), the EU General Data Protection Regulation (GDPR), and relevant local laws in participating countries. All direct identifiers (e.g., names, dates of birth, addresses, contact information) have been removed. Indirect identifiers have also been reviewed and excluded or generalized to prevent re-identification of individuals. No data fields in the public release, either alone or in combination, can reasonably be used to identify a subject. Additionally, there are no retained keys, codes, or linkable information that would allow re-identification of the de-identified dataset by users. This de-identification process has been conducted under the oversight of qualified personnel and in compliance with institutional and regulatory guidelines. As such, the dataset is not considered to involve human subjects and is suitable for unrestricted public dissemination and secondary analysis.