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Updated: Jun 2, 2026
06:07
Matrix-based DNA Extraction for Targeted Next-Generation Sequencing on Decontaminated Sputum Samples
Published on: June 6, 2025
Targeted next-generation sequencing for direct drug-resistant tuberculosis detection in sputum samples in Indonesia:
Bony Wiem Lestari1,2, Rifky Waluyajati Rachman3, Rahmah Aulia Zahra2
1Department of Public Health, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia.
The Lancet Regional Health. Southeast Asia
|June 1, 2026
Summary
Targeted Next Generation Sequencing (tNGS) shows promise for diagnosing drug-resistant tuberculosis (DRTB) in high-incidence settings. Optimization is needed to improve success rates, especially for samples with low bacterial load, and reduce costs for wider adoption.
Area of Science:
- Genomic medicine
- Infectious disease diagnostics
- Molecular epidemiology
Background:
- Targeted Next Generation Sequencing (tNGS) offers advanced diagnostics for drug-resistant tuberculosis (DRTB).
- Optimal implementation, yield, and cost-effectiveness in high TB-incidence settings require further evaluation.
- Understanding these factors is crucial for effective DRTB management.
Purpose of the Study:
- To evaluate the laboratory workflow, implementation cascade, turnaround time, and unit cost of tNGS for DRTB diagnostics.
- To assess the performance of tNGS using the Deeplex Myc-TB assay in Indonesia.
- To identify factors influencing tNGS success and inform optimization strategies.
Main Methods:
- Prospective evaluation of tNGS with Deeplex Myc-TB on sputum samples from patients with rifampicin-resistant TB (RRTB).
- Inclusion of patients from 32 hospitals and 15 community health centers in West Java, Indonesia.
- Analysis of sequencing success, turnaround time, and unit cost.
Main Results:
- Sequencing success varied by bacterial load, with 67.1% of samples completing sequencing and 52.8% yielding complete reads.
- Optimized workflow improved laboratory success to 82.4%.
- Median turnaround time was 8 days, with unit costs of $263.6 (iSeq) and $239.6 (MiSeq).
Conclusions:
- tNGS demonstrates good performance in patients with high sputum bacterial load and offers a relatively rapid turnaround time.
- Optimization for widespread adoption must consider DRTB burden, sample selection, sequencing platform, and cost-effectiveness.
- Further research is needed to maximize tNGS utility in resource-limited settings.
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