Targeted next-generation sequencing for drug-resistant tuberculosis diagnosis: implementation considerations for...

Area of Science:

• Microbiology
• Genomics
• Infectious Diseases

Background:

• Early and accurate diagnosis of drug-resistant tuberculosis (DR-TB) is crucial for effective treatment.
• Phenotypic drug susceptibility testing (pDST) is accurate but slow; rapid molecular assays have limited drug coverage.
• Targeted next-generation sequencing (tNGS) presents a potential solution for broad and rapid resistance detection.

Purpose of the Study:

• To evaluate the performance of two tNGS solutions (Deeplex Myc-TB and ONT) in detecting drug resistance for DR-TB.
• To compare tNGS performance against WHO-recommended molecular assays and pDST.
• To identify factors influencing the integration of tNGS into diagnostic workflows.

Main Methods:

• The study analyzed data from 763 samples across three high-burden DR-TB settings within the Seq&Treat study.
• Sequencing success rates and drug resistance detection were assessed based on initial Xpert MTB/RIF results and WHO-recommended drug regimens.
• Performance was compared to other WHO-endorsed assays, considering potential algorithmic impacts.

Main Results:

• Sequencing success rates were high: 88.5% for GenoScreen and 93.1% for ONT.
• tNGS provided complete resistance data for 73%-86% of drugs in recommended regimens, compared to 92%-93% for pDST.
• Both tNGS solutions demonstrated sensitivity equal to or exceeding that of WHO-recommended molecular assays.

Conclusions:

• tNGS is a valuable centralized tool for comprehensive drug resistance testing to guide DR-TB treatment.
• Integrating tNGS with existing molecular tests optimizes diagnostic workflows for timely and complete resistance detection.
• Findings support policy updates for incorporating tNGS into global TB diagnostic algorithms.