Field evaluation of nanopore targeted next-generation sequencing to predict drug-resistant tuberculosis from native sputum in South Africa and Zambia

作者：Tiana Carina Schwab, Lavania Joseph, Andrew Moono, Pauline C. Göller, Mamello Bride Motsei, Guy Muula, Denise Evans, Stefan Neuenschwander, Gunar Günther, Carolyn Bolton‐Moore, Peter M. Keller, Alban Ramette, Matthias Egger, Shaheed Vally Omar, Lukas Fenner, on behalf of IeDEA Southern Africa (IeDEA-SA) · 发表于：Journal of Clinical Microbiology · 年份：2025 · DOI：10.1128/jcm.01390-24 · 被引用次数：9 · 研究领域：Tuberculosis Research and Epidemiology、Mycobacterium research and diagnosis、Pneumonia and Respiratory Infections

ABSTRACT Rapid and comprehensive drug susceptibility testing (DST) is essential for diagnosing and treating drug-resistant tuberculosis effectively, and next-generation sequencing can be an effective genotypic DST method. We implemented and evaluated the performance of a nanopore targeted sequencing assay, called the Tuberculosis Drug Resistance Test (TBDR, Oxford Nanopore Diagnostics, Ltd., United Kingdom), which predicts drug resistance to 16 TB drugs, at a South African reference laboratory and a district diagnostic laboratory in Zambia. We compared the sequencing success rates between unprocessed and decontaminated sputum samples and determined the diagnostic accuracy against local DST (Xpert MTB/RIF Ultra, Xpert MTB/XDR, and BD BACTEC MGIT phenotypic DST). We prospectively sequenced 236 samples and have 148 samples with sequencing results from unprocessed and decontaminated sputum. We obtained successful sequencing results from 66.4% (94/148) unprocessed sputum samples and 75% (111/148) decontaminated samples. Sequencing success rates at the two sites differed, with 50.7% (36/71) successful sequencing results from unprocessed sputum in Zambia and 75.3% (58/77) in South Africa. Samples with “low” bacterial load, measured by Xpert MTB/RIF Ultra, tended to produce fewer successful sequencing results. TBDR sequencing predicted resistances in 48 samples, detecting resistance for rifampicin ( n = 41) and isoniazid ( n = 20), as well as 10 second-line drugs ( n = 15). Sensitivi...