Comparative assessment of line probe assays and targeted next-generation sequencing in drug-resistant tuberculosis diagnosis.

IF 10.8 1区医学 Q1 MEDICINE, RESEARCH & EXPERIMENTAL

EBioMedicine Pub Date : 2025-09-01 Epub Date: 2025-08-05 DOI:10.1016/j.ebiom.2025.105875

Giovanna Carpi, Marva Seifert, Andres De la Rossa, Swapna Uplekar, Camilla Rodrigues, Nestani Tukvadze, Shaheed V Omar, Anita Suresh, Timothy C Rodwell, Rebecca E Colman

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引用次数: 0

Abstract

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.

Methods: The Seq&Treat clinical study previously evaluated the performance of two targeted next-generation sequencing (tNGS) workflows, GenoScreen Deeplex Myc-TB and Oxford Nanopore Technologies Tuberculosis Drug Resistance Test, on direct sediment samples from persons at risk for DR-TB. Hain Line Probe Assay (LPAs-MTBDRplus and MTBDRsl) 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.

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 < 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.

Funding: Support for the Seq&Treat project was provided through funding from Unitaid (2019-32-FIND MDR).

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线探针检测和靶向新一代测序在耐药结核病诊断中的比较评估。

背景：快速准确地检测耐药结核病（DR-TB）对于确保有效治疗、阻止传播和防止耐药性扩大至关重要。在高负担环境中对分子诊断分析方法进行比较评价对于为耐药结核病治疗的临床决策提供信息至关重要。方法：Seq&Treat临床研究先前评估了两种靶向下一代测序（tNGS）工作流程（GenoScreen Deeplex Myc-TB和Oxford Nanopore Technologies Tuberculosis Drug Resistance Test）对耐药结核病风险人群的直接沉积物样本的性能。Hain Line Probe Assay （LPAs-MTBDRplus和MTBDRsl）使用相同的沉积物样品作为比较试验。采用表型药敏试验和全基因组测序的综合参考标准，比较LPAs的诊断性能和先前建立的tNGS性能，包括对利福平、异烟肼、氟喹诺酮类药物（莫西沙星、左氧氟沙星）和阿米卡星的敏感性和特异性。结果：在720份临床样本中，MTBDRplus LPA对利福平和异烟肼的敏感性分别为92.3% （95% CI 88.9-94.8）和91.9%(88.4-94.4)，均显著低于两种tNGS工作流程的≥95% （p < 0.01）。对于氟喹诺酮类药物（莫西沙星和左氧氟沙星），MTBDRsl LPA和ONT的敏感性相似（分别为94.3%和92.7%，94.8%和93.9%），而GenoScreen的敏感性优于两者（97.3%和96.6%）。与LPAs（88.7%）和ONT（88.3%）相比，GenoScreen对阿米卡星耐药的敏感性最高（94.6%）。LPAs和ONT的完全分析失败率较低（4.9%），而GenoScreen的失败率略高（8.6%），所有分析的单靶点失败率存在差异。解释：与tNGS工作流程相比，LPAs显示出更低的敏感性和更有限的耐药检测，强调了tNGS在改进耐药结核病诊断算法方面的优势。这些发现为指导耐药结核病诊断规划的更新提供了重要证据。资金：Seq&Treat项目由国际药品采购机制（2019-32-FIND MDR）资助。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

EBioMedicine Biochemistry, Genetics and Molecular Biology-General Biochemistry,Genetics and Molecular Biology

CiteScore

17.70

自引率

0.90%

发文量

579

审稿时长

5 weeks

期刊介绍： eBioMedicine is a comprehensive biomedical research journal that covers a wide range of studies that are relevant to human health. Our focus is on original research that explores the fundamental factors influencing human health and disease, including the discovery of new therapeutic targets and treatments, the identification of biomarkers and diagnostic tools, and the investigation and modification of disease pathways and mechanisms. We welcome studies from any biomedical discipline that contribute to our understanding of disease and aim to improve human health.