线探针检测法与靶向新一代测序技术在耐多药结核病诊断中的比较评估
Comparative assessment of line probe assays and targeted next-generation sequencing in drug-resistant tuberculosis diagnosis.
作者信息
Carpi Giovanna, Seifert Marva, De la Rossa Andres, Uplekar Swapna, Rodrigues Camilla, Tukvadze Nestani, Omar Shaheed V, Suresh Anita, Rodwell Timothy C, Colman Rebecca E
机构信息
FIND, Geneva, Switzerland.
FIND, Geneva, Switzerland; Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of San Diego, San Diego, CA, USA.
出版信息
EBioMedicine. 2025 Aug 4;119:105875. doi: 10.1016/j.ebiom.2025.105875.
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).
背景
快速准确地检测耐多药结核病（DR-TB）对于确保有效治疗、阻断传播以及防止耐药性扩散至关重要。在高负担地区对分子诊断检测方法进行比较评估，对于为DR-TB治疗的临床决策提供依据至关重要。
方法
Seq&Treat临床研究先前评估了两种靶向新一代测序（tNGS）工作流程，即GenoScreen Deeplex Myc-TB和牛津纳米孔技术结核病耐药性检测，对来自DR-TB高危人群的直接沉淀物样本的性能。使用相同沉淀物样本的一份等分试样进行Hain线性探针检测（LPAs-MTBDRplus和MTBDRsl）作为对照试验。使用表型药物敏感性检测和全基因组测序的复合参考标准，比较了LPAs的诊断性能和先前确定的tNGS性能，包括对利福平、异烟肼、氟喹诺酮类（莫西沙星、左氧氟沙星）和阿米卡星的敏感性和特异性。
结果
在测试的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工作流程所达到的≥95%（p<0.01）。对于氟喹诺酮类（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%，以及94.8%和93.9%），而GenoScreen的表现优于两者（97.3%和96.6%）。与LPAs（88.7%）和ONT（88.3%）相比，GenoScreen对阿米卡星耐药性的敏感性也最高（94.6%）。LPAs（4.9%）和ONT（5.0%）的完全检测失败率较低，GenoScreen的则略高（8.6%），所有检测方法在单靶点失败方面存在差异。
解读
与tNGS工作流程相比，LPAs的敏感性较低，耐药性检测更有限，这突出了tNGS在改进DR-TB诊断算法方面的优势。这些发现为指导DR-TB诊断项目的更新提供了关键证据。
资金来源
Seq&Treat项目得到了全球药品设施（2019-32-FIND MDR）的资金支持。
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