Microbiology Section, Department of Laboratory Medicine, P.D. Hinduja National Hospital and Medical Research Centre, Mumbai, India.
Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Tuberculosis (Edinb). 2021 Mar;127:102051. doi: 10.1016/j.tube.2021.102051. Epub 2021 Jan 8.
Timely drug resistance detection is essential to global tuberculosis management. Unfortunately, rapid molecular tests assess resistance to only a few drugs, with culture required for comprehensive susceptibility test results.
We evaluated targeted next generation sequencing (tNGS) for tuberculosis on 40 uncultured sputum samples. Resistance profiles from tNGS were compared with profiles from Xpert MTB/RIF, line probe assay (LPA), pyrosequencing (PSQ), and phenotypic testing. Concordance, sensitivity, specificity, and overall test agreement were compared across assays.
tNGS provided results for 39 of 40 samples (97.5%) with faster turnaround than phenotypic testing (median 3 vs. 21 days, p = 0.0068). Most samples were isoniazid and rifampin resistant (N = 31, 79.5%), 21 (53.8%) were fluoroquinolone resistant, and 3 (7.7%) were also resistant to Kanamycin. Half were of the Beijing lineage (N = 20, 51.3%). tNGS from uncultured sputum identified all resistance to isoniazid, rifampin, fluoroquinolones, and second-line injectable drugs that was identified by other methods. Agreement between tNGS and existing assays was excellent for isoniazid, rifampin, and SLDs, very good for levofloxacin, and good for moxifloxacin.
tNGS can rapidly identify tuberculosis, lineage, and drug resistance with faster turnaround than phenotypic testing. tNGS is a potential alternative to phenotypic testing in high-burden settings.
及时发现耐药性对于全球结核病管理至关重要。不幸的是，快速分子检测仅能评估少数几种药物的耐药性，而综合药敏试验结果则需要培养。
我们评估了 40 例未培养痰液样本的靶向下一代测序（tNGS）在结核病中的应用。将 tNGS 的耐药谱与 Xpert MTB/RIF、线性探针分析（LPA）、焦磷酸测序（PSQ）和表型检测的耐药谱进行比较。比较了不同检测方法的一致性、敏感性、特异性和总体检测一致性。
tNGS 为 40 个样本中的 39 个（97.5%）提供了结果，其周转时间比表型检测更快（中位数分别为 3 天和 21 天，p = 0.0068）。大多数样本对异烟肼和利福平耐药（N = 31，79.5%），21 个（53.8%）对氟喹诺酮类耐药，3 个（7.7%）对卡那霉素也耐药。有一半样本属于北京家族（N = 20，51.3%）。tNGS 从未培养的痰液中鉴定出所有对异烟肼、利福平、氟喹诺酮类和二线注射药物的耐药性，这些耐药性是通过其他方法鉴定出来的。tNGS 与现有检测方法在异烟肼、利福平及 SLD 方面的一致性极好，在左氧氟沙星方面的一致性非常好，在莫西沙星方面的一致性良好。
tNGS 可以快速鉴定结核病、谱系和耐药性，其周转时间比表型检测更快。在高负担环境下，tNGS 可能是表型检测的替代方法。
