利用全基因组测序预测中国上海结核分枝杆菌的药物耐药性。
Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Shanghai, China.
机构信息
Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China; Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
Shanghai Municipal Center for Disease Control and Prevention.
出版信息
Int J Infect Dis. 2020 Jul;96:48-53. doi: 10.1016/j.ijid.2020.04.039. Epub 2020 Apr 24.
OBJECTIVE
To evaluate the performance of whole-genome sequencing (WGS) for predicting Mycobacterium tuberculosis (MTB) drug resistance.
METHODS
276 rifampin-resistance tuberculosis (RR-TB) and 30 rifampicin-sensitive clinical isolates were randomly selected from patients with tuberculosis in Shanghai Pulmonary Hospital (SPH). Phenotypic drug susceptibility testing (DST) against six anti-TB drugs was performed, and WGS was used to predict the drug resistance using an online 'TB-Profiler' tool.
RESULTS
Using phenotypic susceptibility as the gold standard, the overall sensitivities and specificities for WGS were 94.53% and 92.00% for isoniazid, 97.10% and 100.00% for rifampicin, 97.46% and 64.36% for ethambutol, 97.14% and 95.83% or streptomycin, 93.02% and 98.87% for ofloxacin, and 75.00% and 100.00% for amikacin, respectively. The concordances of WGS-based DST and phenotypic DST were: isoniazid (94.12%), rifampicin (97.39%), ethambutol (77.12%), streptomycin (96.73%), ofloxacin (96.41%) and amikacin (97.06%).
CONCLUSIONS
WGS could be a promising approach to predict resistance to isoniazid, rifampicin, ethambutol, streptomycin, ofloxacin, and amikacin.
目的
评估全基因组测序（WGS）预测结核分枝杆菌（MTB）药物耐药性的性能。
方法
从上海肺科医院（SPH）的结核病患者中随机选择 276 例利福平耐药性结核病（RR-TB）和 30 例利福平敏感临床分离株。对六种抗结核药物进行表型药物敏感性测试（DST），并使用在线“TB-Profiler”工具使用 WGS 预测药物耐药性。
结果
以表型药敏性为金标准，WGS 对异烟肼的总敏感性和特异性分别为 94.53%和 92.00%，对利福平的敏感性和特异性分别为 97.10%和 100.00%，对乙胺丁醇的敏感性和特异性分别为 97.46%和 64.36%，对链霉素的敏感性和特异性分别为 97.14%和 95.83%，对氧氟沙星的敏感性和特异性分别为 93.02%和 98.87%，对阿米卡星的敏感性和特异性分别为 75.00%和 100.00%。WGS 基于 DST 和表型 DST 的一致性为：异烟肼（94.12%），利福平（97.39%），乙胺丁醇（77.12%），链霉素（96.73%），氧氟沙星（96.41%）和阿米卡星（97.06%）。
结论
WGS 可能是预测异烟肼、利福平、乙胺丁醇、链霉素、氧氟沙星和阿米卡星耐药性的一种很有前途的方法。
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