Direct Whole-Genome Sequencing of Sputum Accurately Identifies Drug-Resistant Mycobacterium tuberculosis Faster than MGIT Culture Sequencing
Direct Whole-Genome Sequencing of Sputum Accurately Identifies Drug-Resistant Mycobacterium tuberculosis Faster than MGIT Culture Sequencing
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DOI：
10.1128/jcm.00666-18
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发表时间：
2018-08-01
影响因子：
9.4
通讯作者：
Breuer, Judith
中科院分区：
文献类型：
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作者：
Doyle, Ronan M.;Burgess, Carrie;Breuer, Judith
目前可用于诊断耐药结核分枝杆菌感染的方法需要培养阳性或仅检测有限数量的耐药相关突变。快速准确地识别抗菌素耐药性，可以迅速开始有效的治疗。在这里，我们确定了直接从常规获得的诊断性痰样本中对结核分枝杆菌进行全基因组测序（WGS）的效用，以提供与分枝杆菌生长指示管（MGIT） WGS相比的全面耐药性概况。我们使用Agilent SureSelectXT试剂盒对43份痰样本进行靶向DNA富集测序，并对每位参与者的43份MGIT阳性样本进行测序。32份（74%）痰液样本和43份（100%）MGIT样本生成了全基因组。并与Xpert MTB/RIF和表型耐药检测结果进行比较。在样品接收后5天内，可通过痰液WGS预测抗生素敏感性，比MGIT培养的WGS早24天，比表型检测早31天。如果只对编码耐药区域进行测序，杂交速度更快，直接痰液结果可缩短至3天。我们表明，直接痰液测序有潜力提供全面的耐药检测，其速度明显快于MGIT全基因组测序或临床培养耐药表型检测。这种改进的周转时间使及时适当的治疗与相关的病人和保健服务的好处。改进样品制备是必要的，以确保可比的灵敏度和完整的耐药谱预测在所有情况下。
The current methods available to diagnose antimicrobial-resistant Mycobacterium tuberculosis infections require a positive culture or only test a limited number of resistance-associated mutations. A rapid accurate identification of antimicrobial resistance enables the prompt initiation of effective treatment. Here, we determine the utility of whole-genome sequencing (WGS) of M. tuberculosis directly from routinely obtained diagnostic sputum samples to provide a comprehensive resistance profile compared to that from mycobacterial growth indicator tube (MGIT) WGS. We sequenced M. tuberculosis from 43 sputum samples by targeted DNA enrichment using the Agilent SureSelectXT kit, and 43 MGIT positive samples from each participant. Thirty two (74%) sputum samples and 43 (100%) MGIT samples generated whole genomes. The times to antimicrobial resistance profiles and concordance were compared with Xpert MTB/RIF and phenotypic resistance testing from cultures of the same samples. Antibiotic susceptibility could be predicted from WGS of sputum within 5 days of sample receipt and up to 24 days earlier than WGS from MGIT culture and up to 31 days earlier than phenotypic testing. Direct sputum results could be reduced to 3 days with faster hybridization and if only regions encoding drug resistance are sequenced. We show that direct sputum sequencing has the potential to provide comprehensive resistance detection significantly faster than MGIT whole-genome sequencing or phenotypic testing of resistance from cultures in a clinical setting. This improved turnaround time enables prompt appropriate treatment with associated patient and health service benefits. Improvements in sample preparation are necessary to ensure comparable sensitivities and complete resistance profile predictions in all cases.