The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs.
The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs.
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DOI：
10.1186/s13073-016-0385-x
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发表时间：
2016-12-22
期刊：
影响因子：
12.3
通讯作者：
Clark TG
中科院分区：
文献类型：
--
作者：
Phelan J;O'Sullivan DM;Machado D;Ramos J;Whale AS;O'Grady J;Dheda K;Campino S;McNerney R;Viveiros M;Huggett JF;Clark TG
抗结核药物耐药性的出现对公共卫生构成了日益严重的威胁。下一代测序作为一种用于调查结核分枝杆菌耐药性的诊断工具，正在迅速获得关注，以帮助做出治疗决定。然而，很少有关于这种测序用于分配抗性谱的精度的数据。我们研究了两个测序平台（Illumina MiSeq, Ion Torrent PGM™）和两个快速分析管道（TBProfiler, Mykrobe predictor），使用表征良好的参考菌株（H37Rv）和对多达13种药物耐药的结核病患者的临床分离株。结果与表型药敏试验比较。为了评估分析稳健性，对个体DNA样本进行重复测序。MiSeq和Ion PGM系统准确预测了耐药谱，并且在生物和技术样品重复之间具有高重复性。估计的变异错误率低（MiSeq 1 / 77 kbp, Ion PGM 1 / 41 kbp），基因组覆盖率高（MiSeq 51倍，Ion PGM 53倍）。MiSeq在富含gc的区域提供了优越的覆盖范围，这转化为假定的基因型药物特异性耐药的增量检测，包括对对氨基水杨酸和吡嗪酰胺的耐药。TBProfiler生物信息学管道与报告的除吡嗪酰胺和对氨基水杨酸外的所有药物的表型敏感性一致，总体一致性为95.3%。当使用Mykrobe预测因子时，与表型检测的一致性为73.6%。在分析一线和二线抗结核药物耐药性时，我们已经证明了两种测序平台的高比较重复性，以及TBProfiler突变文库和分析管道的高预测能力。然而，某些基因组区域覆盖的平台特异性变异性可能对预测对特定药物的耐药性有影响。这些发现可能对未来的临床实践有影响，因此值得进一步审查，在更大的研究中设置并使用更新的突变文库。本文的在线版本（doi:10.1186/s13073-016-0385-x）包含补充材料，可供授权用户使用。
The emergence of resistance to anti-tuberculosis drugs is a serious and growing threat to public health. Next-generation sequencing is rapidly gaining traction as a diagnostic tool for investigating drug resistance in Mycobacterium tuberculosis to aid treatment decisions. However, there are few little data regarding the precision of such sequencing for assigning resistance profiles. We investigated two sequencing platforms (Illumina MiSeq, Ion Torrent PGM™) and two rapid analytic pipelines (TBProfiler, Mykrobe predictor) using a well characterised reference strain (H37Rv) and clinical isolates from patients with tuberculosis resistant to up to 13 drugs. Results were compared to phenotypic drug susceptibility testing. To assess analytical robustness individual DNA samples were subjected to repeated sequencing. The MiSeq and Ion PGM systems accurately predicted drug-resistance profiles and there was high reproducibility between biological and technical sample replicates. Estimated variant error rates were low (MiSeq 1 per 77 kbp, Ion PGM 1 per 41 kbp) and genomic coverage high (MiSeq 51-fold, Ion PGM 53-fold). MiSeq provided superior coverage in GC-rich regions, which translated into incremental detection of putative genotypic drug-specific resistance, including for resistance to para-aminosalicylic acid and pyrazinamide. The TBProfiler bioinformatics pipeline was concordant with reported phenotypic susceptibility for all drugs tested except pyrazinamide and para-aminosalicylic acid, with an overall concordance of 95.3%. When using the Mykrobe predictor concordance with phenotypic testing was 73.6%. We have demonstrated high comparative reproducibility of two sequencing platforms, and high predictive ability of the TBProfiler mutation library and analytical pipeline, when profiling resistance to first- and second-line anti-tuberculosis drugs. However, platform-specific variability in coverage of some genome regions may have implications for predicting resistance to specific drugs. These findings may have implications for future clinical practice and thus deserve further scrutiny, set within larger studies and using updated mutation libraries. The online version of this article (doi:10.1186/s13073-016-0385-x) contains supplementary material, which is available to authorized users.
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影响因子：
16.6
作者：
Bradley P;Gordon NC;Walker TM;Dunn L;Heys S;Huang B;Earle S;Pankhurst LJ;Anson L;de Cesare M;Piazza P;Votintseva AA;Golubchik T;Wilson DJ;Wyllie DH;Diel R;Niemann S;Feuerriegel S;Kohl TA;Ismail N;Omar SV;Smith EG;Buck D;McVean G;Walker AS;Peto TE;Crook DW;Iqbal Z
通讯作者：
Iqbal Z
影响因子：
10.7
作者：
Price MN;Dehal PS;Arkin AP
通讯作者：
Arkin AP
对来自中国的 161 株结核分枝杆菌分离株进行基因组测序，鉴定出与耐药性相关的基因和基因间区域
影响因子：
30.8
作者：
Zhang, Hongtai;Li, Dongfang;Bi, Lijun
通讯作者：
Bi, Lijun
影响因子：
3.7
作者：
Derrien T;Estellé J;Marco Sola S;Knowles DG;Raineri E;Guigó R;Ribeca P
通讯作者：
Ribeca P
DOI：
10.1016/j.tube.2014.02.005
发表时间：
2014-05
期刊：
Tuberculosis (Edinburgh, Scotland)
影响因子：
--
作者：
Coll F;Preston M;Guerra-Assunção JA;Hill-Cawthorn G;Harris D;Perdigão J;Viveiros M;Portugal I;Drobniewski F;Gagneux S;Glynn JR;Pain A;Parkhill J;McNerney R;Martin N;Clark TG
通讯作者：
Clark TG