数字农科院2.0

Deep Amplicon Sequencing Reveals Culture-dependent Clonal Selection of Mycobacterium tuberculosis in Clinical Samples

文献类型： 外文期刊

作者： Jiuxin Qu;Wanfei Liu;Shuyan Chen;Chi Wu;Wenjie Lai;Rui Qin;Feidi Ye;Yuanchun Li;Liang Fu;Guofang Deng;Lei Liu;Qiang Lin;Peng Cui

作者机构：

关键词： （2-1-2）Culture-dependent;Culture-free;Deep amplicon sequencing;Drug susceptibility testing;Mycobacterium tuberculosis

期刊名称： Genomics, Proteomics and Bioinformatics

ISSN： 1672-0229

年卷期： 2025 年 22 卷 6 期

页码：

收录情况： SCIE（2025版） ; ; CSCD（2025-2026年度） ; ; 科技核心（2024版）

摘要： The commonly-used drug susceptibility testing (DST) relies on bacterial culture and faces shortcomings such as long turnaround time and clonal/subclonal selection biases. Here, we developed a targeted deep amplicon sequencing (DAS) method directly applied to clinical specimens. In this DAS panel, we examined 941 drug-resistant mutations (DRMs) associated with 20 anti-tuberculosis drugs with only 4 pg of initial DNA input, and reduced the clinical testing time from 20 days to 2 days. A prospective study was conducted using 115 clinical specimens, predominantly positive for the Xpert® Mycobacterium tuberculosis/rifampicin (Xpert MTB/RIF) assay, to evaluate DRM detection. DAS was performed on culture-free specimens, while culture-dependent isolates were used for phenotypic DST, DAS, and whole-genome sequencing (WGS). For in silico molecular DST, our result based on DAS panel revealed the similar accuracy to three published reports based on WGS. For 82 isolates, application of DAS using the resistance-determining mutation method showed better accuracy (93.03% vs. 92.16%), sensitivity (96.10% vs. 95.02%), and specificity (91.33% vs. 90.62%) than WGS using the Mykrobe software. Compared to culture-dependent WGS, culture-free DAS provides a full picture of sequence variation at the population level, exhibiting in detail the gain-and-loss variants caused by bacterial culture. Our study performs a systematic verification of the advantages of DAS in clinical applications and comprehensively illustrates the discrepancies in Mycobacterium tuberculosis before and after culture.

分类号：

  • 相关文献

[1]Characterization of Rv0394c gene encoding hyaluronidase and chondrosulfatase from Mycobacterium tuberculosis. Yuan, Xianglian,Chen, Liping,Cao, Jun,Yu, Shenye,Liu, Siguo,Yuan, Xianglian,Deng, Xiaoxia,Pang, Hai,Wang Quankai. 2013

[2]Development of one-tube multiplex polymerase chain reaction (PCR) for detecting Mycobacterium bovis. Quan, Zhang,Haiming, Tan,Xiaoya, Cai,Weifeng, Yuan,Hong, Jia,Hongfei, Zhu.

[3]Crystallization and preliminary X-ray analysis of a novel esterase Rv0045c from Mycobacterium tuberculosis. Xu, Lipeng,Liu, Siguo,Xu, Lipeng,Guo, Jiubiao,Zheng, Xiangdong,Pang, Hai,Wen, Tingyi,Sun, Fei. 2010

[4]Expression, Purification and Characterisation of Secreted Esterase Rv2525c from Mycobacterium tuberculosis. Dang, Guanghui,Chen, Liping,Li, Zhaoli,Cui, Yingying,Cao, Jun,Yu, Shenye,Liu, Siguo,Deng, Xiaoxia,Pang, Hai.

[5]C-terminal heat shock protein 70 of Mycobacterium tuberculosis as a molecular adjuvant for DNA vaccination with the porcine circovirus type 2 ORF2 (capsid) gene in mice. Fu, Fang,Tian, Huabin,Li, Xuesong,Lang, Yuekun,Liu, Siguo,Li, Haizhong,Wang, Wei,Li, Xi,Chen, Xin,Li, Xuesong,Tong, Guangzhi. 2013

[6]A novel B cell epitope in cold-shock DEAD-box protein A from Mycobacterium tuberculosis. Wang, Huanan,Zhu, Ting,Yu, Shenye,Liu, Huifang,Wang, Xiumei,Chen, Liping,Si, Wei,Liu, Siguo,Wang, Huanan,Pang, Hai.

[7]Characterization of a novel exported esterase Rv3036c from Mycobacterium tuberculosis. Chen, Liping,Dang, Guanghui,Cao, Jun,Yu, Shenye,Liu, Siguo,Dang, Guanghui,Deng, Xiaoxia,Pang, Hai,Dang, Guanghui,Wu, Defeng.

[8]A VLP-Based Vaccine Displaying HBHA and MTP Antigens of Mycobacterium tuberculosis Induces Protective Immune Responses in M. tuberculosis H37Ra Infected Mice. Juan Wang,Tao Xie,Inayat Ullah,Youjun Mi,Xiaoping Li,Yang Gong,Pu He,Yuqi Liu,Fei Li,Jixi Li,Zengjun Lu,Bingdong Zhu. 2023

[9]Characterization Of A Novel Mycobacterium Tuberculosis Serine Protease (Rv3194C) Activity And Pathogenicity. Li, H, Dang, GH, Liu, HX, Wang, ZX, Cui, ZY, Song, NN, Chen, LP, Liu, SG. 2019

[10]Extracellular Sphingomyelinase Rv0888 Of Mycobacterium T.uberculosis Contributes To Pathological L ung Injury Of Mycobacterium Smegmatis In Mice Via Inducing Formation Of Neutrophil Extracellular Traps. Dang, GH, Cui, YY, Wang, L, Li, TT, Cui, ZY, Song, NN, Chen, LP, Pang, H, Liu, SG. 2018

[11]Pe17 Protein From Mycobacterium Tuberculosis E.nhances Mycobacterium Smegmatis Survival I n Macrophages And Pathogenicity In Mice. Li, Z, Liu, HX, Li, HF, Dang, GH, Cui, ZY, Song, NN, Wang, QK, Liu, SG, Chen, LP. 2019

[12]PE12 interaction with TLR4 promotes intracellular survival of Mycobacterium tuberculosis by suppressing inflammatory response. Jiajun Zhang,Yingying Cui,Xinxin Zang,Tingting Feng,Fanruo Chen,Hui Wang,Guanghui Dang,Siguo Liu. 2023

[13]The combination of Mycobacterium tuberculosis fusion proteins LT33 and LT28 induced strong protective immunity in mice. Pu He,Juan Wang,Daquan Tan,Lina Hu,Yanlin Ma,Youjun Mi,Fei Li,Tingting Zhang,Yunjie Du,Wenhua Zhang,Jixi Li,Lei Jiao,Bingdong Zhu. 2024

[14]Plasma-based ultrasensitive detection of Mycobacterium tuberculosis ESAT6/CFP10 fusion antigen using a CRISPR-driven aptamer fluorescence testing (CRAFT). Siyuan Liu,Guohui Xiao,Peixuan Li,Yating Xu,Xinhao Fan,Lin Tian,Su Zhang,Guoliang Zhang. 2025

[15]Development and application of a curcumin-cinnamon essential oil nanoemulsion agent against mycobacteria. Lei, Zhihui,Ren, Yixuan,Wang, Jinyao,Shi, Haisu,Lin, Hu,Chen, Hong,Bi, Lijun,Wang, Yutang,Zhang, Hongtai. 2025

[16]Cross-sectional analysis of tuberculosis burden and risk factors in Swabi district, Khyber Pakhtunkhwa, Pakistan. Iqbal Ahmad,Madiha Fatima,Ilyas Khan,Sulaiman Bahadar,Abdul Qadeer,Mohamad S. Hakim. 2025

作者其他论文 更多>>