A comparison of phenotypic and WGS drug susceptibility testing in Mycobacterium tuberculosis isolates from the Republic of Korea.
A comparison of phenotypic and WGS drug susceptibility testing in Mycobacterium tuberculosis isolates from the Republic of Korea.
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DOI：
10.1093/jacamr/dlad056
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发表时间：
2023-06
影响因子：
3.4
通讯作者：
中科院分区：
文献类型：
--
作者：
WGS在帮助解决结核病这一重大公共卫生问题方面具有巨大潜力。韩国的结核病发病率在所有经济合作与发展组织国家中排名第三，但迄今为止在结核病方面使用WGS的情况非常有限。回顾性比较2015 - 2017年韩国两个中心结核分枝杆菌（MTB）临床分离株，使用WGS比较表型药敏试验（pDST）和WGS药敏预测（WGS- dsp）。57株结核分枝杆菌分离株提取DNA，并使用Illumina HiSeq平台进行测序。WGS分析采用bwa mem、bcftools和IQ-Tree；使用TB profiler鉴定耐药标记物。表型敏感性在超国家结核病参考实验室（韩国结核病研究所）进行。在一线抗结核药物中，利福平、异烟肼、吡嗪酰胺和乙胺丁醇的一致性分别为98.25%、92.98%、87.72%和85.96%。与pDST相比，WGS-DSP对利福平、异烟肼、吡嗪酰胺和乙胺丁醇的敏感性分别为97.30%、92.11%、78.95%和95.65%。这些一线抗结核药物的特异性分别为100%、94.74%、92.11%和79.41%。对二线药物的敏感性为66.67% ~ 100%，特异性为82.98% ~ 100%。本研究证实了WGS在药物敏感性预测中的潜在作用，这将减少周转时间。然而，需要进一步进行更大规模的研究，以确保目前的耐药突变数据库能够反映韩国目前的结核病情况。
WGS has significant potential to help tackle the major public health problem of TB. The Republic of Korea has the third highest rates of TB of all Organisation for Economic Cooperation and Development countries but there has been very limited use of WGS in TB to date. A retrospective comparison of Mycobacterium tuberculosis (MTB) clinical isolates from 2015 to 2017 from two centres in the Republic of Korea using WGS to compare phenotypic drug susceptibility testing (pDST) and WGS drug susceptibility predictions (WGS-DSP). Fifty-seven MTB isolates had DNA extracted and were sequenced using the Illumina HiSeq platform. The WGS analysis was performed using bwa mem, bcftools and IQ-Tree; resistance markers were identified using TB profiler. Phenotypic susceptibilities were carried out at the Supranational TB reference laboratory (Korean Institute of Tuberculosis). For first-line antituberculous drugs concordance for rifampicin, isoniazid, pyrazinamide and ethambutol was 98.25%, 92.98%, 87.72% and 85.96%, respectively. The sensitivity of WGS-DSP compared with pDST for rifampicin, isoniazid, pyrazinamide and ethambutol was 97.30%, 92.11%, 78.95% and 95.65%, respectively. The specificity for these first-line antituberculous drugs was 100%, 94.74%, 92.11% and 79.41%, respectively. The sensitivity and specificity for second-line drugs ranged from 66.67% to 100%, and from 82.98% to 100%, respectively. This study confirms the potential role for WGS in drug susceptibility prediction, which would reduce turnaround times. However, further larger studies are needed to ensure current databases of drug resistance mutations are reflective of the TB present in the Republic of Korea.
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影响因子：
30.8
作者：
Manson AL;Cohen KA;Abeel T;Desjardins CA;Armstrong DT;Barry CE 3rd;Brand J;TBResist Global Genome Consortium;Chapman SB;Cho SN;Gabrielian A;Gomez J;Jodals AM;Joloba M;Jureen P;Lee JS;Malinga L;Maiga M;Nordenberg D;Noroc E;Romancenco E;Salazar A;Ssengooba W;Velayati AA;Winglee K;Zalutskaya A;Via LE;Cassell GH;Dorman SE;Ellner J;Farnia P;Galagan JE;Rosenthal A;Crudu V;Homorodean D;Hsueh PR;Narayanan S;Pym AS;Skrahina A;Swaminathan S;Van der Walt M;Alland D;Bishai WR;Cohen T;Hoffner S;Birren BW;Earl AM
通讯作者：
Earl AM
影响因子：
--
作者：
Han, Seung Jung;Song, Taeksun;Shin, Sung Jae
通讯作者：
Shin, Sung Jae
DOI：
10.1056/nejmoa1800474
发表时间：
2018-10-11
期刊：
The New England journal of medicine
影响因子：
--
作者：
CRyPTIC Consortium and the 100,000 Genomes Project;Allix-Béguec C;Arandjelovic I;Bi L;Beckert P;Bonnet M;Bradley P;Cabibbe AM;Cancino-Muñoz I;Caulfield MJ;Chaiprasert A;Cirillo DM;Clifton DA;Comas I;Crook DW;De Filippo MR;de Neeling H;Diel R;Drobniewski FA;Faksri K;Farhat MR;Fleming J;Fowler P;Fowler TA;Gao Q;Gardy J;Gascoyne-Binzi D;Gibertoni-Cruz AL;Gil-Brusola A;Golubchik T;Gonzalo X;Grandjean L;He G;Guthrie JL;Hoosdally S;Hunt M;Iqbal Z;Ismail N;Johnston J;Khanzada FM;Khor CC;Kohl TA;Kong C;Lipworth S;Liu Q;Maphalala G;Martinez E;Mathys V;Merker M;Miotto P;Mistry N;Moore DAJ;Murray M;Niemann S;Omar SV;Ong RT;Peto TEA;Posey JE;Prammananan T;Pym A;Rodrigues C;Rodrigues M;Rodwell T;Rossolini GM;Sánchez Padilla E;Schito M;Shen X;Shendure J;Sintchenko V;Sloutsky A;Smith EG;Snyder M;Soetaert K;Starks AM;Supply P;Suriyapol P;Tahseen S;Tang P;Teo YY;Thuong TNT;Thwaites G;Tortoli E;van Soolingen D;Walker AS;Walker TM;Wilcox M;Wilson DJ;Wyllie D;Yang Y;Zhang H;Zhao Y;Zhu B
通讯作者：
Zhu B
DOI：
10.5588/ijtld.18.0658
发表时间：
2019-07-01
影响因子：
4
作者：
Lee, M.;Han, J.;Yim, J-J.
通讯作者：
Yim, J-J.
影响因子：
4.1
作者：
Oh, Juhwan;Lee, Jong-Koo;Hirschhorn, Lisa R.
通讯作者：
Hirschhorn, Lisa R.