Prognostic significance of novel katG mutations in Mycobacterium tuberculosis.
Prognostic significance of novel katG mutations in Mycobacterium tuberculosis.
复制标题
结核分枝杆菌中新型 katG 突变的预后意义。
DOI：
10.1016/j.ijmyco.2014.11.043
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发表时间：
2015
影响因子：
1.2
通讯作者：
Catanzaro,T
中科院分区：
文献类型：
--
作者：
Valafar,F;Ramirez-Busby,SM;Torres,J;Paul,LynthiaV;Rodwell,TC;Victor,TC;Rodrigues,C;Gler,MT;Crudu,V;Catanzaro,T
背景通过全基因组测序（WGS），研究人员开始了解结核分枝杆菌（MTB）的遗传多样性及其在基因组水平上对诊断耐多药结核病（MDR-TB）的影响。全球耐药结核病诊断联盟（GCDD）对来自四个国家的366个临床结核病基因组（主要是MDR/XDR [广泛耐药]）进行了基因组规模变异分析，以告知快速分子诊断的发展。通过对异烟肼（INH）耐药分离株进行进化分析以预测预后，该项目得到了扩展。（130 INHR，21 INHS）印度临床MTB分离株（19：17 INHR，2 INHS）、摩尔多瓦（48：42 INHR，6 INHS）、菲律宾（26：20 INHR，6 INHS）和南非（58：51 INHR，7 INHS）被纳入本研究。INH药敏试验采用MGIT 960和WHO推荐的临界浓度0.1mg/L。使用PacBio RS WGS平台对分离株进行测序。使用圣地亚哥州立大学开发的专有管道（PacDAP）进行全基因组变异分析。为了推断赋予抗性的氨基酸变化，利用PAML来检测正选择下的计算机中的位点。ThedN/dS方法被用于结合贝叶斯经验贝叶斯，以确定网站下的积极选择和卡方分析，以确定所选择的sites.ResultsPacDAP变异分析发现22个新的过氧化氢酶-过氧化物酶（katG产品）突变的意义。其中14个为单核苷酸多态性，8个新突变与katGS 315 T和/或hA启动子内C-15 T联合出现。这些SNPs以前没有报道过。此外，在这些临床分离株中还观察到11种先前观察到但不常见的katG突变。这些结果表明，酶中的17种氨基酸处于正选择压力下;在南非和菲律宾最显着。在摩尔多瓦分离株中没有观察到对315以外密码子的选择压力。由于来自印度的菌株数量少，积极选择下的网站的意义是低的，没有预测印度可以作出基于本study.ConclusionsEleven的14个SNPs的耐药赋予，它被认为是剩余的8个组合突变是补偿性质的，或与已知的SNPs相结合，可以增加耐药水平。阳性选择结果表明，更符合长尾统计的多样化的耐药性进化路径，因此表明偏离了当前分子诊断所基于的传统点突变（或“热点”）模型。阳性选择压力表明“长尾”（即，替代耐药机制）和潜在的典型突变的重要性降低（特别是在南非和菲律宾），这可能对未来的窄靶分子诊断产生重大影响。
BackgroundBy using whole genome sequencing (WGS), researchers are beginning to understand the genetic diversity ofMycobacterium tuberculosis(MTB) and its consequences for the diagnosis of multidrug-resistant tuberculosis (MDR–TB) on a genomic scale. The Global Consortium for Drug-resistant TB Diagnostics (GCDD) conducted a genome scale variant analyses of 366 clinical MTB genomes (mostly MDR/XDR [extensively drug resistant]) from four countries in order to inform the development of rapid molecular diagnostics. This project has been extended by performing an evolutionary analysis of isoniazid (INH)-resistant isolates for prognostic purposes.Methods151 (130 INHR, 21 INHS) clinical MTB isolates from India (19: 17 INHR, 2 INHS), Moldova (48: 42 INHR, 6 INHS), the Philippines (26: 20 INHR, 6 INHS), and South Africa (58: 51 INHR, 7 INHS) were included in this study. INH drug susceptibility was determined by using MGIT 960 and WHO (World Health Organization)-recommended critical concentration of 0.1 mg/L. Isolates were sequenced using PacBio RS WGS platform. A genome-wide variant analysis was conducted using a proprietary pipeline (PacDAP) developed at San Diego State University. To infer the amino acid changes inkatGthat confer resistance, PAML was utilized to detect sitesin silicothat are under positive selection. ThedN/dSmethod was used in combination with Bayes empirical Bayes to determine sites under positive selection and Chi-Squared analysis to determine the significance of the selected sites.ResultsPacDAP variant analysis revealed 22 novel catalase-peroxidase (katGproduct) mutations. Of these, 14 were single nucleotide polymorphisms, while 8 novel mutations appeared in combination withkatGS315T and/or withinhApromoter C-15T. These SNPs have not been previously reported. Additionally, 11 previously observed, but uncommon,katGmutations were also observed in these clinical isolates. These results suggest that 17 amino acids in the enzyme are under positive selective pressure; most significantly in South Africa and the Philippines. No selective pressure on codons other than 315 was observed in isolates from Moldova. Due to the low number of isolates from India, the significance of the sites under positive selection was low and no prediction for India could be made based on this study.ConclusionsEleven of the 14 SNPs are resistance conferring, and it is believed that the remaining 8 combinatorial mutations are either compensatory in nature or, in combination with known SNPs, could increase resistance levels. Positive selection results indicate a diversifying evolutionary path to resistance more in line with long tail statistics and therefore indicate a departure from the traditional point mutation (or “hotspot”) model that current molecular diagnostics are based on. Positive selection pressures indicate a future with elevated diagnostic and prognostic significance of the “long tail” (i.e., alternative mechanisms of resistance) and potentially diminishing significance of the canonical mutations (especially in South Africa and the Philippines), which could have significant future implications on narrowly targeting molecular diagnostics.