The role of mutations in genes associated with phenotypic resistance to bedaquiline (BDQ) and delamanid (DLM) in Mycobacterium tuberculosis complex (MTBc) strains is poorly characterized. A clear understanding of the genetic variants’ role is crucial to guide the development of molecular-based drug susceptibility testing (DST). In this work, we analyzed all mutations in candidate genomic regions associated with BDQ- and DLM-resistant phenotypes using a whole-genome sequencing (WGS) data set from a collection of 4,795 MTBc clinical isolates from six countries with a high burden of tuberculosis (TB). From WGS analysis, we identified 61 and 163 unique mutations in genomic regions potentially involved in BDQ- and DLM-resistant phenotypes, respectively. Importantly, all strains were isolated from patients who likely have never been exposed to these medicines. To characterize the role of mutations, we calculated the free energy variation upon mutations in the available protein structures of Ddn (DLM), Fgd1 (DLM), and Rv0678 (BDQ) and performed MIC assays on a subset of MTBc strains carrying mutations to assess their phenotypic effect. The combination of structural and phenotypic data allowed for cataloguing the mutations clearly associated with resistance to BDQ (n = 4) and DLM (n = 35), only two of which were previously described, as well as about a hundred genetic variants without any correlation with resistance. Significantly, these results show that both BDQ and DLM resistance-related mutations are diverse and distributed across the entire region of each gene target, which is of critical importance for the development of comprehensive molecular diagnostic tools.

中文翻译：

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幼稚结核分枝杆菌临床菌株中与苯达喹啉和德拉曼抗性相关的基因组变异体的表征。

突变在结核分枝杆菌中与苯达喹啉（BDQ）和德拉曼尼德（DLM）表型抗性相关的基因中的作用复杂（MTBc）菌株的特征很差。明确了解遗传变异的作用对于指导基于分子的药物敏感性测试（DST）的开发至关重要。在这项工作中，我们使用来自六个结核病高负担国家的4,795个MTBc临床分离株的全基因组测序（WGS）数据集，分析了与BDQ和DLM耐药表型相关的候选基因组区域中的所有突变（ TB）。通过WGS分析，我们在潜在涉及BDQ和DLM耐药表型的基因组区域中分别确定了61和163个独特突变。重要的是，所有菌株均从可能从未接触过这些药物的患者中分离出来。为了描述突变的作用，我们计算了Ddn（DLM），Fgd1（DLM）和Rv0678（BDQ）的可用蛋白质结构发生突变后的自由能变化，并对带有突变的MTBc菌株的子集进行了MIC分析，以评估其表型效应。结构数据和表型数据的组合可以对明显与BDQ抗性相关的突变进行分类（n = 4）和DLM（n = 35），以前仅描述了其中的两个，以及约一百个与抗性没有任何关系的遗传变异。重要的是，这些结果表明，与BDQ和DLM抗药性相关的突变是多样的，并且分布在每个基因靶标的整个区域，这对于开发全面的分子诊断工具至关重要。