Abstract：
The presence of intermittently dispersed insertion sequences and transposases in the Mycobacterium tuberculosis (Mtb) genome makes intra-genome recombination events inevitable. Understanding their effect on the gene repertoires (GR), which may contribute to the development of drug-resistant Mtb, is critical. In this study, publicly available WGS data of clinical Mtb isolates (endemic region n = 2,601; non-endemic region n = 1,130) were de novo assembled, filtered, scaffolded into assemblies, and functionally annotated. Out of 2,601 Mtb WGS data sets from endemic regions, 2,184 (drug resistant/sensitive: 1,386/798) qualified as high quality. We identified 3,784 core genes, 123 softcore genes, 224 shell genes, and 762 cloud genes in the pangenome of Mtb clinical isolates from endemic regions. Sets of 33 and 39 genes showed positive and negative associations (P < 0.01) with drug resistance status, respectively. Gene ontology clustering showed compromised immunity to phages and impaired DNA repair in drug-resistant Mtb clinical isolates compared to the sensitive ones. Multidrug efflux pump repressor genes (Rv3830c and Rv3855c) and CRISPR genes (Rv2816c-19c) were absent in the drug-resistant Mtb. A separate WGS data analysis of drug-resistant Mtb clinical isolates from the Netherlands (n = 1130) also showed the absence of CRISPR genes (Rv2816c-17c). This study highlights the role of CRISPR genes in drug resistance development in Mtb clinical isolates and helps in understanding its evolutionary trajectory and as useful targets for diagnostics development.IMPORTANCEThe results from the present Pan-GWAS study comparing gene sets in drug-resistant and drug-sensitive Mtb clinical isolates revealed intricate presence-absence patterns of genes encoding DNA-binding proteins having gene regulatory as well as DNA modification and DNA repair roles. Apart from the genes with known functions, some uncharacterized and hypothetical genes that seem to have a potential role in drug resistance development in Mtb were identified. We have been able to extrapolate many findings of the present study with the existing literature on the molecular aspects of drug-resistant Mtb, further strengthening the relevance of the results presented in this study.
摘要：
结核分枝杆菌(Mtb)基因组中间歇性分散的插入序列和转座酶的存在使得基因组内重组事件不可避免。了解它们对基因库(GR)的影响，这可能有助于耐药性Mtb的发展，是至关重要的。在这项研究中,临床Mtb分离株(流行区n=2,601；非流行区n=1,130)的公开WGS数据是从头组装的，过滤，脚手架成组件，和功能注释。在来自流行地区的2,601MtbWGS数据集中，2,184（耐药/敏感：1,386/798）合格为优质。我们确定了3,784个核心基因，123个软核基因，224个外壳基因，和来自流行地区的Mtb临床分离株的pangenome中的762个云基因。33和39组基因与耐药状态呈正相关和负相关(P<0.01),分别。基因本体论聚类显示，与敏感菌株相比，耐药Mtb临床分离株对噬菌体的免疫力受损，DNA修复受损。多药外排泵抑制基因（Rv3830c和Rv3855c）和CRISPR基因（Rv2816c-19c）在耐药Mtb中不存在。来自荷兰的耐药Mtb临床分离株(n=1130)的单独WGS数据分析也显示CRISPR基因(Rv2816c-17c)的缺失。这项研究强调了CRISPR基因在Mtb临床分离株耐药性发展中的作用，并有助于了解其进化轨迹和诊断开发的有用靶标。重要意义本Pan-GWAS研究比较了耐药性和药物敏感性Mtb临床分离株中的基因集的结果，揭示了编码具有基因调节以及DNA修饰和DNA修复作用的DNA结合蛋白的基因的复杂存在-缺失模式。除了具有已知功能的基因，鉴定出一些似乎在Mtb耐药性发展中具有潜在作用的未表征和假设的基因.我们已经能够推断本研究的许多发现与现有的有关耐药Mtb的分子方面的文献，进一步加强了本研究结果的相关性。
