Front Cell Infect Microbiol:中科院北京基因组所陈非研究组发现基因型
近日，《Front Cell Infect. Microbiol》杂志在线发表了中国科学院北京基因组研究所陈非研究组与首都医科大学附属北京胸科医院暨国家结核病临床实验室黄海荣研究组合作的一篇研究论文，研究选取了分属不同谱系(包括标准株H37Ra、H37Rv、牛结核、卡介苗)、适应于不同宿主且表现出不同致病性的12株MTBC菌株，借助比较基因组学手段，全面揭示了导致MTBC宿主适应性、毒力和免疫原性差异的遗传基础。
结核病已连续两年超过HIV成为全球第一大传染病。据WHO结核年报报道，2015年全球新增结核病例1,040万，死亡180万。另外，目前全球约有三分之一人口(约20亿)为结核菌携带者，感染者中约1/10的人最终会发展为活动性结核。结核分枝杆菌复合群(MTBC)是引发结核病的元凶，其成员在基因组序列上极为保守，一致性超过99%，但是不同谱系的菌株在毒力、宿主适应性等方面存在较大表型差异，这可能是MTBC菌株与不同的宿主之间长期共进化的结果。长期的地理隔离导致了基因型隔离与遗传隔离，从而进一步造成MTBC表型的差异。为了揭示不同MTBC菌株致病性、宿主适应性等表型差异的遗传基础，探寻高度保守的MTBC基因型和多样化表型之间的联系。
科研人员通过对感染不同宿主的结核杆菌的比较分析，发现了三类只存在于人源菌株中的基因，包括2个烯酰辅酶A水合酶、5个PE/PPE家族蛋白和8个mce3家族蛋白。这些基因中的绝大多数已被实验证明在结核毒力和免疫中发挥重要的作用，它们在动物源菌株中的特异性缺失极有可能导致结核杆菌宿主适应性差异。通过对MTBC毒力因子的分析发现13个只存在北京系中的SNPs，它们很可能是导致北京系菌株毒力更强的原因之一;对实验室最常用的标准有毒株H37Rv与无毒株H37Ra的比较，发现3个可能导致H37Ra毒力减弱的突变位点，包括已被实验验证的S219L (PhoP)、A219E (MazG) 和1个新发现的I228M (EspK);对动物源有毒株牛结核杆菌和弱毒株(卡介苗及田鼠分枝杆菌)的分析发现，RD1区域的前4个基因而非传统观念所认为的整个RD1区可能是导致动物源结核杆菌毒力减弱的原因。通过对MTBC抗原决定簇的分析发现，北京系菌株特异缺失了4个抗原决定簇，它们的缺失可能导致北京系菌株的免疫逃逸，从而毒性更强。此外，不同宿主的结核杆菌在抗原决定簇上也存在差异，反应了不同宿主的结核杆菌与相应宿主之间特异的免疫反应。
研究揭示了导致MTBC菌株表型差异的基因组突变，增强了对于MTBC基因组如此保守而表型差异如此显著的理解。此外，在整个MTBC范围内系统的比较基因组学研究为更好的理解MTBC的致病机制奠定了基础，为结核病的防治提供了新的检测靶标，进一步促进了针对结核病疫苗的研发。
高度保守的基因型和差异显著的表型
原文链接：
The BioInformatics Analysis of Comparative Genomics of Mycobacterium tuberculosisComplex (MTBC) Provides Insight into Dissimilarities between Intraspecific Groups Differing in Host Association, Virulence, and Epitope Diversity
原文摘要：
Tuberculosis now exceeds HIV as the top infectious disease cause of mortality, and is caused by the Mycobacterium tuberculosis complex (MTBC). MTBC strains have highly conserved genome sequences (similarity >99%) but dramatically different phenotypes. To analyze the relationship between genotype and phenotype, we conducted the comparative genomic analysis on 12 MTBC strains representing different lineages (i.e., Mycobacterium bovis; M. bovis BCG; M. microti; M. africanum; M. tuberculosis H37Rv; M. tuberculosis H37Ra, and sixM. tuberculosis clinical isolates). The analysis focused on the three aspects of pathogenicity: host association, virulence, and epitope variations. Host association analysis indicated that eight mce3 genes, two enoyl-CoA hydratases, and five PE/PPE family genes were present only in human isolates; these may have roles in host-pathogen interactions. There were 15 SNPs found on virulence factors (including five SNPs in three ESX secretion proteins) only in the Beijing strains, which might be related to their more virulent phenotype. A comparison between the virulent H37Rv and non-virulent H37Ra strains revealed three SNPs that were likely associated with the virulence attenuation of H37Ra: S219L (PhoP), A219E (MazG) and a newly identified I228M (EspK). Additionally, a comparison of animal-associated MTBC strains showed that the deletion of the first four genes (i.e., pe35, ppe68, esxB, esxA), rather than all eight genes of RD1, might play a central role in the virulence attenuation of animal isolates. Finally, by comparing epitopes among MTBC strains, we found that four epitopes were lost only in the Beijing strains; this may render them better capable of evading the human immune system, leading to enhanced virulence. Overall, our comparative genomic analysis of MTBC strains reveals the relationship between the highly conserved genotypes and the diverse phenotypes of MTBC, provides insight into pathogenic mechanisms, and facilitates the development of potential molecular targets for the prevention and treatment of tuberculosis.
作者：陈非
