Espinoza Monica E, Swing Ashley M, Elghraoui Afif, Modlin Samuel J, Valafar Faramarz
Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, California, USA.
San Diego State University/University of California, San Diego | Joint Doctoral Program in Public Health (Global Health), San Diego, California, USA.
mSystems. 2025 Apr 22;10(4):e0049924. doi: 10.1128/msystems.00499-24. Epub 2025 Mar 6.
complex successfully adapts to environmental pressures through mechanisms of rapid adaptation which remain poorly understood despite knowledge gained through decades of research. In this study, we used 110 reference-quality, complete assembled, long-read sequenced clinical genomes to study patterns of structural adaptation through a graph-based pangenome analysis, elucidating rarely studied mechanisms that enable enhanced clinical phenotypes offering a novel perspective to the species' adaptation. Across isolates, we identified a pangenome of 4,325 genes (3,767 core and 558 accessory), revealing 290 novel genes, and a substantially more complete account of difficult-to-sequence genes. Seventy-four percent of core genes were deemed non-essential , 38% of which support the pathogen's survival , suggesting a need to broaden current perspectives on essentiality. Through information-theoretic analysis, we reveal the genes that contribute most to the species' diversity-several with known consequences for antigenic variation and immune evasion. Construction of a graph pangenome revealed topological variations that implicate genes known to modulate host immunity (), defense against phages/viruses ( and ), and others associated with host tissue colonization. Here, the prominent trehalose transport pathway stands out for its involvement in caseous granuloma catabolism and the development of post-primary disease. We show paralogous duplications of genes implicated in bedaquiline ( in all L1 isolates) and ethambutol () resistance, with a paralogous duplication of its regulator () in 96 isolates. We provide hypotheses for novel mechanisms of immune evasion and antibiotic resistance through gene dosing that can escape detection by molecular diagnostics.IMPORTANCE complex (MTBC) has killed over a billion people in the past 200 years alone and continues to kill nearly 1.5 million annually. The pathogen has a versatile ability to diversify under immune and drug pressure and survive, even becoming antibiotic persistent or resistant in the face of harsh chemotherapy. For proper diagnosis and design of an appropriate treatment regimen, a full understanding of this diversification and its clinical consequences is desperately needed. A mechanism of diversification that is rarely studied systematically is MTBC's ability to structurally change its genome. In this article, we have assembled 110 clinical genomes (the largest assembled set to date) and performed a pangenomic analysis. Our pangenome provides structural variation-based hypotheses for novel mechanisms of immune evasion and antibiotic resistance through gene dosing that can compromise molecular diagnostics and lead to further emergence of antibiotic resistance.
结核分枝杆菌复合群（MTBC）通过快速适应机制成功适应环境压力，尽管经过数十年研究已积累了相关知识，但这些机制仍未得到充分理解。在本研究中，我们使用了110个参考质量、完整组装、长读长测序的临床基因组，通过基于图的泛基因组分析来研究结构适应模式，阐明了一些鲜为人知的机制，这些机制促成了增强的临床表型，为该物种的适应提供了新视角。在所有分离株中，我们鉴定出一个由4325个基因组成的泛基因组（3767个核心基因和558个辅助基因），发现了290个新基因，并更全面地描述了难以测序的基因。74%的核心基因被认为是非必需的，其中38%支持病原体的存活，这表明有必要拓宽目前对基因必需性的认识。通过信息论分析，我们揭示了对物种多样性贡献最大的基因——其中一些基因对抗原变异和免疫逃逸具有已知影响。构建图泛基因组揭示了拓扑变异，这些变异涉及已知调节宿主免疫（）、抵抗噬菌体/病毒（和）以及与宿主组织定植相关的其他基因。在此，突出的海藻糖转运途径因其参与干酪样肉芽肿分解代谢和原发性疾病后发展而引人注目。我们展示了与贝达喹啉（在所有L1分离株中）和乙胺丁醇（）耐药相关基因的旁系同源重复，以及其调节因子（）在96个分离株中的旁系同源重复。我们通过基因剂量提出了免疫逃逸和抗生素耐药新机制的假设，这些机制可能逃避分子诊断的检测。
仅在过去200年中，结核分枝杆菌复合群（MTBC）就已导致超过10亿人死亡，并且每年仍继续导致近150万人死亡。该病原体具有在免疫和药物压力下多样化并存活的多种能力，甚至在面对严厉化疗时会变得抗生素持续存在或耐药。为了进行正确诊断和设计合适的治疗方案，迫切需要全面了解这种多样化及其临床后果。一种很少被系统研究的多样化机制是MTBC在结构上改变其基因组的能力。在本文中，我们组装了110个临床基因组（迄今为止组装的最大数据集）并进行了泛基因组分析。我们的泛基因组通过基因剂量为免疫逃逸和抗生素耐药新机制提供了基于结构变异的假设，这些机制可能损害分子诊断并导致抗生素耐药性的进一步出现。
