Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies.
Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies.
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选择性全基因组扩增直接从患者皮肤活检中揭示巴西利什曼原虫的群体遗传学。
DOI：
10.1371/journal.ppat.1011230
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发表时间：
2023-03
期刊：
影响因子：
6.7
通讯作者：
中科院分区：
文献类型：
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作者：
在巴西，巴西利什曼原虫是被忽视的热带疾病皮肤利什曼病（CL）的主要病原体。CL表现为一系列疾病严重程度，治疗失败率高。然而，导致疾病表现和治疗结果的寄生虫因素尚未得到很好的理解，部分原因是成功地从患者病变中分离和培养寄生虫仍然是一个重大的技术挑战。在这里，我们描述了利什曼原虫的选择性全基因组扩增（SWGA）的发展，并表明这种方法使直接从原发性患者皮肤样本中获得的寄生虫基因组的文化独立的分析，使我们能够规避文物与适应文化。我们表明，SWGA可以适用于多个利什曼原虫物种居住在不同的宿主物种，这表明这种方法是广泛有用的实验感染模型和临床研究。直接对从巴西巴伊亚的Corte de佩德拉的患者收集的皮肤活检进行的SWGA显示出广泛的基因组多样性。最后，作为概念验证，我们证明了SWGA数据可以与已发表的培养寄生虫分离株的全基因组数据相结合，以识别巴西特定地理区域特有的变异，其中已知治疗失败率很高。SWGA提供了一种相对简单的方法，直接从患者样本中生成利什曼原虫基因组，从而释放了将寄生虫遗传学与宿主临床表型联系起来的潜力。巴西利什曼原虫是巴西皮肤利什曼病的主要病因。由于培养的局限性，重要的是以不依赖培养的方式研究寄生虫。我们使用选择性全基因组扩增（SWGA）直接从患者活检中探索寄生虫基因组多样性。这种方法是廉价的，可以广泛用于产生寄生虫基因组序列数据从不同的利什曼原虫物种感染不同的哺乳动物宿主。我们发现L.来自巴西巴伊亚的巴西亚种基因组与地理位置相关。通过将这些数据与来自南美洲四个国家的其他研究的公开可用的基因组序列相结合，我们确定了巴西东北部特有的变异，这些变异可能与高区域治疗失败率有关。
In Brazil, Leishmania braziliensis is the main causative agent of the neglected tropical disease, cutaneous leishmaniasis (CL). CL presents on a spectrum of disease severity with a high rate of treatment failure. Yet the parasite factors that contribute to disease presentation and treatment outcome are not well understood, in part because successfully isolating and culturing parasites from patient lesions remains a major technical challenge. Here we describe the development of selective whole genome amplification (SWGA) for Leishmania and show that this method enables culture-independent analysis of parasite genomes obtained directly from primary patient skin samples, allowing us to circumvent artifacts associated with adaptation to culture. We show that SWGA can be applied to multiple Leishmania species residing in different host species, suggesting that this method is broadly useful in both experimental infection models and clinical studies. SWGA carried out directly on skin biopsies collected from patients in Corte de Pedra, Bahia, Brazil, showed extensive genomic diversity. Finally, as a proof-of-concept, we demonstrated that SWGA data can be integrated with published whole genome data from cultured parasite isolates to identify variants unique to specific geographic regions in Brazil where treatment failure rates are known to be high. SWGA provides a relatively simple method to generate Leishmania genomes directly from patient samples, unlocking the potential to link parasite genetics with host clinical phenotypes. Leishmania braziliensis is the main cause of cutaneous leishmaniasis in Brazil. Due to limitations in culturing, it is important to study the parasite in a culture-independent manner. We use selective whole genome amplification (SWGA) to explore parasite genomic diversity directly from patient biopsies. This method is inexpensive and can be broadly used to generate parasite genome sequence data from different Leishmania species infecting different mammalian hosts. We found high diversity among the L. braziliensis genomes from Bahia, Brazil, which correlated with geographic location. By integrating these data with publicly available genome sequences from other studies spanning four countries in South America, we identified variants unique to Northeast Brazil that may be linked to high regional rates of treatment failure.
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影响因子：
6.4
作者：
Dumetz F;Imamura H;Sanders M;Seblova V;Myskova J;Pescher P;Vanaerschot M;Meehan CJ;Cuypers B;De Muylder G;Späth GF;Bussotti G;Vermeesch JR;Berriman M;Cotton JA;Volf P;Dujardin JC;Domagalska MA
通讯作者：
Domagalska MA
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1.2
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影响因子：
3.9
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Argimón S;Abudahab K;Goater RJE;Fedosejev A;Bhai J;Glasner C;Feil EJ;Holden MTG;Yeats CA;Grundmann H;Spratt BG;Aanensen DM
通讯作者：
Aanensen DM
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
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