PDF(Pubmed)
Abstract：
Although several studies have investigated genetic diversity of Leishmania infantum in North Africa, genome-wide analyses are lacking. Here, we conducted comparative analyses of nuclear and mitochondrial genomes of seven L. infantum isolates from Tunisia with the aim to gain insight into factors that drive genomic and phenotypic adaptation. Isolates were from cured (n=4) and recurrent (n=3) visceral leishmaniasis (VL) cases, originating from northern (n=2) and central (n=5) Tunisia, where respectively stable and emerging VL foci are observed. All isolates from relapsed patients were from Kairouan governorate (Centre); one showing resistance to the anti-leishmanial drug Meglumine antimoniate. Nuclear genome diversity of the isolates was analysed by comparison to the L. infantum JPCM5 reference genome. Kinetoplast maxi and minicircle sequences (1 and 59, respectively) were extracted from unmapped reads and identified by blast analysis against public data sets. The genome variation analysis grouped together isolates from the same geographical origins. Strains from the North were very different from the reference showing more than 34 587 specific single nucleotide variants, with one isolate representing a full genetic hybrid as judged by variant frequency. Composition of minicircle classes within isolates corroborated this geographical population structure. Read depth analysis revealed several significant gene copy number variations correlating with either geographical origin (amastin and Hsp33 genes) or relapse (CLN3 gene). However, no specific gene copy number variation was found in the drug-resistant isolate. In contrast, resistance was associated with a specific minicircle pattern suggesting Leishmania mitochondrial DNA as a potential novel source for biomarker discovery.
摘要：
尽管有几项研究调查了北非婴儿利什曼原虫的遗传多样性，缺乏全基因组分析。这里,我们对来自突尼斯的7个婴儿乳球菌分离株的核基因组和线粒体基因组进行了比较分析,目的是深入了解驱动基因组和表型适应的因素.分离来自治愈（n=4）和复发（n=3）内脏利什曼病（VL）病例，起源于北部（n=2）和中部（n=5）突尼斯，其中分别观察到稳定和出现的VL灶。复发患者的所有分离株都来自Kairouan省（中心）；一个显示出对抗利什曼原药葡甲胺的耐药性。通过与婴儿乳杆菌JPCM5参考基因组进行比较，分析了分离株的核基因组多样性。从未映射的读段中提取了叶绿体最大和小环序列（分别为1和59），并通过针对公共数据集的爆炸分析进行了鉴定。基因组变异分析将来自相同地理起源的分离株组合在一起。来自北方的菌株与参考文献有很大不同，显示超过34587种特定的单核苷酸变体，根据变异频率判断，一个分离株代表全遗传杂种。分离物中微环类的组成证实了这种地理种群结构。阅读深度分析揭示了与地理起源(amastin和Hsp33基因)或复发(CLN3基因)相关的几个显著的基因拷贝数变异。然而,在耐药分离株中没有发现特定的基因拷贝数变异.相比之下,耐药性与特定的微环模式相关,提示利什曼原虫线粒体DNA是发现生物标志物的潜在新来源.
