利什曼原虫毒力机制的基因组学研究：来自一个非典型菌株的证据。

BACKGROUND: Leishmaniasis is a neglected tropical disease with diverse clinical phenotypes, determined by parasite, host and vector interactions. Despite the advances in molecular biology and the availability of more Leishmania genome references in recent years, the association between parasite species and distinct clinical phenotypes remains poorly understood. We present a genomic comparison of an atypical variant of Leishmania donovani from a South Asian focus, where it mostly causes cutaneous form of leishmaniasis. RESULTS: Clinical isolates from six cutaneous leishmaniasis patients (CL-SL); 2 of whom were poor responders to antimony (CL-PR), and two visceral leishmaniasis patients (VL-SL) were sequenced on an Illumina MiSeq platform. Chromosome aneuploidy was observed in both groups but was more frequent in CL-SL. 248 genes differed by 2 fold or more in copy number among the two groups. Genes involved in amino acid use (LdBPK_271940) and energy metabolism (LdBPK_271950), predominated the VL-SL group with the same distribution pattern reflected in gene tandem arrays. Genes encoding amastins were present in higher copy numbers in VL-SL and CL-PR as well as being among predicted pseudogenes in CL-SL. Both chromosome and SNP profiles showed CL-SL and VL-SL to form two distinct groups. While expected heterozygosity was much higher in VL-SL, SNP allele frequency patterns did not suggest potential recent recombination breakpoints. The SNP/indel profile obtained using the more recently generated PacBio sequence did not vary markedly from that based on the standard LdBPK282A1 reference. Several genes previously associated with resistance to antimonials were observed in higher copy numbers in the analysis of CL-PR. H-locus amplification was seen in one cutaneous isolate which however did not belong to the CL-PR group. CONCLUSIONS: The data presented suggests that intra species variations at chromosome and gene level are more likely to influence differences in tropism as well as response to treatment, and contributes to greater understanding of parasite molecular mechanisms underpinning these differences. These findings should be substantiated with a larger sample number and expression/functional studies.

背景：利什曼病是一种被忽视的热带病，具有多种临床表型，由寄生虫、宿主和媒介的相互作用决定。尽管近年来分子生物学取得了进展，并且有更多的利什曼原虫基因组参考资料可用，但寄生虫物种与不同临床表型之间的关联仍知之甚少。我们展示了南亚一个利什曼原虫异常变体的基因组比较，该变体主要引起皮肤利什曼病。

结果：对来自皮肤利什曼病患者（CL-SL）的 6 个临床分离株进行测序；其中 2 个对锑治疗反应不佳（CL-PR），2 个内脏利什曼病患者（VL-SL）在 Illumina MiSeq 平台上进行测序。两组均观察到染色体非整倍性，但 CL-SL 更为频繁。两组之间有 248 个基因的拷贝数差异超过 2 倍。VL-SL 组中氨基酸利用（LdBPK_271940）和能量代谢（LdBPK_271950）相关基因占主导地位，同样的分布模式反映在基因串联数组中。VL-SL 和 CL-PR 中的阿米斯汀基因具有更高的拷贝数，CL-SL 中的阿米斯汀基因也被预测为假基因。染色体和 SNP 图谱均显示 CL-SL 和 VL-SL 形成两个不同的群体。虽然 VL-SL 的预期杂合度要高得多，但 SNP 等位基因频率模式并没有表明潜在的近期重组断点。使用最近生成的 PacBio 序列获得的 SNP/indel 图谱与基于标准 LdBPK282A1 参考的图谱没有明显差异。在对 CL-PR 的分析中，观察到几个先前与抗锑药物耐药相关的基因具有更高的拷贝数。在一个皮肤分离株中观察到 H 基因座扩增，但该分离株不属于 CL-PR 组。

结论：所提出的数据表明，种内染色体和基因水平的变异更有可能影响嗜性和对治疗的反应差异，并有助于更好地理解寄生虫分子机制，这些差异是这些机制的基础。这些发现应该通过更大的样本数量和表达/功能研究来证实。