Genome-Scale Multilocus Microsatellite Typing of Trypanosoma cruzi Discrete Typing Unit I Reveals Phylogeographic Structure and Specific Genotypes Linked to Human Infection

Trypanosoma cruzi is the most important parasitic infection in Latin America and is also genetically highly diverse, with at least six discrete typing units (DTUs) reported: Tc I, IIa, IIb, IIc, IId, and IIe. However, the current six-genotype classification is likely to be a poor reflection of the total genetic diversity present in this undeniably ancient parasite. To determine whether epidemiologically important information is ��hidden�� at the sub-DTU level, we developed a 48-marker panel of polymorphic microsatellite loci to investigate population structure among 135 samples from across the geographic distribution of TcI. This DTU is the major cause of resurgent human disease in northern South America but also occurs in silvatic triatomine vectors and mammalian reservoir hosts throughout the continent. Based on a total dataset of 12,329 alleles, we demonstrate that silvatic TcI populations are extraordinarily genetically diverse, show spatial structuring on a continental scale, and have undergone recent biogeographic expansion into the southern United States of America. Conversely, the majority of human strains sampled are restricted to two distinct groups characterised by a considerable reduction in genetic diversity with respect to isolates from silvatic sources. In Venezuela, most human isolates showed little identity with known local silvatic strains, despite frequent invasion of the domestic setting by infected adult vectors. Multilocus linkage indices indicate predominantly clonal parasite propagation among all populations. However, excess homozygosity among silvatic strains and raised heterozygosity among domestic populations suggest that some level of genetic recombination cannot be ruled out. The epidemiological significance of these findings is discussed.克氏锥虫（Trypanosoma cruzi）是拉丁美洲最为重要的寄生虫病病原体，同时具有极高的遗传多样性，目前已报道至少6个分型单元（discrete typing units, DTUs）：TcI、IIa、IIb、IIc、IId及IIe。然而当前的六基因型分类或许难以全面反映这一公认古老寄生虫的全部遗传多样性。为探究亚分型单元层面是否隐藏着具有流行病学意义的信息，我们开发了一套包含48个多态性微卫星位点（microsatellite loci）的标记组合，对覆盖TcI全地理分布范围的135份样本开展群体结构分析。TcI是南美洲北部人类锥虫病疫情复燃的主要病因，同时也在整个美洲大陆的野生栖居锥蝽媒介（triatomine vectors）和哺乳动物储存宿主（reservoir hosts）中广泛存在。基于总计12329个等位基因（alleles）的数据集，我们证实野生型TcI群体具有极高的遗传多样性，在大陆尺度上呈现空间结构特征，且近期发生了生物地理学层面的扩张，蔓延至美国南部地区。与之相反，多数被采样的人类菌株仅分布于两个截然不同的类群中，相较于野生来源分离株，这两类群的遗传多样性显著降低。在委内瑞拉，尽管受感染的成虫锥蝽频繁侵入人居环境，但多数人类分离株与当地已知的野生菌株几乎无遗传同源性。多位点连锁指数（linkage indices）显示，所有群体的寄生虫繁殖均以无性克隆为主要方式。不过，野生菌株中存在的纯合性过剩以及家养群体中升高的杂合性表明，一定程度的遗传重组仍无法排除。本文对上述发现的流行病学意义进行了讨论。