Evolution of Cryptococcus neoformans strains from patients with HIV/AIDS

描述（由申请人提供）：目前有超过一百万的HIV/AIDS患者患有真菌性脑膜脑炎，并且由此产生的发病率和死亡率非常显著。这些感染中的绝大多数是由新型隐球菌变种菌株引起的。Grubii，其通过具有荚膜血清型A而被识别。这种酵母在环境中无处不在，与鸟类栖息地和植物残骸有关。感染不是传染性的，而是通过吸入干燥的酵母细胞或担孢子而获得的。尽管感染哺乳动物的能力并没有为真菌提供明显的进化优势，但大多数天然分离株都能够在哺乳动物宿主中定殖，这表明致病性是在环境中进化的。 在初步研究中，我们开发了强大的多位点基因分型方法，并发现了两个独特的，遗传隔离的血清型A亚群：（i）一个全球亚群，由与野鸽排泄物相关的普遍存在的，高度克隆的单态性菌株组成，（ii）一个独特的，高度可变的，与非洲本土树木相关的南部非洲重组亚群。这一南部非洲人群的遗传多样性是前所未有的，表明这一人群可能代表了血清型A的现存全球菌株的祖先起源。我们还分析了临床和环境样本中多位点基因型的频率，发现并非所有菌株（或基因型）都同样可能导致人类隐球菌病。尽管非洲人群的基因型存在巨大的多样性，但博茨瓦纳几乎一半的患者（46%）和南非大部分患者（17%）感染了三种密切相关的基因型菌株。相比之下，在非洲的环境菌株之间的基因型分布是可比的，没有占主导地位。在全球分离株中，大多数基因型在患者和主要的非非洲生态位鸽子粪便中同样流行，尽管一种基因型（A2）在环境中高度流行，但从未从患者中分离出来。 本研究旨在探讨C.在群体遗传和基因组水平上对新生儿进行研究。该项目涉及两个独立但互补的目标。目的1将利用群体遗传学和系统发育分析的方法来检验血清型A的非洲起源假说。目标2将使用比较基因组学、全基因组关联图谱和表型分析的方法来鉴定基因组区域，这些基因组区域可以区分经常引起感染的菌株和很少从人类中分离出来的菌株。本文介绍了全基因组方法在自然界中的应用。新形式病毒将鉴定与人类致病性显著相关的基因或基因组区域。

DESCRIPTION (provided by applicant): Over a million patients with HIV/AIDS are currently afflicted with fungal meningoencephalitis, and the resultant morbidity and mortality are profoundly significant. The vast majority of these infections are caused by strains of Cryptococcus neoformans var. grubii, which have been recognized by possessing capsular serotype A. This yeast is ubiquitous in the environment, where it is associated with avian habitats and vegetative debris. Infection is not contagious but acquired exogenously by the inhalation of desiccated yeast cells or basidiospores. Although the ability to infect mammals offers no obvious evolutionary advantage to the fungus, most natural isolates are capable of colonizing mammalian hosts, which suggests that pathogenicity evolved in the environment. In preliminary studies, we developed robust multilocus genotyping methods and discovered two unique, genetically isolated subpopulations of serotype A: (i) a global subpopulation comprised of ubiquitous, highly clonal monomorphic strains associated with the excreta of feral pigeons and (ii) a unique, highly-variable, recombining subpopulation in southern Africa that is associated with indigenous African trees. The genetic diversity of this southern African population is unprecedented and suggests that this population may represent ancestral origin of the extant, global strains of serotype A. We also analyzed the frequencies of multilocus genotypes among clinical and environmental samples and discovered that not all strains (or genotypes) are equally likely to cause cryptococcal disease in humans. Despite the enormous diversity of genotypes in the African population, almost half of all patients in Botswana (46%) and a major proportion of patients in South Africa (17%) were infected by strains with three closely related genotypes. In contrast, the distribution of genotypes among environmental isolates in Africa is comparable, and none are dominant. Among global isolates, most genotypes were equally prevalent in both patients and the predominant non-African ecological niche, pigeon feces, although one genotype (A2) was highly prevalent in the environment but never isolated from patients. This proposal will investigate the evolution of pathogenicity in C. neoformans at the population genetic and genomic levels. This project involves two independent but complementary aims. Aim 1 will use methods of population genetic and phylogenetic analysis to test the hypothesis of the African origin of serotype A. Aim 2 will use methods of comparative genomics, genome-wide association mapping and phenotypic assays to identify genomic regions that differentiate strains that frequently cause infection from strains that are rarely, if ever, isolated from humans. This application of whole-genome methods to natural strains of C. neoformans will identify genes or genomic regions that are significantly associated with pathogenicity for humans.