Evolution of Cryptococcus neoformans strains from patients with HIV/AIDS

描述(申请人提供)：目前有100多万艾滋病毒/艾滋病患者患有真菌性脑膜脑炎，由此导致的发病率和死亡率是非常显著的。这些感染中的绝大多数是由新生隐球菌变种引起的。这种酵母普遍存在于环境中，与鸟类栖息地和植被碎片有关。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外源性获得的。虽然感染哺乳动物的能力对真菌没有明显的进化优势，但大多数自然分离株都能够定植哺乳动物宿主，这表明致病性是在环境中进化的。在初步研究中，我们发展了强大的多位点基因分型方法，并发现了A型血清的两个独特的、遗传隔离的亚群：(I)全球亚群，由与野鸽排泄物相关的无处不在的高度克隆的单态菌株组成；(Ii)在南部非洲，与非洲本土树木相关的独特、高度可变的重组亚群。这个南部非洲群体的遗传多样性是史无前例的，这表明这个群体可能代表着现存的全球A型血清毒株的祖先起源。我们还分析了临床和环境样本中多位点基因型的频率，发现并不是所有的菌株(或基因型)都同样有可能导致人类患上隐球菌疾病。尽管非洲人口的基因类型千差万别，但博茨瓦纳几乎一半的患者(46%)和南非的大部分患者(17%)感染了具有三种密切相关基因类型的菌株。相比之下，非洲环境分离株的基因类型分布具有可比性，没有一个是占主导地位的。在全球分离株中，大多数基因型在两名患者和占主导地位的非非洲生态位--鸽子粪便中同样流行，尽管有一种基因型(A2)在环境中高度流行，但从未从患者身上分离出来。这一建议将从种群、遗传和基因组水平上研究新生隐孢子虫致病性的进化。该项目涉及两个独立但相辅相成的目标。Aim 1将使用群体遗传和系统发育分析的方法来检验A型血清起源于非洲的假设。Aim 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识别区分经常引起感染的菌株与很少从人类分离的菌株的基因组区域。这种将全基因组方法应用于新生葡萄球菌自然菌株的方法将识别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.