Within-patient Candida auris strain diversity in a tertiary hospital

项目摘要 金黄色念珠菌最近已成为全球侵袭性感染的一种原因，这种感染与高危因素有关 尽管使用棘球菌素类、一线抗真菌药和其他药物治疗，死亡率仍然很高。 金黄色葡萄球菌由于其抗真菌耐药性的倾向和在医院持续存在的能力，构成了独特的挑战 并导致长期暴发。金黄色葡萄球菌是单倍体酵母，在进化上与 类似白色念珠菌的二倍体念珠菌和大多数致病菌。菌株隶属于5个系统地理支系。多数 感染是由分支I、III或IV菌株引起的。有越来越多的证据表明，支系之间存在遗传多样性， 包括核心基因组单核苷酸多态、核型改变、基因拷贝数变异、 多倍体和非整倍体。同一分支内的菌株也表现出抗真菌敏感性的差异， 毒力属性和致病性。到目前为止，很少有特定的基因被确认为毒力。 决定因素、发病机制和棘球绦虫耐受性仍然知之甚少。机制： 耐受性、抗药性、毒力和致病力不一定是从其他念珠菌中推断出来的。 或者在C.Auris分枝之间。长期以来的模式是，几乎所有念珠菌感染的血液或其他 正常情况下，无菌部位来源于单一的克隆生物体。然而，在初步研究中，我们已经表明， 至少从个别患者的血培养阳性中恢复了一些金黄色葡萄球菌和光滑葡萄球菌 我们的中心表现出未被识别的基因和表型多样性。我们的数据表明，一个新的、以人口为基础的 念珠菌感染的范例。这个项目的目标是描述遗传和表型。 从个体患者中恢复的金黄色葡萄球菌菌株的多样性及其与特定的金黄色葡萄球菌基因和基因的关系 棘球菌素耐受性和抗药性以及毒力的变异体。在目标1中，我们将表演短和长- 阅读全基因组测序并建立多个分支I和III C的系统发育图 每个患者的培养，包括基线和持续和复发感染期间，尽管 棘球菌素治疗。然后，我们将测试每个患者的遗传差异菌株的表型，包括 棘球绦虫的耐受性和抗药性，以及毒力相关的表型。在目标2中，我们将优先考虑基因 和基因变异体，并在分支I和分支III背景下创造等基因突变的金黄色葡萄球菌菌株。同基因菌株 将在体外和小鼠血流模型中评估棘球绦虫的反应和毒力 感染。这一结果将为金色棘球绦虫的反应和致病机理提供新的见解，并确定 参与这些过程的基因。我们的研究结果将为下一步的力学研究提供基础 棘球绦虫的耐受性、耐药性和毒力，以及确定金黄色葡萄球菌临床意义的试验 基因类型和表型多样性。我们的微生物遗传多样性范例具有潜在的深远影响 用于患者护理、临床微生物学实践以及对抗真菌治疗反应和发病机制的了解。

Project Summary Candida auris has recently emerged as a cause of invasive infections worldwide that are associated with high mortality rates despite treatment with echinocandins, the frontline class of antifungal agents, and other drugs. C. auris poses unique challenges due to its propensity for antifungal resistance, and ability to persist in hospital environments and cause long-tern outbreaks. C. auris are haploid yeasts that are evolutionarily divergent from diploid Candida like C. albicans and most pathogenic spp. Strains fall in 5 phylogeographic clades. Most infections are caused by clade I, III or IV strains. There is mounting evidence for genetic diversity within clades, including core genome single nucleotide polymorphisms, karyotype alterations, gene copy number variations, polyploidy and aneuploidy. Strains within a given clade also demonstrate differences in antifungal susceptibility, virulence attributes and pathogenicity. To date, few specific genes have been validated as virulence determinants, and pathogenesis and echinocandin tolerance remain poorly understood. Mechanisms of tolerance, resistance, virulence and pathogenesis cannot necessarily be extrapolated from other Candia spp., or between C. auris clades. The long-standing paradigm is that almost all Candida infections of blood or other normally sterile sites stem from a single, clonal organism. However, in preliminary studies, we have shown that at least some C. auris and C. glabrata strains recovered from positive blood cultures from individual patients at our center exhibit unrecognized genotypic and phenotypic diversity. Our data suggest a new, population-based paradigm for Candida infections. The objectives of this project are to characterize the genetic and phenotypic diversity of C. auris strains recovered from individual patients, and to implicate specific C. auris genes and gene variants in echinocandin tolerance and resistance, and in virulence. In aim 1, we will perform short- and long- read whole genome sequencing and establish phylogeny of multiple clade I and III C. auris recovered from cultures from each patient, including at baseline and during persistent and recurrent infections despite echinocandin treatment. We will then test phenotypes of genetically distinct strains from each patient, including echinocandin tolerance and resistance, and virulence-associated phenotypes. In aim 2, we will prioritize genes and gene variants, and create isogenic mutant C. auris strains in clade I and III backgrounds. Isogenic strains will be assessed for echinocandin responses and virulence in vitro and in a mouse model of bloodstream infection. Results will afford new insights into echinocandin responses and pathogenesis by C. auris, and identify genes that contribute to these processes. Our results will provide a foundation for mechanistic studies of echinocandin tolerance, resistance and virulence, and for trials establishing the clinical significance of C. auris genotypic and phenotypic diversity. Our paradigm of microbial genetic diversity has potentially profound implications for patient care, clinical microbiology practice, and understanding of antifungal treatment responses and pathogenesis.