Within-patient Candida auris strain diversity in a tertiary hospital

项目摘要 耳念珠菌最近已成为世界范围内侵袭性感染的原因， 尽管使用棘白菌素（一线抗真菌药物）和其他药物治疗， C.由于其抗真菌耐药性的倾向和在医院持续存在的能力， 环境，并导致长期爆发。C. auris是单倍体酵母， 二倍体假丝酵母样C.白色念珠菌和大多数致病菌属。菌株属于5个地理分支。最 感染由进化枝I、III或IV菌株引起。越来越多的证据表明进化枝内存在遗传多样性， 包括核心基因组单核苷酸多态性，核型改变，基因拷贝数变异， 多倍体和非整倍体。同一进化枝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。迄今为止，很少有特定的基因已被验证为毒力 决定因素，发病机制和棘白菌素耐受性仍然知之甚少。机制 耐受性、抗性、毒力和致病性不一定能从其他念珠菌属物种推断， 或C.耳支长期以来的范式是，几乎所有的血液或其他念珠菌感染， 通常无菌的场所源自单一的克隆生物。然而，在初步研究中，我们已经表明， 至少有一些C。auris和C.从个体患者的阳性血培养中回收的光滑菌株， 我们的中心表现出未被识别的基因型和表型多样性。我们的数据表明，一种新的，基于人口的 念珠菌感染的范例。该项目的目标是表征遗传和表型 C.多样性从个别患者中回收的耳念珠菌菌株，并涉及特定的C.耳基因与基因 棘白菌素耐受性和抗性以及毒力的变异。在目标1中，我们将执行短期和长期- 读取全基因组测序并建立多个进化枝I和III C的同源性。耳恢复， 每例患者的培养物，包括基线时以及持续性和复发性感染期间， 棘白菌素治疗。然后，我们将测试来自每个患者的基因不同菌株的表型，包括 棘白菌素耐受性和抗性，以及毒力相关表型。在aim 2中，我们将优先考虑基因 和基因变体，并产生同基因突变体C。auris菌株在进化枝I和III背景中。等基因菌株 将在体外和小鼠血流模型中评估棘白菌素反应和毒力 感染结果将为棘白菌素反应和C.耳，并确定 这些基因参与了这些过程。我们的研究结果将提供一个基础的机制研究 棘白菌素耐受性、抗性和毒力，以及确定C. Auris 基因型和表型多样性。我们对微生物遗传多样性的研究具有潜在的深远意义 用于患者护理、临床微生物学实践以及了解抗真菌治疗反应和发病机制。

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.