Project 3 Population studies of major human fungal pathogens: genomic and transcriptomic analyses of interactions with the host and microbiome and the rise of antifungal resistance

项目 3 主要人类真菌病原体的群体研究：与宿主和微生物组相互作用以及抗真菌耐药性上升的基因组和转录组分析

• 批准号: 10163679
• 负责人: Christina A Cuomo
• 金额: $ 71.94万
• 依托单位: BROAD INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-04-10 至 2024-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10163679
• 关键词: Address; Animal Model; Antifungal Agents; Antifungal Therapy; Area; Blood; Blood Circulation; Candida; Cells; Central Nervous System Infections; Cessation of life; Clinical; Clinical Treatment; Clinical Trials; Collection; Communicable Diseases; Cryptococcus; Cryptococcus neoformans; Data; Development; Diagnosis; Drug resistance; Evolution; Fungal Drug Resistance; Gastrointestinal tract structure; Gene Deletion; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genetic Transcription; Genetic Variation; Genetic study; Genome; Genomic approach; Genomics; Growth; Health; Heterogeneity; High-Throughput Nucleotide Sequencing; Human; Hybrids; Immune response; Immunocompromised Host; Individual; Infection; Innate Immune Response; Intervention; Lung infections; Maps; Measures; Mediating; Metadata; Metagenomics; Methods; Monitor; Mycoses; Neuraxis; Outcome; Pathogenesis; Patient Isolators; Patients; Penicillium; Phenotype; Population; Population Study; Property; Risk Factors; Sampling; Sepsis; Site; Skin; Stream; Talaromyces; Technology; Testing; Variant; Virulence; Virulent; Work; candidemia; chronic infection; cohort; combat; deletion library; effective therapy; fungus; genome sequencing; genome wide association study; genome-wide; genomic data; host microbiome; in vivo; individual patient; microbiome; mortality; mycobiome; novel strategies; pathogen; pathogen genomics; pathogenic fungus; phenotypic data; prospective; reference genome; response; synergism; transcriptome sequencing; transcriptomics; trial comparing; whole genome

Fungal pathogens have a major impact on human health; the lack of effective antifungal therapies, the diversity of species infecting humans, and the emergence of new lineages, species and drug resistance represent major challenges to treatment. This proposal will examine two species causing the largest number of opportunistic invasive mycoses and a third species representing a major cause of endemic dimorphic mycoses. We will compare clinical isolates from each pathogen to determine the genetic basis of highly virulent or antifungal resistant isolates, and to discriminate how isolates that cause invasive infections differ from those of low virulence or that are part of a healthy mycoflora. In the first aim, we will study the genetic basis of pathogenesis of Cryptococcus neoformans, a major cause of infection in immunocompromised individuals, by combining large- scale phenotyping, whole genome sequencing, and transcriptional analysis of natural isolates. We will characterize how natural isolates differ in in vivo growth during pulmonary infection and dissemination to the central nervous system and will use these measures to carry out genome-wide association screens of the pathogen; in parallel, we will measure the growth of the Cryptococcus gene deletion collection of over 4,000 strains. To highlight changes in gene regulation between isolates and pinpoint genes that are highly expressed at different infection stages, we will carry out RNA-Seq of in vivo stages and key cells involved in fungal interactions. We will also examine the microevolution of this pathogen during host infection and compare that to changes observed in an animal model. In the second aim, we will address a major question about the origin of bloodstream Candida infections, which are a major cause of mortality in immunocompromised patients. We will examine the intra-host diversity of Candida isolates between commensal sites in the gut and the skin and isolates from patients with candidemia to trace the origin of these bloodstream infections. We will adapt new enrichment approaches to increase the proportion of Candida reads in metagenomic samples. Lastly, we will test isolates that are more frequently associated with the bloodstream origin to confirm their relative virulence in an animal model. In aim 3, we will examine isolates of Talaromyces (Penicillium) marneffei collected from patients in a recent clinical trial comparing two antifungal treatments. This represents the largest collection of clinical isolates collected for a clinical trial with patient metadata for an endemic mycosis. We will use whole genome and RNA- Seq analyses to define properties associated with drug resistance and aggressive infections with high mortality. While these three aims represent independent projects to examine fungal pathogenesis, each utilizes large-scale ‘omics approaches to extend and develop new paradigms for studying and understanding fungal virulence in the context of natural population variation. This work will provide an unprecedented whole-genome view into pathogens associated with clinical samples, and a synthesis of its findings will suggest new approaches for diagnosis and treatment for individual patients and risk factors to monitor prospectively.

真菌病原体对人类健康具有重大影响；缺乏有效的抗真菌疗法，多样性 感染人类的​​物种数量，以及新谱系、物种和耐药性的出现代表了主要的 该提案将研究造成最多机会性感染的两个物种。 侵袭性真菌病和代表地方性二形性真菌病主要原因的第三种。 比较每种病原体的临床分离株，以确定高毒力或抗真菌的遗传基础 耐药菌株，并区分引起侵袭性感染的菌株与低毒力菌株的区别 或者是健康菌群的一部分 在第一个目标中，我们将研究发病机制的遗传基础。 新型隐球菌是免疫功能低下个体感染的主要原因，通过结合大 我们将进行规模表型分析、全基因组测序和天然分离株的转录分析。 描述自然分离株在肺部感染和传播到全身过程中体内生长的差异 中枢神经系统，并将利用这些措施进行全基因组关联筛选 同时，我们将测量 4,000 多个隐球菌基因缺失集合的生长情况 突出菌株之间基因调控的变化并查明高表达的基因。 在不同的感染阶段，我们将进行体内阶段和参与真菌的关键细胞的RNA-Seq 我们还将检查这种病原体在宿主感染过程中的微进化，并将其与宿主感染进行比较。 在动物模型中观察到的变化在第二个目标中，我们将解决有关起源的主要问题。 血液念珠菌感染，这是免疫功能低下患者死亡的主要原因。 检查肠道和皮肤共生位点之间念珠菌分离株的宿主内多样性 我们将采用新的浓缩方法从念珠菌血症患者身上追踪这些血液感染的起源。 增加宏基因组样本中念珠菌读数比例的方法最后，我们将测试分离株。 更频繁地与血流起源相关，以确认它们在动物中的相对毒力 在目标 3 中，我们将检查从患者身上收集的马尔尼菲青霉分离株。 最近比较两种抗真菌治疗的临床试验这是最大的临床分离株集合。 收集用于地方性真菌病患者元数据的临床试验，我们将使用全基因组和 RNA-。 Seq 分析可定义与耐药性和高死亡率侵袭性感染相关的特性。 虽然这三个项目旨在代表检查真菌发病机制的独立项目，但每个项目都利用大规模 “组学方法扩展和开发研究和理解真菌毒力的新范式 这项工作将为研究提供前所未有的全基因组视角。 与临床样本相关的病原体，及其研究结果的综合将提出新的方法 个体患者的诊断和治疗以及前瞻性监测的危险因素。