Genomic diversity of Candida bloodstream infections

念珠菌血流感染的基因组多样性

• 批准号: 10358615
• 负责人: M. Hong Thi NGUYEN
• 金额: $ 21.9万
• 依托单位: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-03-01 至 2025-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10358615
• 关键词: Adhesions; Antifungal Agents; Antimicrobial susceptibility; Attention; Bacteria; Biological Process; Blood; Blood Circulation; Candida; Candida albicans; Candida glabrata; Candidiasis; Cell Wall; Cells; Clinical; Clinical Microbiology; Complement; DNA Sequence Rearrangement; Data; Diploidy; Disease; Exhibits; Experimental Models; Foundations; Fungal Drug Resistance; Gastrointestinal tract structure; Genes; Genetic; Genetic Determinism; Genetic Variation; Genetic study; Genome; Genomics; Growth; Haploidy; Hematogenous; Human; In Vitro; Infection; Laboratories; Morphology; Mucous Membrane; Organism; Organism Cloning; Pathogenesis; Patients; Phenotype; Phylogenetic Analysis; Population; Population Heterogeneity; Recurrence; Recurrent disease; Regulation; Resistance; Resistance development; Sepsis; Single Nucleotide Polymorphism; Site; State Hospitals; Stimulus; Surface; Testing; Time; Treatment Failure; United States; Virulence; Virulent; candidemia; chronic infection; clinically relevant; echinocandin resistance; genetic variant; genome analysis; genome sequencing; individual patient; insertion/deletion mutation; insight; mortality; mouse model; mutant; nanopore; novel; opportunistic pathogen; pathogen; recurrent infection; reference genome; response; stem; treatment response; whole genome

Project Abstract Candida species are fourth leading cause of bloodstream infections (BSIs) in United States hospitals. BSIs due to C. albicans and C. glabrata, the most common Candida species to cause invasive infections, are 20%-40% despite treatment with echinocandins, the frontline antifungal agents. Echinocandin resistance is increasingly described among C. albicans and C. glabrata clinical isolates. Nevertheless, most echinocandin treatment failures are not associated with emergence of resistance. Echinocandin tolerance, in which Candida growth is inhibited but cells remain viable, may predispose to subsequent development of resistance, but clinical relevance of this phenotype is unclear. The longstanding paradigm is that almost all candidemia and other BSIs stem from a single, clonal organism. In preliminary studies, however, we showed by whole genome sequencing (WGS) and phylogenetic analyses that C. albicans and C. glabrata BSIs are caused by mixed populations of genetically diverse strains, which are not typically recognized by the clinical microbiology laboratory. Upon deeper analysis of C. albicans WGS data, we found that gene variants identified in multiple patients with BSIs were enriched for biological processes that are known to be important in echinocandin responses and virulence. Our objectives in this project are to characterize in greater detail the genetic and phenotypic diversity of bloodstream C. albicans and C. glabrata strains, with particular attention to strains associated with persistent or recurrent infections despite echinocandin treatment, and to implicate specific Candida genes and gene variants in echinocandin tolerance, resistance and virulence. We hypothesize that by studying strains from longitudinal BCs and extra- blood sites of patients with persistent or recurrent C. albicans or C. glabrata bloodstream infections despite echinocandin treatment, we will identify novel genes or gene variants that are responsible for echinocandin tolerance/resistance and virulence. In our first aim, we will complete WGS and analyses of C. albicans and C. glabrata from baseline BCs (10 patients each). Then, we will perform WGS and analyses of strains from positive longitudinal blood and extra-blood cultures collected during or after echinocandin treatment. Finally, we will determine phenotypes of genetically diverse strains from BCs, including echinocandin tolerance and resistance. In our second aim, we will construct isogenic mutant and complemented C. albicans and C. glabrata strains for genes and gene variants that are identified and prioritized in aim 1. We will test strains for phenotypes in vitro and for echinocandin treatment responses and virulence using mouse models of hematogenously disseminated infections. Results will affirm the extent and type of C. albicans and C. glabrata genetic diversity in BCs, afford new insights into Candida responses to echinocandins during persistent or recurrent BSIs, and identify novel genetic determinants of echinocandin treatment failure and virulence. Our findings will challenge current clinical and microbiology laboratory practices, and provide a foundation for studies of genetic diversity during BSIs by other Candida species and bacteria, and mechanisms of antifungal tolerance, resistance and pathogenesis.

项目摘要 念珠菌是美国医院血液感染(BSI)的第四大原因。BSIS到期 对白念珠菌和光滑念珠菌这两种最常见的引起侵袭性感染的念珠菌来说，20%-40% 尽管使用棘球菌素治疗，但一线抗真菌药物。棘球绦虫耐药性日益增强 在白色念珠菌和光滑念珠菌临床分离株中描述。尽管如此，大多数棘球菌素治疗 失败与抵抗的出现无关。棘球菌素耐受性，其中念珠菌生长 被抑制但细胞仍然存活，可能易于随后发生耐药，但与临床相关 这种表型的类型尚不清楚。长期以来的模式是，几乎所有的念珠菌症和其他细菌感染都源于 一种单一的克隆生物体。然而，在初步研究中，我们通过全基因组测序(Wgs)显示 系统发育分析表明，白色念珠菌和光滑念珠菌是由混合种群遗传引起的。 不同的菌株，通常不被临床微生物学实验室识别。根据更深层次的分析 在白色念珠菌WGS数据中，我们发现在多个BSI患者中发现的基因变异对 已知在棘球绦虫反应和毒力中起重要作用的生物过程。我们的目标是 这个项目是为了更详细地描述血液中白色念珠菌的遗传和表型多样性。 和光滑假丝酵母菌株，特别注意与持续或反复感染有关的菌株 尽管接受棘球菌素治疗，但与棘球菌素相关的特定念珠菌基因和基因变异有关 耐受性、抵抗力和毒性。我们假设，通过研究来自纵向BCS和外部的菌株- 持续或复发的白色念珠菌或光滑念珠菌血流感染患者的血液部位 棘球绦虫治疗，我们将确定与棘球绦虫相关的新基因或基因变体 耐受性/抗药性和致病力。在我们的第一个目标中，我们将完成WGS和对白色念珠菌和C. 基础BCS的光滑度(各10例)。然后，我们将对阳性菌株进行WGS和分析 在棘球绦虫治疗期间或治疗后收集纵向血和血外培养。最后，我们会 确定BCS遗传多样性菌株的表型，包括棘球绦虫的耐受性和抗药性。 在我们的第二个目标中，我们将构建等基因突变和互补的白色念珠菌和光滑念珠菌菌株 在目标1中确定和优先考虑的基因和基因变体。我们将在体外测试菌株的表型 用小鼠血行播散性模型观察棘球绦虫的治疗反应和毒力 感染。结果将肯定白念珠菌和光滑念珠菌在BCS中的遗传多样性的范围和类型， 对念珠菌在持续性或复发性BSI期间对棘球菌素的反应的新见解，并确定新的 棘球绦虫治疗失败和毒力的遗传决定因素。我们的发现将挑战目前的临床 和微生物学实验室实践，并通过以下方式为生物多样性研究提供基础 其他念珠菌和细菌的耐药、耐药和致病机制。

项目成果

Unveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics from either short- or long-read sequencing.

使用 VEBA 2.0 揭开微生物领域的面纱：模块化生物信息学套件，用于通过短读长或长读长测序进行端到端基因组解析的原核生物、（微）真核生物和病毒多组学。

• DOI: 10.1101/2024.03.08.583560
• 发表时间: 2024
• 期刊: bioRxiv : the preprint server for biology
• 作者: Espinoza,JoshL;Phillips,Allan;Prentice,MelanieB;Tan,GeneS;Kamath,PaulineL;Lloyd,KarenG;Dupont,ChrisL
• 通讯作者: Dupont,ChrisL

Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures.

• DOI: 10.1038/s41467-023-41509-x
• 发表时间: 2023-09-22
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Badrane, Hassan;Cheng, Shaoji;Dupont, Christopher L.;Hao, Binghua;Driscoll, Eileen;Morder, Kristin;Liu, Guojun;Newbrough, Anthony;Fleres, Giuseppe;Kaul, Drishti;Espinoza, Josh L.;Clancy, Cornelius J.;Nguyen, M. Hong
• 通讯作者: Nguyen, M. Hong