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 念珠菌物种是美国医院血液感染（BSI）的第四主要原因。 BSIS应得 对于白色念珠菌和C. glabrata而言，最常见的念珠菌物种引起侵入性感染，为20％-40％ 尽管用棘突素治疗前线抗真菌剂。 eChinocandin抗性越来越多 在白色念珠菌和glabrata临床分离株中描述。然而，大多数echinocandin治疗 失败与抵抗的出现无关。 chinocandin的耐受性，其中念珠菌的生长是 抑制但细胞仍然可行，可能会易于随后的抗性发展，但临床相关性 这种表型尚不清楚。长期以来的范式是，几乎所有的候选血症和其他BSI都源于 一个单一的克隆生物。然而，在初步研究中，我们通过整个基因组测序（WGS）表明 系统发育分析表明，白色念珠菌和C. glabrata bsis是由遗传上混合种群引起的 多种菌株，通常不受临床微生物实验室的认可。经过更深入的分析 在白色念珠菌WGS数据中，我们发现在多个BSI患者中鉴定出的基因变异量富含 已知在echinocandin反应和毒力中很重要的生物过程。我们的目标 该项目将更详细地表征血统白色念珠菌的遗传和表型多样性 和C. glabrata菌株，特别注意与持续或复发感染相关的菌株 尽管进行了棘手的治疗，并牵涉到echinocandin中的特定念珠菌基因和基因变异 耐受性，抗性和毒力。我们假设通过研究纵向BC和外部的菌株 尽管 echinocandin治疗，我们将确定负责echinocandin的新型基因或基因变体 耐受性/抗性和毒力。在我们的第一个目标中，我们将完成白色念珠菌和C.的WGS和分析。 基线BC的Glabrata（每个患者10例）。然后，我们将对正面进行WGS和分析菌株的分析 在echinocandin治疗期间或之后收集的纵向血液和血外培养物。最后，我们会的 确定来自BCS的遗传多样性菌株的表型，包括echinocandin的耐受性和耐药性。 在我们的第二个目标中，我们将构建异基因突变体和互补的白色念珠菌和C. glabrata菌株 在AIM 1中鉴定和优先级的基因和基因变体。我们将在体外测试表型的菌株 以及使用血源性散布的小鼠模型用于棘手的治疗反应和毒力 感染。结果将肯定白色念珠菌的程度和类型和BCS中的C. glabrata遗传多样性可负担 对持久性或经常性BSIS期间对脑虫响应的念珠菌反应的新见解，并确定新颖 echinocandin治疗衰竭和毒力的遗传决定因素。我们的发现将挑战当前的临床 和微生物学实验室实践，并为BSI期间遗传多样性的研究提供了基础 其他念珠菌物种和细菌，以及抗真菌耐受性，耐药性和发病机理的机制。

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