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。 BSI 到期 白色念珠菌和光滑念珠菌（引起侵袭性感染的最常见念珠菌）的感染率为 20%-40% 尽管使用一线抗真菌药物棘白菌素进行治疗。棘白菌素耐药性日益增加 描述了白色念珠菌和光滑念珠菌临床分离株。尽管如此，大多数棘白菌素治疗 失败与阻力的出现无关。棘白菌素耐受性，其中念珠菌生长 受到抑制，但细胞仍然存活，可能容易随后产生耐药性，但临床相关性 该表型的具体情况尚不清楚。长期存在的范式是，几乎所有念珠菌血症和其他 BSI 都源于 一个单一的、克隆的有机体。然而，在初步研究中，我们通过全基因组测序（WGS）表明 系统发育分析表明白色念珠菌和光滑念珠菌 BSI 是由遗传上的混合种群引起的 临床微生物学实验室通常无法识别的不同菌株。经过更深入的分析 根据白色念珠菌 WGS 数据，我们发现在多名 BSI 患者中鉴定出的基因变异丰富了 已知对棘白菌素反应和毒力很重要的生物过程。我们的目标是 该项目旨在更详细地描述血流白色念珠菌的遗传和表型多样性 和光滑念珠菌菌株，特别注意与持续性或复发性感染相关的菌株 尽管进行了棘白菌素治疗，并暗示了棘白菌素中特定的念珠菌基因和基因变异 耐受性、抵抗力和毒力。我们假设通过研究纵向 BC 和额外的菌株 持续或复发性白色念珠菌或光滑念珠菌血流感染患者的血液部位，尽管 棘白菌素治疗，我们将鉴定导致棘白菌素的新基因或基因变体 耐受性/耐药性和毒力。我们的第一个目标是完成全基因组测序以及白色念珠菌和念珠菌的分析。 光滑从基线 BC（每个 10 名患者）。然后，我们将对阳性菌株进行全基因组测序和分析 在棘白菌素治疗期间或之后收集的纵向血液和血外培养物。最后，我们将 确定来自 BC 的遗传多样性菌株的表型，包括棘白菌素耐受性和抗性。 在我们的第二个目标中，我们将构建同基因突变体和互补的白色念珠菌和光滑念珠菌菌株 目标 1 中确定并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 并使用血源性传播的小鼠模型研究棘白菌素治疗反应和毒力 感染。结果将确认 BC 中白色念珠菌和光滑念珠菌遗传多样性的程度和类型， 关于念珠菌在持续性或复发性 BSI 期间对棘白菌素反应的新见解，并确定新的 棘白菌素治疗失败和毒力的遗传决定因素。我们的研究结果将挑战当前的临床 和微生物学实验室实践，并为 BSI 期间的遗传多样性研究提供基础 其他念珠菌属物种和细菌，以及抗真菌耐受、耐药和发病机制的机制。

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