Within-patient Candida auris strain diversity in a tertiary hospital

三级医院患者内耳念珠菌菌株多样性

基本信息

批准号：
10732309
负责人：
M. Hong Thi NGUYEN
金额：
$ 23.85万
依托单位：
UNIVERSITY OF PITTSBURGH AT PITTSBURGH
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-08-14 至 2025-07-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10732309
关键词：
Adherence Aneuploidy Antibiotic Resistance Antifungal Agents Blood Blood Circulation Candida Candida albicans Candida auris Cell Wall Cells Clinical Microbiology Copy Number Polymorphism Data Diploidy Disease Outbreaks Environment Exhibits Foundations Fungal Drug Resistance Gene Dosage Genes Genetic Genetic Determinism Genetic Variation Genome Genomics Genotype Growth Haploidy Hematogenous Hospitals In Vitro Individual Infection International Karyotype Lipase Microbial Biofilms Microbial Genetics Minimum Inhibitory Concentration measurement Morphogenesis Morphology Multi-Drug Resistance Mutation Mycoses Organism Paper Pathogenesis Pathogenicity Patient Care Patients Peptide Hydrolases Pharmaceutical Preparations Phenotype Phylogeny Point Mutation Polyploidy Population Predisposition Process Production Public Health Regulation Research Design Resistance Resistance development Sepsis Single Nucleotide Polymorphism Site Sterility Testing Treatment Failure Variant Virulence Yeasts antibiotic tolerance biological adaptation to stress carbapenem resistance chronic infection clinically relevant clinically significant echinocandin resistance falls fitness genetic variant genome sequencing health organization individual patient insight mortality mouse model mutant neutrophil novel population based priority pathogen recurrent infection resistant Klebsiella pneumoniae response stem treatment response whole genome

项目摘要

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.

项目概要耳念珠菌最近已成为全球侵袭性感染的一个原因，这些感染与高感染率有关。尽管使用一线抗真菌药物棘白菌素和其他药物进行治疗，死亡率仍然很高。耳念珠菌由于其抗真菌耐药性以及在医院中持续存在的能力而带来了独特的挑战环境并导致长期爆发。 C. auris 是单倍体酵母，在进化上与二倍体念珠菌，如白色念珠菌和大多数致病菌种。菌株分为 5 个系统发育分支。最多感染由 I、III 或 IV 分支菌株引起。越来越多的证据表明进化枝内的遗传多样性，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。给定分支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，很少有特定基因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、毒力和发病机制不一定能从其他念珠菌属中推断出来，或 C. auris 进化枝之间。长期存在的范式是，几乎所有血液或其他部位的念珠菌感染通常无菌位点源自单一克隆生物体。然而，在初步研究中，我们已经表明至少有一些耳念珠菌和光滑念珠菌菌株是从个体患者的阳性血培养中回收的我们的中心展现出未被认识的基因型和表型多样性。我们的数据表明了一种新的、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从个体患者中回收的耳念珠菌菌株的多样性，并暗示特定的耳念珠菌基因和基因棘白菌素耐受性和耐药性以及毒力的变异。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从 C. auris 中回收的多个进化枝 I 和 III 的系统发育来自每位患者的培养物，包括基线以及持续和反复感染期间棘白菌素治疗。然后，我们将测试每位患者遗传上不同的菌株的表型，包括棘白菌素耐受性和耐药性以及毒力相关表型。在目标 2 中，我们将优先考虑基因和基因变异，并在进化枝 I 和 III 背景中创建等基因突变耳念珠菌菌株。同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。结果将为耳念珠菌的棘白菌素反应和发病机制提供新的见解，并确定有助于这些过程的基因。我们的结果将为机制研究提供基础棘白菌素耐受性、耐药性和毒力，以及用于确定耳念珠菌临床意义的试验基因型和表型多样性。我们的微生物遗传多样性范式具有潜在的深远影响用于患者护理、临床微生物学实践以及抗真菌治疗反应和发病机制的了解。