RNA based diagnostics for rapid pathogen identification and drug resistance

基于 RNA 的快速病原体识别和耐药性诊断

基本信息

批准号：
8876094
负责人：
DEBORAH T HUNG
金额：
$ 155.26万
依托单位：
BROAD INSTITUTE, INC.
依托单位国家：
美国
项目类别：
财政年份：
2015
资助国家：
美国
起止时间：
2015-02-15 至 2020-01-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8876094
关键词：
Acceleration Acinetobacter Acute Address Antibiotic Resistance Antibiotic susceptibility Antibiotics Bacteria Biological Assay Blood Cells Clinic Clinical Clinical Data Communicable Diseases Complex Computational algorithm Coupled Cytolysis DNA Data Data Set Decision Making Derivation procedure Detection Development Devices Diagnosis Diagnostic Drug resistance Elements Engineering Enterobacter Enterococcus faecium Escherichia coli Exposure to Fractionation Genes Genetic Genetic Markers Genetic Transcription Genomics Genotype Growth Hospitals Hour Individual Klebsiella pneumonia bacterium Knowledge Life Measurable Medical Messenger RNA Methods Microfluidics Molecular Profiling Morbidity - disease rate Mutation Nanotechnology Nucleic Acids Pathogen detection Patients Pattern Pharmaceutical Preparations Phenotype Physicians Physiological Predisposition Primary Health Care Process Pseudomonas aeruginosa Public Health RNA Reaction Recovery Reporting Research Resistance Ribosomal RNA Sampling Scanning Scientist Sensitivity and Specificity Specificity Specimen Staphylococcus aureus Stress Syndrome Technology Testing Therapeutic Therapeutic Intervention Time Training Transcript Variant Work base cost digital genome-wide improved industry partner meetings microbial mortality multidisciplinary nano-string particle pathogen pathogen exposure prototype public health relevance rapid detection resistant strain response single molecule tertiary care transcriptome sequencing

项目摘要

DESCRIPTION (provided by applicant): Rapid diagnostics for infectious diseases that both identify the pathogen and provide drug susceptibility data in real-time would transform patient management and critical public health issues such as the current antibiotic resistance crisis. Their application would reach broadly from clinics and primary care offices to tertiary care hospitals, providing immediate guidance for therapeutic intervention thereby resulting in more prudent and appropriate use of antibiotics, in some cases with mortality benefit. The need to generate real- time drug susceptibility patterns is particularly acute in the face of escalating antibiotic resistance that is challenging empiric antibiotic decision-making. We propose to develop a rapid, universal RNA hybridization-based diagnostic platform that would provide both real-time identification of microbial pathogens and reveal their susceptibility to diverse antibiotics. Pathogen identification will be achieved by the detection of species-specific sequence variations in highly abundant ribosomal RNAs. Drug susceptibility will be determined by detection of transcriptional signatures that are extremely rapidly induced (within minutes) by antibiotic exposure in susceptible but not resistant strains. Importantly, in contrast o existing DNA-based diagnostics, this RNA-based approach will enable pathogen identification without nucleic acid amplification and drug susceptibility profiling without a priori knowledge of the genes or mutations that confer drug resistance. Moreover, since transcriptional responses to antibiotics occur much earlier than measurable changes in growth, this platform would provide a phenotypic readout much earlier than culture-based assays. Significantly, this work is coupled with microfluidic technology to obviate the need for culture. Proof of principle studies have demonstrated the feasibility of this approach. We now propose to expand upon and optimize our RNA-signatures for pathogen identification and drug susceptibility for the high priority antibiotic resistant ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter species), to solve individual engineering challenges required for development of a diagnostic device, and to integrate these elements into a microfluidic prototype for rapid pathogen identification and antibiotic susceptibility. To that ed, we have formed a multidisciplinary team of scientists, engineers, and industry partners that will work collaboratively to carry out the proposed research.

描述（应用程序提供）：既鉴定病原体又提供药物易感性数据的传染病的快速诊断将改变患者管理和关键的公共健康问题，例如当前的抗生素耐药性危机。他们的应用将从诊所和初级保健办公室到三级护理医院，从而为治疗干预提供了直接的指导，从而在某些情况下会更加审慎，适当地使用抗生素。面对抗生素抗生素的耐药性不断提高，挑战经验性抗生素决策的抗生素耐药性，产生实时药物敏感性模式的需求尤其急切。我们建议开发一个基于RNA杂交的快速，通用的诊断平台，该平台将提供对微生物病原体的实时鉴定并揭示其对潜水抗生素的敏感性。病原体鉴定将通过检测高度丰富的核糖体RNA中的特异性序列变化来实现。药物敏感性将通过检测转录特征来确定，这些特征是通过易感性但没有抗性菌株的抗生素暴露诱导（几分钟之内）的转录特征。重要的是，与现有的基于DNA的诊断相比，这种基于RNA的方法将在没有核酸扩增和药物敏感性分析的情况下实现病原体鉴定，而没有对赋予药物抗性的基因或突变的先验知识。此外，由于对抗生素的转录反应比可测量的生长变化要早得多，因此该平台将提供比基于培养的测定的表型读数。值得注意的是，这项工作与微流体技术相结合，以消除对培养的需求。原则研究证明证明了这种方法的可行性。 We now propose to expand upon and optimize our RNA-signatures for pathogen identification and drug susceptibility for the high priority antibiotic resistant ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumaii, Pseudomonas aeruginosa, and Enterobacter species), to solve individual engineering challenges开发诊断装置所需的，并将这些元素整合到微流体原型中，以快速病原体鉴定和抗生素易感性。在此期间，我们组成了一个由科学家，工程师和行业合作伙伴组成的多学科团队，他们将共同努力进行拟议的研究。