Multiplex diagnostic for biothreat C. psittaci & non-threat respiratory pathogens

生物威胁鹦鹉热衣原体的多重诊断

• 批准号: 8268884
• 负责人: DEBORAH Anne DEAN
• 金额: $ 124.67万
• 依托单位: CHILDREN'S HOSPITAL & RES CTR AT OAKLAND
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-06-06 至 2017-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8268884
• 关键词: Adenoviruses; Antibiotic Resistance; Antibiotics; Bacillus anthracis; Biological; Biological Assay; Burkholderia pseudomallei; Categories; Cervical; Chlamydia; Chlamydia trachomatis; Chlamydophila pneumoniae; Chlamydophila psittaci; Clinic; Clinical; Clinical Research; Clinical Trials; Clinics and Hospitals; Collection; Coxiella burnetii; DNA; DNA amplification; DNA purification; Data; Detection; Development; Diagnostic; Disease; Drug resistance; Early Diagnosis; Early identification; Epidemiology; Evaluation; Fluorescence; Francisella tularensis; Future; Genome; Genomics; Goals; Health Personnel; Hospitals; Hour; Housing; Human; Individual; Infection; Influenza; Lasers; Lead; Legionella pneumophila; Life; Location; Lung diseases; Measles; Medical; Methods; Microfluidics; Military Personnel; Mycoplasma pneumoniae; Names; National Institute of Allergy and Infectious Disease; New Agents; Nucleic Acid Amplification Tests; Organism; Parainfluenza; Pathogenesis; Patients; Performance; Population; Predictive Value; Prevalence; Procedures; Readiness; Reading; Respiratory syncytial virus; Reverse Transcriptase Polymerase Chain Reaction; Sampling; Sensitivity and Specificity; Sexually Transmitted Diseases; Source; Specificity; Sputum; Staging; Swab; Symptoms; System; Technical Expertise; Technology; Testing; Therapeutic; United States National Institutes of Health; Urethra; Vagina; Virulence; Virulent; Work; Yersinia pestis; age group; atypical pneumonia; base; biodefense; biothreat; comparative genomics; design; genome sequencing; human DNA; innovation; instrument; microbial; novel; nucleic acid detection; pathogen; respiratory; treatment strategy

DESCRIPTION (provided by applicant): There is an urgent need to develop rapid sample-to-answer clinic and field deployable diagnostics for NIAID Category A, B and C biothreat pathogens to protect both military and civilian populations. The goal of this application is to advance and validate a lead candidate diagnostic - a novel microfluidics nucleic acid detection and sequencing diagnostic platform recently developed by NetBio-to identify Category B pathogen Chlamydia psittaci (Cps) that causes life-threatening respiratory diseases and has historically been a focus of bioweapons development as well as being a vastly understudied pathogen. We will also detect emerging Cps pathogens and non-biothreat pathogens that are the leading cause of atypical pneumonia and often confused with biothreat agents in clinical presentation: Chlamydia trachomatis (Ct), Chlamydia pneumoniae (Cpn), Mycoplasma pneumoniae (Mp) and Legionella pneumophila (Lp). Indeed, the Biodefense RFA-AI-11-014 we are responsive to states, "Medical diagnostics that use platforms to rapidly distinguish whether an individual is infected with a biological threat agent or a common infection with similar, generalized symptoms are of high priority." There are currently few or no commercial diagnostics for these pathogens in the US. The NetBio platform consists of a ruggedized, analytic instrument that accepts a biochipset (BCS)-shown in Preliminary Studies to purify genomic DNA from clinical samples, amplify, electrophoretically separate and laser detect and type Ct. The entire system from DNA purification to detection takes ~1 hour. The Aims are to: 1) genome sequence representative Cps biothreat and non- biothreat atypical respiratory pathogens for robust primer selection; 2) modify the BCS to purify genomic DNA from human clinical nasopharyngeal (NP) swab and sputum samples; 3) employ the primer selection pipeline developed by Dr. Read to identify primers based on comparative genomics of available genomes and those sequenced in Aim 1 for differentiating biothreat and non-biothreat atypical respiratory pathogens, and develop a multiplexed assay for DNA amplification to distinguish each pathogen; and 4) evaluate the sensitivity, specificity and positive and negative predictive value of the NetBio assay using first spiked samples and then clinical NP swabs and sputum samples compared to the available commercial nucleic acid amplification tests for Ct, Cpn, Mp and Lp (none exist for Cps), and compared to highly sensitive in-house RT-PCR assays prior to clinical trials for FDA approval. A future goal will be to expand the assay to other biothreat respiratory pathogens. We envision that the NetBio sample-to-answer assay will be used in ERs, MD offices, clinics, military facilities, hospitals and the field to advance our understanding of the epidemiology of atypical respiratory diseases and best treatment strategies, which will inform biothreat preparedness. A broadly used diagnostic will detect patients with common but also biothreat infection, enabling early identification of an attack and rapid treatment of infecte military and civilian populations. PUBLIC HEALTH RELEVANCE: Chlamydia psittaci is a Category B Biodefense agent that is difficult to distinguish from the clinical presentation of Chlamydia pneumoniae, Chlamydia trachomatis, Mycoplasma pneumoniae and Legionella pneumophila; all are respiratory pathogens and represent the major causes of atypical pneumonia in the world today. There are no reliable commercial diagnostics available for any of these human pathogens. We plan to develop an easy to use, cheap, one-hour diagnostic that will detect and differentiate each pathogen for use in ERs, clinics, hospitals, military facilities and the field to advance our understanding of the epidemiology of atypical respiratory diseases and the best therapeutic strategies, which will inform biothreat preparedness. A broadly-used diagnostic will identify patients with common but also with biothreat infections, enabling the identification of an attack i the early stages and assisting health care personnel in rapidly treating infected military and civilian populations to save lives.

描述（由申请人提供）：迫切需要为NIAID A，B和C生物治疗病原体开发快速的样本到临时诊所和现场可部署的诊断，以保护军事和平民。该应用的目的是提高和验证主要的候选诊断 - 一种新型的微流体核酸检测和测序诊断平台最近由Netbio开发而成，可识别类别B病原体Chlamydia psittaci（CPS），可引起生命危及生命的呼吸疾病，并史无前例地构成了生物过多的焦点，并且一直在广泛地理解。我们还将检测出新出现的CPS病原体和非生物治疗病原体，这些病原体是非典型肺炎的主要原因，并且经常与临床表现中的生物治疗剂混淆：沙眼衣原体（CT）（CT），衣原体肺炎（CPN），mimcoplasma pneumonia and lbneumonia and logumopla（mpnecra）（mpnecral）（mp）（mp）（pe）。的确，生物形式RFA-AI-11-014我们对国家的反应：“使用平台来迅速区分个人是否感染了生物威胁剂或具有类似广义症状的常见感染的医学诊断，这是很高的优先事项。”目前，在美国，这些病原体几乎没有商业诊断。 NetBio平台由一种耐用的，分析仪器组成，该仪器接受初步研究中的生物芯片（BCS），以从临床样品中净化基因组DNA，并放大，电泳分离和激光检测和类型CT。从DNA纯化到检测的整个系统需要约1小时。目的是：1）基因组序列代表性CPS Biothreat和非生物疗法非典型呼吸病原体用于健壮的底漆； 2）修改BCS以纯化人类鼻咽（NP）拭子和痰液样品中的基因组DNA； 3）采用Read博士开发的底漆选择管道来鉴定基于可用基因组的比较基因组学，以及在AIM 1中测序的底漆，以区分生物治疗和非生物治疗非典型呼吸道病原体，并为DNA扩增开发多发性测定，以区分每种病原体； 4）与可用的商业核酸扩增测试相比，使用先发出的样本和临床NP拭子和痰样品，评估NetBio测定的敏感性，特异性以及正面和负预测值，与CT，CPN，MP和LP的可用商业核酸扩增测试相比，与以前具有高度敏感的In House RT-PCR RT-PCR clins进行了比较。未来的目标是将测定法扩展到其他生物治疗呼吸道病原体。我们设想，Netbio样本与答案测定将用于ERS，MD办公室，诊所，军事设施，医院和领域，以促进我们的理解 非典型呼吸道疾病和最佳治疗策略的流行病学，这将为生物治疗准备。广泛使用的诊断将检测患有常见但生物治疗感染的患者，从而能够早期鉴定出攻击并快速治疗感染军事和平民人群。 公共卫生相关性：衣原体psittaci是B类生物形式的剂，很难与肺炎衣原体，沙眼衣原体，霉菌肺炎和肺炎菌群的临床表现区分开。所有人都是呼吸道病原体，代表了当今世界上非典型肺炎的主要原因。这些人类病原体中的任何一种都没有可靠的商业诊断。我们计划开发一种易于使用的，便宜的一个小时的诊断，该诊断将检测和区分每种病原体，以用于ERS，诊所，医院，军事设施和领域，以促进我们对异型呼吸道疾病的流行病学以及最佳治疗策略的理解，这些策略将为BiothReat准备好生物剂。广泛使用的诊断将确定患有常见的患者，但也会患有生物治疗感染，从而使I次发作的早期阶段识别，并协助迅速治疗受感染的军事和平民人群挽救生命的医疗保健人员。