An Automated Multi-target Diagnostic System for Gastrointestinal Pathogens

胃肠道病原体自动多靶点诊断系统

• 批准号: 8103988
• 负责人: Margarita B Rogatcheva
• 金额: $ 109.12万
• 依托单位: BIOFIRE DEFENSE, LLC.
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-07-02 至 2013-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8103988
• 关键词: 5 year old; Acute; Adenoviruses; Adopted; Algorithms; Archives; Bacteria; Biological Assay; Campylobacter jejuni; Categories; Cause of Death; Cessation of life; Child; Cities; Clinical; Clostridium difficile; Complex; Computer software; Cryptosporidium parvum; Cyclospora; DNA; Data; Data Analyses; Detection; Development; Devices; Diagnosis; Diagnostic; Diagnostic tests; Diarrhea; Disease Outbreaks; Documentation; Drug Formulations; Ensure; Entamoeba histolytica; Enteral; Epidemiology; Escherichia coli; Escherichia coli EHEC; Etiology; Evaluation; Feces; Food; Gene Targeting; Genes; Giardia lamblia; Goals; Gold; Health; Hour; Human; Idaho; In Vitro; Individual; Listeria monocytogenes; Medical center; Methods; Microbiology; Molecular; National Institute of Allergy and Infectious Disease; Norovirus; Nucleic Acids; Organism; Patients; Performance; Process; Production; Protocols documentation; Protozoa; Public Health; Quality Control; RNA; Reaction; Reagent; Reporting; Reproducibility; Reverse Transcription; Risk; Rotavirus; Salmonella; Sampling; Sensitivity and Specificity; Shigella; Shigella dysenteriae; Shigella flexneri; Shigella sonnei; Sodium Chloride; Surveys; System; Technology; Testing; Time; Training; United States; Update; Validation; Vibrio; Vibrio cholerae; Vibrio vulnificus; Virus; Water; Yersinia enterocolitica; biothreat; clinically relevant; cost; cost effective; design; enteropathogenic Escherichia coli; enterotoxigenic Escherichia coli; foodborne; gastrointestinal; gastrointestinal system; improved; innovation; instrument; novel; nucleic acid purification; pathogen; pilot lot production; point of care; rapid detection; research and development; scale up; skills; tool; usability

DESCRIPTION (provided by applicant): An estimated 3-4 million children below the age of 5 years die each year as a result of complications related to diarrhea. Every year in the United States, there are an estimated 211 to 375 million episodes of acute diarrhea resulting in 5,000 deaths. The number and diversity of diarrhea causing pathogens, including viruses, bacteria, and protozoa along with the similarities in clinical presentation pose significant problems for diagnosis. Current microbiological methods used to identify the responsible pathogen are slow and laborious requiring days for a result. While individual patients suffer from these testing limitations, public health is also threatened by outbreaks that spread undetected. Idaho Technology Inc. (ITI) has developed the FilmArray System, an innovative molecular diagnostics device that streamlines pathogen identification in human samples. The FilmArray System simultaneously identifies up to 27 organisms in ~1 hour, and requires only a minimally trained operator to perform the test. The FilmArray System comprises a uniquely designed "lab-in-a-pouch", which together with the FilmArray instrument, automatically performs all steps needed for detection and identification of pathogens, from nucleic acid extraction to multiplex real time PCR and data analysis. The goal of this project is to adopt this technology and incorporate assays, protocols and consumables to accurately identify the presence of 22 diarrhea- associated pathogens. ITI proposes the following Aims to develop and evaluate the FilmArray Gastrointestinal (GI) Pathogen System. In Aim 1, the assays to detect diarrhea causing pathogens and the protocols to extract nucleic acids from stool will be developed and then combined to make the FilmArray GI pouch. The FilmArray instrument software will be adapted for the interpretation of the GI pathogen assays. The assays in FA GI pouch will be validated using stool samples that have been shown to be positive by conventional tests. After validation the FA GI pouches will be transferred from R & D to ITI's production facility so that pouches can be produced under current Good Manufacturing Practices (cGMP). Transfer will require quality control (QC) of raw materials and the final product, documentation of formulations and dispense protocols for reaction mixtures and pilot lot production. In Aim 2, analytic testing will be performed to determine the sensitivity and specificity of the system, examine reproducibility, identify possible interferants in stool, and evaluate the potential for contamination between tests. The performance of the FA GI System will be evaluated in a clinical setting as a test of the feasibility of applying for FDA clearance of the FA GI System as an In Vitro Diagnostic Device. A large set of previously characterized archived stool samples and a small set of fresh samples will be tested using the FA GI Diagnostic System at Primary Children Medical Center (PCMC), Salt Lake City, UT. The challenge in diagnosing infectious diarrhea is the large number and diversity of the pathogens that are known to cause diarrhea, including viruses, bacteria and protozoa. We propose to develop the FilmArray Gastrointestinal Pathogen System, a rapid (<1 hour), automated, sensitive, objective and inexpensive test able to detect 22 diarrhea causing pathogens in a single step. This novel tool will overcome diagnostic difficulties, improve the treatment and reduce the cost of diarrheal illness for individual patients, and improve public health by rapid detection of outbreaks. Relevance: The challenge in diagnosing infectious diarrhea is the large number and diversity of the pathogens that are known to cause diarrhea, including viruses, bacteria and protozoa. We propose to develop the FilmArray Gastrointestinal Pathogen System, a rapid (<1 hour), automated, sensitive, objective and inexpensive test able to detect 22 diarrhea causing pathogens in a single step. This novel tool will overcome diagnostic difficulties, improve the treatment and reduce the cost of diarrheal illness for individual patients, and improve public health by rapid detection of outbreaks.

描述（由申请人提供）： 据估计，每年有 3-400 万 5 岁以下儿童死于腹泻相关并发症。在美国，每年估计会发生 211 至 3.75 亿次急性腹泻，导致 5,000 人死亡。引起腹泻的病原体（包括病毒、细菌和原生动物）的数量和多样性以及临床表现的相似性给诊断带来了重大问题。目前用于识别致病病原体的微生物学方法缓慢且费力，需要数天才能得出结果。虽然个别患者受到这些检测的限制，但公共卫生也受到未被发现的疫情爆发的威胁。爱达荷科技公司 (ITI) 开发了 FilmArray 系统，这是一种创新的分子诊断设备，可简化人类样本中病原体的识别。 FilmArray 系统可在大约 1 小时内同时识别多达 27 种生物体，并且只需要经过最低限度培训的操作员即可执行测试。 FilmArray 系统包括一个独特设计的“袋式实验室”，它与 FilmArray 仪器一起自动执行检测和识别病原体所需的所有步骤，从核酸提取到多重实时 PCR 和数据分析。该项目的目标是采用该技术并结合检测、方案和耗材来准确识别 22 种腹泻相关病原体的存在。 ITI 提出以下目标来开发和评估 FilmArray 胃肠 (GI) 病原体系统。在目标 1 中，将开发检测引起腹泻的病原体的检测方法和从粪便中提取核酸的方案，然后将其组合起来制作 FilmArray 胃肠道袋。 FilmArray 仪器软件将适用于解释胃肠道病原体检测。 FA GI 袋中的检测将使用常规测试显示呈阳性的粪便样本进行验证。验证后，FA GI 袋将从研发部门转移到 ITI 的生产设施，以便可以根据现行良好生产规范 (cGMP) 生产袋。转移将需要对原材料和最终产品进行质量控制（QC）、反应混合物和中试批量生产的配方和分配方案的记录。在目标 2 中，将进行分析测试以确定系统的灵敏度和特异性，检查重现性，识别粪便中可能的干扰物，并评估测试之间污染的可能性。 FA GI 系统的性能将在临床环境中进行评估，以测试 FA GI 系统作为体外诊断设备申请 FDA 许可的可行性。将使用犹他州盐湖城初级儿童医疗中心 (PCMC) 的 FA GI 诊断系统对大量先前已表征的存档粪便样本和一小部分新鲜样本进行测试。诊断感染性腹泻的挑战是已知引起腹泻的病原体数量众多且多样性，包括病毒、细菌和原生动物。我们建议开发 FilmArray 胃肠道病原体系统，这是一种快速（<1 小时）、自动化、灵敏、客观且廉价的测试，能够一步检测 22 种引起腹泻的病原体。这种新颖的工具将克服诊断困难，改善治疗并降低个体患者腹泻疾病的费用，并通过快速检测疫情来改善公共卫生。 相关性：诊断感染性腹泻的挑战是已知引起腹泻的病原体数量众多且多样性，包括病毒、细菌和原生动物。我们建议开发 FilmArray 胃肠道病原体系统，这是一种快速（<1 小时）、自动化、灵敏、客观且廉价的测试，能够一步检测 22 种引起腹泻的病原体。这种新颖的工具将克服诊断困难，改善治疗并降低个体患者腹泻疾病的费用，并通过快速检测疫情来改善公共卫生。