Mining the phage playbook to create a potent, generic phage therapy

挖掘噬菌体剧本以创建有效的通用噬菌体疗法

• 批准号: 10723647
• 负责人: Michele LeRoux
• 金额: $ 45.86万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-07-21 至 2028-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10723647
• 关键词: Adoption; Antibiotic Resistance; Antibiotics; Automobile Driving; Back; Bacteria; Bacterial Infections; Bacteriophages; Biological; Biology; Collection; DNA cassette; Defense Mechanisms; Development; Engineering; Evolution; Future; Genomic approach; Immune; Immune system; Immunity; Individual; Infection; Maps; Mining; Molecular; Multi-Drug Resistance; Pathway interactions; Patients; Phage Display; Population Heterogeneity; Printing; Process; Production; Pseudomonas aeruginosa; Specificity; System; Therapeutic; Viral; Virus; Vision; Work; arms race; bacterial resistance; clinically relevant; high throughput screening; innovation; insight; novel; opportunistic pathogen

PROJECT SUMMARY Phage therapy, the practice of treating bacterial infections with bacteria-targeting viruses, bacteriophage (or phage), is a promising and urgently needed alternative to antibiotics. A major challenge holding this approach back from widespread adoption is that phage treatments need to be customized for the infecting strains in each patient, a slow and labor-intensive process. This requirement arises from the exquisitely narrow host-range that many phages display, even among closely related bacterial strains. A major factor driving phage host range is the immense collection of bacterial anti-phage immune mechanisms that are unevenly distributed across bacterial strains. However, the underlying molecular arms race between bacteria and phage has given rise to an equally impressive set of corresponding phage counter-defense pathways, and thus collectively phage have already evolved mechanisms by which to overcome most bacterial defenses. Similar to their bacterial counterparts, each phage strain encodes only a miniscule fraction of existing counter-defenses, thus explaining the narrow host-range of individual phages. Developing a phage treatment that could amass these naturally occurring phage solutions into a “super phage cocktail” would enable production of an off-the-shelf phage treatment with a greatly expanded species range and the ability to forestall bacterial resistance. Here, I propose developing a pipeline leveraging existing phage counter-defense mechanisms to create a powerful proof-of-principle phage cocktail for the opportunistic pathogen, Pseudomonas aeruginosa. To realize this vision, I will take an experimental genomic approach to map the immune system of clinically relevant P. aeruginosa isolates and thereby determine which bacterial defenses the phage will encounter during infections. I will then develop a powerful, high throughput screen to identify existing phage counter-defense mechanisms that can overcome these bacterial defenses. Finally, I will create a super phage cocktail encoding an extensive collection of counter-defense gene cassettes with the ability to infect a broad set of P. aeruginosa strains. These studies seek to leverage the existing biology underlying the bacterial-phage molecular arms race to overcome a major hurdle in the development of phage therapy. This work will provide unprecedented insight into the breadth and diversity of both bacterial immunity and phage counter-defenses and uncover a multitude of novel biological mechanisms to be characterized in future studies. The engineered phage cocktail also constitutes an innovative experimental system that can be used to answer fundamental questions about viral population diversity and evolution. This initial study will serve as the blue print for development of phage therapy for other multi-drug resistant opportunistic pathogens.

项目概要 噬菌体疗法，用针对细菌的病毒、噬菌体（或 噬菌体）是一种有前途且迫切需要的抗生素替代品。采取这种方法的一个主要挑战 广泛采用后的一个问题是，噬菌体治疗需要针对每个感染菌株进行定制 患者，这是一个缓慢且劳动密集型的过程。这一要求源于极其狭窄的宿主范围 许多噬菌体都表现出这一点，即使是在密切相关的细菌菌株中也是如此。驱动噬菌体宿主的主要因素 范围是分布不均匀的细菌抗噬菌体免疫机制的巨大集合 跨细菌菌株。然而，细菌和噬菌体之间潜在的分子军备竞赛已经给了 产生一组同样令人印象深刻的相应噬菌体反防御途径，从而共同 噬菌体已经进化出克服大多数细菌防御的机制。类似于他们的 与细菌对应物相比，每种噬菌体菌株仅编码现有反防御的一小部分，因此 解释单个噬菌体的狭窄宿主范围。开发一种可以聚集这些物质的噬菌体治疗方法 将天然存在的噬菌体溶液转化为“超级噬菌体混合物”将能够生产现成的噬菌体 噬菌体处理大大扩大了物种范围并具有预防细菌耐药性的能力。 在这里，我建议开发一个利用现有噬菌体反防御机制的管道来创建一个 针对机会性病原体铜绿假单胞菌的强大原理验证噬菌体混合物。实现 为了实现这一愿景，我将采用实验性基因组方法来绘制临床相关疟原虫的免疫系统图谱。 铜绿假单胞菌分离，从而确定噬菌体在感染过程中将遇到哪些细菌防御。 然后我将开发一个强大的高通量筛选来识别现有的噬菌体反防御机制 可以克服这些细菌的防御。最后，我将创建一个超级噬菌体鸡尾酒，编码广泛的 能够感染多种铜绿假单胞菌菌株的反防御基因盒的集合。 这些研究试图利用细菌-噬菌体分子军备竞赛背后的现有生物学原理来 克服了噬菌体疗法发展的主要障碍。这项工作将提供前所未有的见解 深入研究细菌免疫和噬菌体反防御的广度和多样性，并揭示大量 未来研究中要表征的新生物机制。工程噬菌体鸡尾酒还 构成了一个创新的实验系统，可用于回答有关病毒的基本问题 人口多样性和进化。这项初步研究将作为噬菌体开发的蓝图 治疗其他多重耐药机会性病原体。