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

项目总结 噬菌体疗法，用以细菌为靶标的病毒治疗细菌感染的实践，噬菌体(或 噬菌体)，是一种很有前途和迫切需要的抗生素替代品。坚持这种方法的一个主要挑战 从广泛采用中恢复过来的是，需要为每个感染菌株定制噬菌体治疗 耐心，这是一个缓慢和劳动密集型的过程。这一要求源于微妙狭窄的主机范围 许多噬菌体都有这种表现，即使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 Range是分布不均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 上升到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 噬菌体已经进化出了克服大多数细菌防御的机制。类似于他们的 细菌的对应物，每个噬菌体菌株只编码一小部分现有的反防御系统，因此 解释了单个噬菌体寄主范围狭窄的原因。开发一种噬菌体疗法，可以积聚这些 将自然产生的噬菌体溶液制成“超级噬菌体鸡尾酒”将使现成的生产成为可能。 噬菌体处理大大扩大了菌种范围，并具有预防细菌耐药性的能力。 在这里，我建议开发一条利用现有噬菌体反防御机制的管道，以创建 针对条件致病菌铜绿假单胞菌的强大原则证明噬菌体鸡尾酒。要意识到 在这个愿景中，我将采取一种实验性的基因组方法来绘制临床相关的P。 铜绿假单胞菌分离，从而确定在感染期间噬菌体将遇到哪些细菌防御。 然后，我将开发一个强大的、高通量的筛选来识别现有的噬菌体反防御机制 可以克服这些细菌防御系统。最后，我将创建一个超级噬菌体鸡尾酒，编码广泛的 收集能够感染广泛的铜绿假单胞菌菌株的反防御基因盒。 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来 克服噬菌体疗法发展中的一个主要障碍。这项工作将提供前所未有的洞察力 深入研究细菌免疫和噬菌体对抗防御的广度和多样性，并发现 新的生物学机制将在未来的研究中得到表征。经过改造的噬菌体鸡尾酒也 构成了一个创新的实验系统，可以用来回答关于病毒的基本问题 种群多样性和进化。这项初步研究将作为发展噬菌体的蓝图 治疗其他多药耐药的条件致病菌。

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.