Engineered phage for expanded host range and increased payload capacity

抗菌素耐药性的迅速上升使人们重新关注控制病原体传播的替代战略，包括耐多药战略。噬菌体（一种感染并杀死细菌的病毒）治疗作为抗生素的一种可行替代疗法重新引起了人们的兴趣，但选择和生产用于生物医学应用的噬菌体以预防或治疗人类和动物的细菌感染仍然是一项具有挑战性的任务。目前的解决方案可能涉及不同噬菌体的复杂鸡尾酒，以产生有效的结果。因此，目前正在探索基因工程方法来优化噬菌体的抗微生物活性，例如使用噬菌体作为CRISPR-Cas递送载体，并解决诸如单个噬菌体宿主范围狭窄等问题，这些问题限制了作为有效治疗干预措施的广泛应用。该项目旨在通过将计算（即人工智能）与分子遗传/合成生物学方法相结合，创造出新的工程化噬菌体，以改善或增加治疗用途所需的特性。使用计算/生物信息学工具挖掘大型、公开可用的数据集将识别噬菌体受体变体和噬菌体抗防御系统，这些系统可以进行筛选和功能评估。显示有利特性的单个元素将用于合理设计和遗传组装具有增强特性的新型噬菌体，例如改善宿主范围和感染潜力。整合编码遗传有效载荷的附加模块，如具有进一步提高修饰噬菌体效能潜力的CRISPR-Cas系统，将需要构建能够容纳添加的遗传物质的最小噬菌体基因组。选定的噬菌体将进行几轮基因组还原，以确定最小可行基因组，用于重新组装整合有效载荷模块的修饰噬菌体。

The rapid rise of antimicrobial resistance has resulted in renewed interest in alternative strategies to control the spread of pathogens including multidrug resistant ones. Phage (virus that infects and kills bacteria) therapy has gathered renewed interest as a viable alternative to antibiotics but selection and production of phages for biomedical applications to prevent or treat bacterial infections in humans and animals remains a challenging task. Current solutions can involve a complex cocktail of different phages to produce efficient results. Consequently, genetic engineering approaches are now being explored to optimize phage anti-microbial activity, e.g. by use of phages as CRISPR-Cas delivery vehicles, and address problems such as the narrow host range of individual phages that limit broader use as effective therapeutic interventions.The project aims to create novel, engineered bacteriophages that will improve or add desired traits for therapeutic use by combining computational (i.e., artificial intelligence) with molecular genetic/synthetic biology approaches. Mining large, publicly available datasets using computational/bioinformatic tools will identify phage receptor variants and phage anti-defence systems that can be screened and assessed for functionality. Individual elements displaying favourable characteristics will be used to rationally design and genetically assemble novel phages with enhanced properties such as improved host range and infectious potential. Integration of additional modules encoding genetic payloads such as CRISPR-Cas systems with the potential to further increase efficacy of the modified phages will require the construction of minimal phage genomes able to accommodate the added genetic material. The selected phage(s) will be subjected to several rounds of genome reduction to determine the minimal viable genome(s) that will be used to re-assemble modified phages integrating the payload module.