Engineered phage for expanded host range and increased payload capacity

抗菌素耐药性的迅速上升重新引起了人们对控制病原体传播的替代战略的兴趣，其中包括耐多药病原体。噬菌体(感染和杀死细菌的病毒)疗法作为抗生素的可行替代品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来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，例如通过使用噬菌体作为CRISPR-CAS递送载体，并解决诸如单个噬菌体宿主范围狭窄等限制其作为有效治疗干预措施的更广泛使用的问题。该项目旨在创造新型的工程噬菌体，通过结合计算(即人工智能)和分子遗传/合成生物学方法来改进或增加治疗所需的特征。使用计算/生物信息学工具挖掘可公开获得的大型数据集，将识别噬菌体受体变体和可以筛选和评估功能的噬菌体反防御系统。具有良好特性的单个元件将被用于合理设计和遗传组装具有增强特性的新型噬菌体，如改善寄主范围和感染潜力。整合其他编码基因有效载荷的模块，如CRISPR-CAS系统，有可能进一步提高修饰噬菌体的效力，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(S)将经历几轮基因组缩减，以确定最小可存活基因组(S)，该基因组将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.