Building re-usable phage and antibiotic treatments via exploitation of bacteria-phage co-evolutionary dynamics

项目摘要 慢性(长期)细菌感染是一个重大的医疗和公共卫生挑战， 抗生素耐药性上升。由于抗生素往往不能治疗这些病例，越来越多的注意力正转向 替代疗法，包括噬菌体(噬菌体)疗法。就像抗生素一样，噬菌体疗法面临着 抵抗的挑战。与药物不同，噬菌体可以进化来克服细菌的防御，为 与他们的目标共同进化的动力。噬菌体进化已被标记为一个潜在有用的属性 在提高总体效率方面，但也作为确保监管合规性的陷阱，因为 所需的治疗。这项应用表明，操纵细菌之间的共同进化动态 而且噬菌体可以促进针对单一进化细菌的特定噬菌体处理的可重用性 人口。 共同进化可以通过两种主要方式发生，一种是不断升级的“军备竞赛动态”(ARD)模型，另一种是多样化的 “波动选择动态”(FSD)模型。这两个都是在噬菌体-细菌系统中观察到的，以及试点数据 显示包括抗生素在内的应激源的加入有利于FSD的发生。试点数据进一步表明，消防处 动力学促进标准噬菌体制剂对单一进化细菌的有效再利用 由于在FSD制度下，细菌不会进化出广泛的普遍耐药性。取而代之的是消防处 导致对共同进化的噬菌体产生特殊的抗性，代价是恢复对祖先的易感性 以及可能获得许可/批准的噬菌体。 主要的假设是，随着抗生素的加入，共同进化的动力可以改变-- 通过减少细菌负荷和允许重复使用来提高长期治疗效果 一种标准的特许噬菌体制剂。该提案将在两个具体目标上检验这一假设： 目的1：评估体恤释放患者临床噬菌体治疗期间的共同进化动力学 样本。为了评估治疗背景下的共同进化动力学，研究人员将使用临床 8名囊性纤维化患者的样本，他们接受了一种噬菌体鸡尾酒作为体恤释放护理的一部分 目的2：确定改变PA临床分离株共同进化动力学的噬菌体和抗生素因子。目标1 提供了一个了解临床共同进化动力学的窗口，但不允许直接测试 不同的治疗方案。评估促进FSD共同进化动力学和治疗的因素 可重用性，研究人员将进行体外模拟噬菌体疗法，以总结和扩展 同情的释放在合成痰介质中起作用。

Project Summary Chronic (long-term) bacterial infections are a major medical and public-health challenge, exacerbated by the rise in antibiotic resistance. As antibiotics often fail to treat these cases, increasing attention is turning to alternate therapeutics, including bacteriophage (phage) therapy. Like antibiotics, phage therapy faces the challenge of resistance. Unlike drugs, phages can evolve to overcome bacterial defenses, opening potential for co-evolutionary dynamics with their targets. Phage evolution has been flagged as a potentially useful attribute in enhancing total efficacy, but also as a pitfall in ensuring regulatory compliance due to the changing nature of required treatment. This application proposes that manipulating the co-evolutionary dynamic between bacteria and phage can promote the re-usability of defined phage treatments against a single evolving bacterial population. Co-evolution can occur in two main ways, an escalating ‘arms race dynamic’ (ARD) model, or a diversifying ‘fluctuating selection dynamic’ (FSD) model. Both are observed in phage-bacteria systems, and pilot data shows that FSD is favored by the addition of stressors including antibiotics. Pilot data further shows that FSD dynamics promote the effective re-use of a standard phage preparation against a single evolving bacterial population, as under the FSD regime, bacteria do not evolve broadly generalized resistance. Instead FSD leads to specialized resistance to the co-evolved phage at the cost of a return to susceptibility to the ancestral and potentially licensed/approved phage. The primary hypothesis is that co-evolutionary dynamics can be shifted with the addition of antibiotics – improving the long-term treatment efficacy by reducing bacterial burden and allowing for repeated application of a standard licensed phage preparation. The proposal will test this hypothesis in two specific aims: Aim 1: Assess co-evolutionary dynamics during clinical phage therapy using compassionate release patient samples. To assess co-evolutionary dynamics in a therapeutic context, the investigators will use clinical samples from 8 cystic fibrosis patients who received a phage cocktail as part of compassionate release care Aim 2: Identify phage and antibiotic factors that shift co-evolutionary dynamics in clinical PA isolates. Aim 1 provides a window into clinical co-evolutionary dynamics but does not allow a direct test of the impact of different treatment designs. To assess the factors that promote FSD co-evolutionary dynamics and treatment re-usability, the investigators will conduct in vitro mock phage therapy to recapitulate and expand on the compassionate release work in a synthetic sputum medium.