Attacking failure of antibiotic treatment by targeting antimicrobial resistance enabler cell-states

摘要 新的抗菌药的部署迅速被耐药性的快速演变所绕过，强调 迫切需要新的战略，以在与细菌病原体的军备竞赛中保持领先地位。开发一个 详细了解哪种抗生素的情况以及遗传和机制基础 耐药性的发展为先发制人地颠覆这一进程提供了机会。而由病毒引起的感染 携带抗菌素耐药(AMR)基因的微生物是抗生素治疗失败(ATF)的主要原因， ATF多发生在传统药敏试验不是AMR的病原体时。它正在成为 越来越多的人认识到，耐受性、持久性和异质抗性等瞬时细胞状态是至关重要的 导致治疗失败的驱动因素。然而，关于基因和基因的数据很少 这些细胞状态的机制基础以及缺乏诊断-检测方法。ATF单元格状态 最初作为少数变异存在于群体中，并表现出一种瞬变的表型，这种表型往往随着 压力消退，使它们难以检测，因此在目前的诊断分析中被遗漏。 这些使能细胞状态在机制上仍然知之甚少，并且似乎优先出现在 波动的治疗方案，例如由药物的PK/PD特性引起的，由此ATF细胞状态 在抗生素压力减弱后，可能会导致(易感)细菌感染的重新出现。重要的是 这创造了机会，让多步高水平抗性突变有更长的机会 浮出水面。因此，由于抗生素耐药变种通常紧随其后发生 ATF细胞状态，这些细胞状态可被视为抗生素治疗失败和AMR的促进剂。这 提案的重点是解开ATF细胞状态在抗生素出现中的重要性 耐药性和治疗失败，并设计新的方法和战略来识别、跟踪和瞄准 他们。主要团队由4名首席调查人员组成，他们都有非常成功的合作历史。 他们将共同应对分布在3个项目中的5项挑战，并由一名行政人员和一名 基因组学和生物信息学核心。挑战：1)可能的遗传途径的完整轮廓，可以诱导 确定ATF细胞状态；2)确定促使ATF细胞状态出现的治疗方案； 3)确定ATF细胞状态如何使AMR出现；4)筛选药物和化合物 5)提出了一种计算反卷积的方法 这预测了复杂细菌群体中ATF细胞状态的存在和频率。总体而言， Proposal包含一系列概念和技术创新方面的内容，旨在 低估了抗药性出现的根源所在的遗传机制和进化力量， 最终目标是设计新的诊断和抗菌策略，以减缓甚至阻止 当前无休止的军备竞赛“需要我们竭尽所能地奔跑，以保持原地不动”。

SUMMARY Deployment of new antimicrobials is promptly circumvented by the rapid evolution of resistance, underscoring the critical need for new strategies to stay ahead in the arms-race against bacterial pathogens. Developing a detailed understanding of the circumstances as well as genetic and mechanistic basis for which antibiotic resistance develops provides opportunities for pre-emptively subverting this process. While infections caused by organisms harboring antimicrobial resistance (AMR) genes are a major cause of antibiotic treatment failure (ATF), ATF frequently occurs when the etiological agents are not AMR by traditional susceptibility testing. It is becoming increasingly recognized that transient cell-states such as tolerance, persistence and hetero-resistance are critical drivers underlying treatment failure. However, there is a paucity of data with regards to the genetic and mechanistic basis for these cell-states as well as a lack of diagnostic-detection approaches. ATF cell-states initially exist as minority variants within a population and display a transient phenotype that tends to dissipate as the stress subsides, making them challenging to detect and consequently missed in current diagnostic assays. These enabler cell-states remain mechanistically poorly understood and seem to preferentially arise during fluctuating treatment regimens, for instance caused by a drug’s PK/PD characteristics, whereby ATF cell-states can drive the re-emergence of the (susceptible) bacterial infection after antibiotic pressure wanes. Importantly, this creates opportunities where multi-step high-level resistance mutations are given an extended opportunity to emerge. Therefore, because antibiotic resistant variants often follow closely on the heels of the occurrence of ATF cell-states, these cell-states can be viewed as enablers of antibiotic treatment failure and AMR. This proposal focuses on untangling the importance of ATF cell-states in the emergence of antibiotic resistance and treatment failure, and designs new approaches and strategies to identify, track and target them. The main team consists of 4 principal investigators that have a very successful collaboration history. Together they will work on 5 challenges distributed across 3 projects and supported by an administrative and a genomics and bioinformatics core. In Challenge: 1) the full profile of possible genetic pathways that can induce ATF cell-states is determined; 2) treatment regimens that drive the emergence of ATF-cell states are determined; 3) it is determined how ATF cell-states enable the emergence of AMR; 4) drugs and compounds are screened for, that target ATF cell-state collateral sensitivities; 5) a computational deconvolution approach is developed that predicts the presence and frequency of ATF cell-states in a complex bacterial population. Overall this proposal contains a collection of conceptually and technically innovative aspects that are geared towards understating the genetic mechanisms and evolutionary forces that sit at the root of the emergence of resistance, with the ultimate goal to design new diagnostics and antimicrobial strategies that can slow or even stop the current endless arms-race “that takes all the running we can do, to keep in the same place”.