Connecting the Spatiotemporal Organization of Gut Bacterial Communities to the Emergence and Spread of Antibiotic Resistance

项目总结 抗药性细菌对人类的健康和福祉构成全球威胁。新的战略 抗击耐药性是当务之急，因为目前的药物开发管道跟不上 随着有效抗生素供应的减少。我建议调查和操纵地球的生态 抗生素耐药性的获得和宿主到宿主的传播。具体地说，我将确定如何在物理上 肠道内细菌群落的结构--这是抗生素耐药性的主要储存库 细菌--影响耐药特性的进化和耐药细胞的传播。这是一种动机 研究方向是抗生素耐药性从根本上取决于空间和时间 寄主-微生物系统的组织。例如，细菌之间的抗药性基因共享 通过横向基因转移通常要求细胞彼此靠近。此外， 耐药细菌在宿主之间的传播需要它们被物理置换并被驱逐到 环境。因此，可以使用改变肠道细菌群落的时空组织 在耐药细菌成为感染剂之前预防和遏制它们。然而，剖析 管理抗生素耐药性的时空复杂机制是一个重大挑战，使用 目前的方法。我克服这一局限的解决方案是将合成生物学与遗传学相结合 工程设计的细菌群落，以及实时成像来跟踪和控制细菌在 活体动物的肠道。我将使用幼虫斑马鱼作为脊椎动物的宿主模型，因为它们能够 对宿主-微生物系统的研究，跨越复杂性、空间和时间的尺度，很难在 无论是老鼠还是人类。使用这种实验方法，我之前发现肠道流动，细菌 游泳动力和亚致命抗生素分别代表宿主、细菌和环境因素， 这可以调节肠道细菌的时空组织和生理格局。我会驾驭 这些因素和我的实验方法解决了以下三个假设。首先，我将测试 假设肠道细菌的时空组织控制着肠道细菌的获得和持久性 肠道内的耐药性特征。其次，我将检验这样一种假设，即 肠道细菌调节耐药细胞在宿主之间的传播。第三，我将测试 细菌协调获得抗性特征和宿主到宿主传播的假说 通过特定的遗传途径。我提出的研究有可能启发基于生态学的 通过肠道治疗性操作减少抗生素耐药性的策略 微生物组的物理结构。这种生态知情和不含抗生素的策略将保护 在最需要的时候发挥当前抗生素的效力，并避免 抗生素对有益的常驻细菌。

PROJECT SUMMARY Antibiotic resistant bacteria pose a global threat to human health and wellbeing. New strategies for combating resistance are urgently needed because current drug development pipelines are not keeping up with the dwindling supply of effective antibiotics. I propose to investigate and manipulate the ecology of antibiotic resistance acquisition and host-to-host transmission. Specifically, I will determine how the physical structure of bacterial communities within the intestine—which is a major reservoir of antibiotic resistant bacteria—affects the evolution of resistance traits and transmission of resistant cells. A motivation for this research direction is that antibiotic resistance fundamentally dependends on the spatial and temporal organization of host–microbe systems. For example, the sharing of resistance genes between bacteria through lateral gene transfer often requires cells to be in close proximity to one another. In addition, the transmission of resistant bacteria between hosts requires that they are physically displaced and expelled into the environment. Thus, altering the spatiotemporal organization of gut bacterial communities could be used to prevent and contain resistant bacteria before they become agents of infection. However, dissecting the spatially and temporally complex mechanisms governing antibiotic resistance is a significant challenge using current approaches. My solution to overcome this limitation is to combine synthetic biology, genetically engineered bacterial communities, and live imaging to track and control bacterial behavior inside the intestines of living animals. I will employ larval zebrafish as a vertebrate host model because they enable studies of host–microbe systems across scales of complexity, space, and time that are difficult to perform in mice or humans. Using this experimental approach, I previously discovered that intestinal flow, bacterial swimming motility, and sublethal antibiotics represent host, bacterial, and environmental factors, respectively, that can modulate the spatiotemporal organization and physiological landscape of gut bacteria. I will harness these factors and my experimental approach to address the following three hypotheses. First, I will test the hypothesis that the spatiotemporal organization of gut bacteria controls the acquisition and persistence of resistance traits within the intestine. Second, I will test the hypothesis that the spatiotemporal organization of gut bacteria regulates the transmission of antibiotic resistant cells between hosts. And third, I will test the hypothesis that bacteria coordinate both the acquisition of resistance traits and host-to-host transmission through specific genetic pathways. My proposed research has the potential to inspire ecology-based strategies for curtailing antibiotic resistance through the therapeutic manipulation of the intestinal microbiome’s physical structure. Such ecology-informed and antibiotic-free strategies would preserve the potency of current antibiotics for when they are needed most and avoid the unintended side effects of antibiotics on beneficial resident bacteria.