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

项目摘要 抗生素耐药性细菌对人类健康和福祉构成全球性威胁。新战略 由于目前的药物开发渠道跟不上， 有效抗生素的供应越来越少我提议调查和操纵 抗生素抗性的获得和宿主到宿主的传播。具体地说，我将确定如何物理 细菌群落的结构在大肠杆菌-这是一个主要的水库抗生素耐药性 细菌-影响抗性性状的进化和抗性细胞的传播。一个动机 研究方向是抗生素耐药性从根本上取决于空间和时间 宿主微生物系统的组织。例如，细菌之间的耐药基因共享 通过横向基因转移通常需要细胞彼此非常接近。此外该 宿主之间的耐药细菌的传播需要它们被物理移位并被驱逐到宿主体内。 环境保护因此，改变肠道细菌群落的时空组织可以被用于 以防止和遏制耐药细菌成为感染媒介。然而，解剖 控制抗生素耐药性的空间和时间复杂机制是一个重大挑战， 目前的做法。我克服这个局限性的方法是将联合收割机， 工程化的细菌群落，以及实时成像来跟踪和控制 活动物的肠子。我将采用斑马鱼幼虫作为脊椎动物宿主模型，因为它们能够 宿主微生物系统的研究跨越复杂性，空间和时间的尺度，难以在 老鼠或人类。使用这种实验方法，我以前发现肠道流动，细菌 游泳运动性和亚致死抗生素分别代表宿主、细菌和环境因素， 可以调节肠道细菌的时空组织和生理景观。我将驾驭 这些因素和我的实验方法来解决以下三个假设。首先，我将测试 假设肠道细菌的时空组织控制的收购和持久性 肠道内的抵抗特性。第二，我将测试的假设，时空组织的 肠道细菌调节宿主之间抗生素抗性细胞的传递。第三，我将测试 假设细菌协调抗性性状的获得和宿主到宿主的传播 通过特定的遗传途径。我提出的研究有可能激发基于生态学的 通过肠道治疗性操作减少抗生素耐药性的策略 微生物的物理结构。这种生态知情和无虫害的战略将保护 目前抗生素的效力，当他们最需要的，并避免意外的副作用， 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.