Microbiota Intervention Strategies Limiting Selection and Transmission of Antibiotic Resistance burden in the One Health domain

抗菌素耐药性（AMR）是对人类健康的主要威胁，通常被描述为一种缓慢蔓延的全球流行病。推动抗微生物药物耐药性的一个关键因素是在人类、动物和环境中广泛使用抗微生物药物，这导致了耐药细菌和基因的选择，并促进了耐药细菌和抗微生物药物耐药性基因在不同的“同一个健康”领域（人类、动物和环境）之间的传播。MISTAR项目旨在降低抗菌素耐药性感染猖獗的环境（医院和农场）中的抗菌素耐药性水平，最终目标是在不同的“同一个健康”环境中阻止抗菌素耐药性的选择和传播。为此，我们将开发、测试和实施干预策略，使用一系列不同的方法来促进微生物群的保存。首先，我们将开发基于肠道微生物群的干预措施（粪便微生物群移植（FMT）和基于护理点的微生物群指数），并测试其在住院患者中的效果，以减少AMR。具体来说，我们将分析FMT如何调节AMR基因的丰度、多样性和动态。此外，将开发和验证用于监测高风险地区入院时抗菌素耐药性携带情况的工具，以及将FMT相关变化定性为选择和/或传播指标的工具。这将允许患者接受量身定制的干预措施，包括FMT，大大缩短到结果的时间，防止无意的抗生素处方/FMT，并允许及时切换到所需的靶向抗菌治疗。这一目标的研究还将帮助我们确定微生物群落中与AMR基因丰度负相关的细菌种类，然后可以测试它们作为潜在生物治疗药物的用途，将在目标3中进行测试。其次，我们将在三个不同的“同一健康”环境（社区、农场和医院）和三个不同的国家（巴西、荷兰和西班牙）开发和测试旨在减少空气中粉尘污染和抗生素耐药性传播的干预措施的效果。具体而言，我们将实施以下干预措施(i)家用空气净化器，（ii）养猪喂养方法，以及（iii）医院空气过滤系统，并测试它们对通过空气和尘埃颗粒传播AMR的影响。为此，我们将分析医院空气中的生物气溶胶、农场风尘、人类、狗和猪的肠道和鼻腔微生物群以及抗性组。第三，我们将开发和测试新的实验干预策略，以调节微生物群，消除肠道微生物群落中的AMR。这些方法基于微生物群落组成可以通过不同群落成员之间的竞争而改变的想法。第一种干预使用细菌拮抗剂，可以在群落环境中胜过耐药细菌，而第二种干预使用天然存在的核酸内切酶CRISPR-Cas9作为移动工具，从微生物群落中去除AMR基因。在体外验证后，我们将使用昆虫模型melonella测试这两种干预措施在体内的有效性，并通过使用小鼠肠道定植模型进行最后的概念验证实验。MISTAR提供关键的科学见解、新的技术技能和新的干预措施，以帮助阻止抗微生物药物耐药性的蔓延，这些见解、技术技能和干预措施可在高收入和低收入国家应用。

Antimicrobial resistance (AMR) is a major threat to human health, often described as a slow spreading global pandemic. A key factor in driving AMR is the extensive use of antimicrobial drugs in humans, animals and environment, which leads to selection for resistant bacteria and genes, and facilitates spread of resistant bacteria and AMR genes between the different One Health domains (human, animals and the environment). The MISTAR project aims to reduce AMR levels in environments where AMR infections thrive - hospitals and farms, with the ultimate goal to block the selection and transmission of AMR within different One Health settings. To do so we will develop, test and implement intervention strategies that promote microbiota preservation using a range of different approaches. Firstly, we will develop gut microbiota-based interventions (fecal microbiota transplantation (FMT) and microbiota-based index at point-of-care) and test their effect in hospitalized patients to reduce AMR. Specifically, we will analyze how FMT modulates the abundance, diversity, and dynamics of AMR genes. In addition, tools for monitoring the AMR carriage at admission to hospital high-risk areas, and for characterizing FMT associated changes as indicators of selection and/or transmission will be developed and validated. This will allow patients to receive tailored interventions including FMT, substantially shorten the time-to-result, preventing inadvertent antibiotic prescription/FMT, and allowing a timely switch to the required targeted antibacterial therapy. Research in this objective will also help us to identify bacterial species in a microbial community that are inversely correlated with the abundance of AMR genes, which can then be tested for their use as potential biotherapeutics to be tested in Objective 3. Second, we will develop and test the effects of interventions aimed at reducing airborne dust-bound pollution and transmission of AMR, in three different One Health settings (community, farm and hospital) and in three different countries (Brazil, Netherlands, and Spain). Specifically, we will implement the following interventions (i) household air purifiers, (ii) feeding practices in farmed pigs, and (iii) hospital air filtration systems, and test their effect on AMR transmission via air and dust particles. To do so, we will analyze the bioaerosols from hospital air, farm wind-borne dust, gut and nasal microbiota and resistomes of humans, dogs and pigs.Thirdly, we will develop and test novel experimental intervention strategies to modulate the microbiota to eradicate AMR in gut microbial communities. These approaches are based on the idea that microbial community composition can be altered through competition between different community members. The first intervention uses bacterial antagonists that can outcompete resistant bacteria in a community context, while the second one uses the naturally occurring endonuclease CRISPR-Cas9 as a mobile tool to remove AMR genes from the microbial community. After in vitro validation we will test the efficacy of both interventions in vivo using the insect model Galleria melonella and by a final proof-of-concept experiment using a mouse gut colonization model.MISTAR delivers key scientific insights, new technical skills and new interventions to help stop the spread of AMR, that can be applied in both high- and low income countries.