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

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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.