CRISPR-Cas9 gene drives to fight antimicrobial resistance

CRISPR-Cas9基因驱动对抗抗生素耐药性

• 批准号: BB/R010781/1
• 负责人: Stineke Van Houte
• 金额: $ 41.67万
• 依托单位: UNIVERSITY OF EXETER
• 依托单位国家: 英国
• 项目类别: Fellowship
• 财政年份: 2018
• 资助国家: 英国
• 起止时间: 2018 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FR010781%2F1
• 关键词: CRISPR; Cas9; gene; drives; fight

Antimicrobial resistance (AMR) is one of the greatest threats of our time causing a predicted 10 million human deaths per year by 2050 with a total cost of $100 trillion. Recently, a revolutionary technology has been developed, known as CRISPR-Cas9, which can be used to eradicate AMR from microbial communities. However, this technology has only been tested under laboratory conditions, and is not yet ready for use in the real world. My proposed research will take the development of this technology to the next level by testing for the first time whether CRISPR-Cas9 can eradicate AMR from a complex microbial community, isolated from the pig gut. The pig gut microbial community is a highly relevant study system, since decades of consistent overuse of antibiotics in animal industries to boost animal growth and limit disease has selected for very high levels of AMR in the animal gut, causing severe risks for human and animal health. The resulting AMR enters the environment due to the application of animal manure for soil fertilization, which is thought to also contribute to AMR emergence in human populations.In my research I will first develop genetic tools that will help to spread CRISPR-Cas9 through a microbial community. I will monitor the spread of CRISPR-Cas9 and the associated AMR decline. Crucially, I will also carefully monitor the consequences: too often have promising pest and disease control strategies been applied without considering the ecological and evolutionary risks, sometimes leaving a devastating impact on ecosystem functioning and causing resistance to emerge. I foresee two scientific challenges associated with implementing this new technology. First, removal of an AMR gene may cause unwanted or unanticipated increases in other AMR genes that are functionally redundant. Second, the AMR gene that is targeted by CRISPR-Cas9 may evolve to become resistant to targeting, which could undermine the technology.To address these challenges, I will monitor the changes in a pig gut microbial community caused by the removal of AMR genes, and whether resistance to CRISPR-Cas9 will evolve. This will involve introducing CRISPR-Cas9 to the pig gut community in a long-term (12 months) experiment, and in parallel introducing CRISPR-Cas9 to simpler derived communities in short-term experiments (2 months). For both types of experiments, I will then examine the ecological and evolutionary changes that occur. These experiments will take place in a contained laboratory environment, to avoid unintended release of the CRISPR-Cas9 into the environment. Crucially, the data from these experiments will feed into a mathematical model to generate a theoretical framework that allows me to predict these ecological and evolutionary consequences in other microbial communities. This research will be carried out at the University of Exeter, one of the centers of excellence for studying microbial community ecology, evolution of AMR and CRISPR-Cas9. I will be embedded in a highly collaborative research environment, sharing laboratory space with key experts from the relevant disciplines. The BBSRC Future Leader Fellowship will allow me to start building my own research group, and to become a fully independent researcher. I will use this fellowship as a springboard to attract further funding to expand the scope of my research program, and to pursue novel lines of research that dovetail from this project.AMR is now recognized by the UN General Assembly as one of the most urgent problems that our society is facing, and a key strategic priority for BBSRC research funding. Discovering new strategies to minimize the burden of AMR in both humans and animals would be truly groundbreaking. Testing whether CRISPR-Cas9 can eradicate AMR from a complex microbial community and understanding the consequences of AMR removal will be a major step forward to push such a breakthrough.

抗菌素耐药性 (AMR) 是当今时代最大的威胁之一，预计到 2050 年，每年将导致 1000 万人死亡，总损失达 100 万亿美元。最近，一项革命性的技术被开发出来，称为 CRISPR-Cas9，可用于根除微生物群落中的 AMR。然而，这项技术仅在实验室条件下进行了测试，尚未准备好在现实世界中使用。我提出的研究将通过首次测试 CRISPR-Cas9 能否从猪肠道中分离出的复杂微生物群落中根除 AMR，将这项技术的发展提升到一个新的水平。猪肠道微生物群落是一个高度相关的研究系统，因为几十年来，动物工业中持续过度使用抗生素来促进动物生长和限制疾病，导致动物肠道中的 AMR 水平非常高，对人类和动物健康造成严重风险。由于使用动物粪便进行土壤施肥，由此产生的 AMR 进入环境，这被认为也导致了 AMR 在人类群体中的出现。在我的研究中，我将首先开发有助于在微生物群落中传播 CRISPR-Cas9 的遗传工具。我将监测 CRISPR-Cas9 的传播以及相关的 AMR 下降。至关重要的是，我还将仔细监测后果：在没有考虑生态和进化风险的情况下应用有前景的病虫害控制策略，有时会对生态系统功能造成毁灭性影响，并导致出现抗药性。我预见到与实施这项新技术相关的两个科学挑战。首先，去除 AMR 基因可能会导致其他功能冗余的 AMR 基因出现不必要或意外的增加。其次，CRISPR-Cas9靶向的AMR基因可能会进化出对靶向的抗性，这可能会破坏该技术。为了应对这些挑战，我将监测因去除AMR基因而引起的猪肠道微生物群落的变化，以及是否会进化出对CRISPR-Cas9的抗性。这将涉及在长期（12 个月）实验中将 CRISPR-Cas9 引入猪肠道群落，同时在短期实验（2 个月）中将 CRISPR-Cas9 引入更简单的衍生群落。对于这两种类型的实验，我将检查所发生的生态和进化变化。这些实验将在封闭的实验室环境中进行，以避免 CRISPR-Cas9 意外释放到环境中。至关重要的是，这些实验的数据将输入一个数学模型，以生成一个理论框架，使我能够预测其他微生物群落的这些生态和进化后果。这项研究将在埃克塞特大学进行，该大学是研究微生物群落生态学、AMR 和 CRISPR-Cas9 进化的卓越中心之一。我将融入一个高度协作的研究环境，与相关学科的主要专家共享实验室空间。 BBSRC 未来领袖奖学金将使我能够开始建立自己的研究小组，并成为一名完全独立的研究员。我将利用这笔奖学金作为跳板，吸引更多资金来扩大我的研究计划范围，并追求与该项目相吻合的新研究方向。AMR 现在被联合国大会认为是我们社会面临的最紧迫问题之一，也是 BBSRC 研究资助的关键战略优先事项。发现新的策略来最大限度地减少人类和动物的抗菌素耐药性负担将是真正具有开创性的。测试 CRISPR-Cas9 是否可以从复杂的微生物群落中消除 AMR 并了解 AMR 消除的后果将是推动这一突破的重要一步。

项目成果

Table S4 from CRISPR-Cas immunity leads to a coevolutionary arms race between

表 S4 来自 CRISPR-Cas 免疫导致了之间的共同进化军备竞赛

• DOI: 10.6084/m9.figshare.7764248
• 发表时间: 2019
• 作者: Common J

Table S3 from CRISPR-Cas immunity leads to a coevolutionary arms race between

表 S3 来自 CRISPR-Cas 免疫导致了之间的共同进化军备竞赛

• DOI: 10.6084/m9.figshare.7764251
• 发表时间: 2019
• 作者: Common J

Table S2 from CRISPR-Cas immunity leads to a coevolutionary arms race between

表 S2 来自 CRISPR-Cas 免疫导致了之间的共同进化军备竞赛

• DOI: 10.6084/m9.figshare.7764257
• 发表时间: 2019
• 作者: Common J

Supplementary Information from CRISPR-Cas immunity leads to a coevolutionary arms race between

CRISPR-Cas免疫的补充信息导致了之间的共同进化军备竞赛

• DOI: 10.6084/m9.figshare.7764254
• 发表时间: 2019
• 作者: Common J

Evolutionary emergence of infectious diseases in heterogeneous host populations.

• DOI: 10.1371/journal.pbio.2006738
• 发表时间: 2018-09
• 期刊: PLoS biology
• 影响因子: 9.8
• 作者: Chabas H;Lion S;Nicot A;Meaden S;van Houte S;Moineau S;Wahl LM;Westra ER;Gandon S
• 通讯作者: Gandon S