CRISPR-Cas9 gene drives to fight antimicrobial resistance

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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.