Farmed salmon is a major source of high quality protein and fatty acids essential for human health. Salmon aquaculture is worth approximately £1Bn to the UK economy, and supports many rural and coastal communities. However, sea lice are a major perennial problem for salmon aquaculture worldwide. These parasites attach to the skin of salmon and feed on tissue, mucus and blood. Infected fish show impaired growth and increased occurrence of secondary infections. They cause significant negative impacts on salmonid health and welfare, while lice prevention and treatment costs are a large economic burden for salmon farming, over £800M per annum. Encouragingly there is substantial genetic variation in resistance to sea lice both within and across salmonid species. While the commonly farmed Atlantic salmon are generally susceptible to infection, other salmonid species such as coho salmon are fully resistant. Improving the innate genetic resistance of the farmed salmon to sea lice is an environmentally friendly, but underexploited approach to lice control. Incremental improvements have been achieved via selective breeding of Atlantic salmon, but their long generation interval slows progress. Genome editing raises the possibility of rapidly increasing the resistance of salmon via precise targeted changes to their genomes; the key is knowing which specific genes to target. This project focusses on understanding the genetic mechanisms underlying resistance to sea lice, and identifying gene targets for genome editing to develop lice-resistant Atlantic salmon. To identify target lice resistance genes for editing, several different approaches will be taken, each exploiting the latest genomic technologies. Firstly, whole genome sequences will be obtained from a large population of farmed salmon on which sea lice counts following challenge have been collected. These will be used to map individual genes that contribute to variation in resistance in the commercial Atlantic salmon population. Secondly, it is known that the mechanisms underlying resistance to sea lice are due to a successful localised immune response close to the attachment site of the louse. Therefore, a detailed gene expression comparison of the immune response of Atlantic and coho salmon in the first four days following a lice challenge will be undertaken, using single cell sequencing approaches to highlight different responses in distinct cell populations at louse attachment sites. This will be complemented by profiling of the gene expression of the lice, and identification of potential immunomodulatory proteins and their targets in the host. Thirdly, genome editing approaches will be used to assess the impact of perturbing candidate resistance genes on response to sea lice both in cell culture and in the fish themselves. The former will be used to assess the cellular response to proteins secreted from the sea lice, and the consequences of knocking out each of the target genes on that response. This will lead to a final set of target genes for editing in salmon embryos, after which the edited fish will be challenged with sea lice. The resistance of the edited fish compared to full sibling control fish will then be assessed. The scientific programme of the project will be complemented by co-development of a strategy for the breeding and dissemination of edited lice resistant salmon, together with industrial partner Benchmark PLC. Furthermore, public and stakeholder engagement events are planned to communicate the research plans and outcomes, with a particular focus on the benefits and risks of genome editing in aquaculture. A successful outcome of lice resistant salmon would have major animal welfare and economic impacts via prevention of outbreaks, and removal of the need for chemical treatments. It would also provide a high profile example of the power of genome editing technology to understand biology and to improve food security and animal health.

Antibiotics are used to prevent and treat bacterial infections in humans and animals. Antibiotics are natural products of microbes and have been present in the environment in small amounts for millions of years. Some environmental bacteria have therefore had time to evolve resistance to these antibiotics. Once we started using antibiotics to treat infections, we set off a chain of events that has led to pre-evolved resistance moving from its environmental origins into bacteria that cause disease. This "mobile" resistance can spread through bacterial populations, leading to long-term consequences when these bacteria cause infections. One example is the CTX-M enzyme, which gives resistance to 3rd generation cephalosporin (3GC) antibiotics. CTX-M was discovered 30 years ago, but it is now found in bacteria causing about 5% of urinary tract and bloodstream infections in humans in the UK. 3GCs are used to treat infections in humans and animals. However, because they are considered Highest Priority Critically Important Antimicrobials for use in humans, their use in farm animals in the UK has now almost stopped. This is because the Red Tractor farm assurance scheme, which is followed by 95% of UK farms, introduced new regulations around antibiotic use in mid 2018. One aim is to reduce the number of 3GC resistant bacteria in farm animals, which might spread to humans and cause resistant infections. Some antibiotics, in contrast, are used to treat infections in farmed animals but never in humans (in the UK). One example is spectinomycin, which has been extensively used to treat sheep in the UK for decades. There are no rules specifically preventing the use of "farmed animal specific" antibiotics like spectinomycin, but in many countries, there is a general downward trend in antibiotic usage in farming. Furthermore, since late 2021, spectinomycin has no longer been available in the UK for treatment of sheep because its manufacturers have withdrawn it from sale. This might be expected to reduce rates of spectinomycin resistance in the UK sheep flock. We also see spectinomycin - and other farmed animal specific antibiotic resistance - in bacteria causing human infections, suggesting that there is a flow of resistant bacteria from farmed animals to humans. Maybe this will now start to reduce? Moves to reduce antibiotic usage in farming are ongoing in many countries. This project aims to build a partnership between UK (University of Bristol) researchers and those in Canada (Universities of Montreal, Guelph, Calgary and Prince Edward Island) who are experts in antibiotic use and resistance in farmed animals, and/or in humans. In Canada, there has been variation in regulatory and industry-led changes to antibiotic usage in farming at provincial level, but generally, a downward trajectory in usage started later than it did in the UK. Our partnership will be built though a variety of activities, but predominantly by collaborative research aiming to understand whether antibiotic usage reduction in farming is driving down antibiotic resistance levels on farms, and also in human infections. To do this, we will take advantage of natural experiments in the UK and Canada that are uniquely possibly for us to undertake, become of our ongoing involvement in large-scale longitudinal farm antibiotic usage and resistance surveillance projects, and the fact that antibiotic usage is being reduced in both countries at different rates and in subtly different ways. It is very difficult to validly demonstrate a significant association between antibiotic usage reduction in farming on antibiotic resistance in bacteria on farms, and even more difficult to show and effect on human populations. This is because of all the potential confounding factors occurring in parallel that might also be driving down resistance. The value of our partnership is that we can pool our cutting edge technical expertise and so make these analysis possible.