Cross-species transmission of pathogens from the animal reservoir to domestic species and ultimately to humans constitutes a major risk for animal or human health. Recent studies in the United States of America and our preliminary work in France have identified a new Genus tentatively named Influenzavirus D within the Orthomyxoviridae family. The novel virus was shown to infect swine and cattle and to efficiently replicate and transmit in ferrets, the animal model of choice for the study of influenza viruses pathogenesis for humans, suggesting that humans could be infected. Our project aims at assessing the emergence threat associated with influenza D viruses’ circulation such to provide essential information about host range; origin, diversity, and evolution; pathogenesis; stability in different environments and putative routes of transmission, of influenza D virus in France. The virus will first be studied in its known hosts: cattle and swine, but emphasis will be put on predicting possible human infections thanks to surveillance in humans but also through adequate in vitro assays using human and ferret cells. We will also look at potential other host species that might serve as virus reservoir: wild ruminants (Cervidae) and wild boars (closest species to known domestic animals influenza D virus host species), small carnivores and equine (in very close contact with humans and susceptible to influenza A viruses). This will pave the way towards development of effective strategies for diagnostic and control of the disease.

Clostridium perfringens and Clostridioides difficile are major pathogenic bacteria involved in human infections. C. perfringens is also one of the bacterial hazards identified in the Guides to Good Hygiene Practices and of application of HACCP principles in the slaughtering and cutting of bovine, pig and poultry sectors. As animals are healthy carriers of both species in their digestive tract, animal meats are privileged targets to explain the occurrence of toxic episodes involving these pathogens. Without questioning the adequacy and relevance of the control measures implemented, little or no data are currently available in France on the importance of these two hazards in slaughterhouses and cutting plants. The ClostAbat project brings together academic partners and technical institutes with a wide range of expertise in food sciences and human clinical practice to develop knowledge and decision support tools to enable the sectors to have objective information on the importance of these hazards in slaughterhouses/cutting plants. This project will allow: i) to assess the contamination of the three meat sectors with regards to C. perfringens and C. difficile hazards and to consider the correlation between the occurrence of the digestive carriage at the slaughterhouse, contamination of carcasses, meat cuts and the production environment, as well as the bacterial profile within each slaughterhouse; ii) to determine the pathogenic potential of the isolated strains for humans; iii) to identify epidemiological markers allowing the isolates traceability according to the animal sectors; iv) to define their persistence in slaughterhouse and the potential correlation between their presence and the abundance of other bacterial taxa in surface populations; v) to determine the relative importance of the different transmission routes (animal or environmental) and their possible implication in infectious diseases in humans; vi) to transfer the methodologies used for data processing to the technical institutes for the characterization and monitoring of the two pathogens in the different meat sectors; vii) to set up recommendations by drafting guidelines describing strategies to be carried out by operators in order to efficiently reduce their involvement in contamination and their impact on Public Health; viii) to propose an alternative exploratory strategy for the management of these hazards by LED light treatment and to assess its impact on meat quality. The project has 5 Work Packages (WP): the WP1 concerns the organization of the sample collection in the slaughterhouses according to the specificities of each sector, the WP2 aims at determining the contamination frequencies of the meat sectors with regard to the hazards C. perfringens and C. difficile, the WP3 aims to determine the pathogenic potential of the isolated strains for humans, the WP4 aims to identify the relative importance of the sectors with respect to the two hazards and the WP5 aims to investigate the possibility of using LED combined with relative humidity/temperature to destroy the spores of C. perfringens and C. difficile. Thus, the meat sectors’ operators will be better able to justify the adequacy and relevance of the control measures implemented with regard to the C. perfringens and C. difficile hazards, and, if necessary, to re-examine them and disseminate selected prevention practices.

Global aquaculture has expanded continuously over the last 30 years to meet the increasing demand of fish for human consumption, which can no longer be met by fisheries captures. The growth of aquaculture has generated an increasing demand of raw materials for aquafeeds. However, the volume of fish meal (FM) and fish oil (FO), the traditional major ingredients of aquafeeds produced from feed-grade fisheries, remained stable over the last 20 years. This has forced a shift from marine resources towards plant products as ingredients for fish feed. The proportion of FM and FO in fish feeds has been reduced by one third as a result of recent research efforts. Nevertheless, trials using highly substituted (little or no FM and FO) plant-based diets highlighted physiological bottlenecks. These limits in the adaptive capacity of the fish to the unavoidable changes in dietary formulations urged us to explore a new paradigm: “adapting the fish to the new diets”. Having now demonstrated genetic variability for such adaptation in rainbow trout, we propose to take advantage of the existence of divergent genotypes to (i) decipher the mechanisms underlying the differences in short and long term adaptive response to plant-based diets and (ii) find markers of short or long term adaptation of fish to plant ingredients which will enhance the efficiency of future selection for fish adapted to new diets. This is the core of the AGREENFISH project. Using rainbow trout as a model of fish relying on marine ingredients, the research will be conducted by a consortium gathering French experts in fish genetics, nutrition, physiology and behavior, pathology, immunology, microbiology, and representatives of the French aquaculture industry. We will investigate (i) rainbow trout isogenic lines that we previously identified as highly divergent for responses to plant-based diets and (ii) a population of rainbow trout which we selected for its aptitude (survival and growth) to cope with plant-based diets. We will compare the responses of the different groups when fed a plant-based diet free of marine ingredients versus a diet containing FM and FO to decipher the adaptive mechanisms implemented at short and long terms by the contrasting genotypes. The characterization of isogenic lines, used here as a model of strong genetic divergence in adaptive capacity, will both use "sans a priori approach" and focus on specific targets known to be affected by plant ingredients: feed intake, gut and associated microbiota, liver metabolism, nutrient utilization and growth. The comparison of the selected (3rd generation) and control populations will target the selection criteria (survival, growth), the major nutritional bottlenecks and the responses to challenging situations and to several pathogens, in order to assess the fish robustness as a major determinant of fish production efficiency. Also, the soundest biomarkers (functional phenotypes, gene expression…) of adaptation found in the isogenic lines will be tested in the selected and control populations. Signatures of selection will be searched in the genome of the selected line, and combined with results from transcript analysis in the isogenic lines to mine candidate genes. The most consistent signatures will be then tested in a commercial population, in the individuals showing the largest difference when fed a diet devoid of FM and FO from the first feeding. Finally, all data will be gathered into an integrative map chart of the functional alterations and adaptive mechanisms induced by diet according to genetic groups, from which relevant biomarkers of the adaptive capacity of fish fed plant-based diets will be identified. This knowledge and the new tools generated will allow enhancing the genetic selection for better adaptation of domestic fish populations to the major diet shifts in feed composition and to improve formulation of aquafeeds, and will be disseminated for application in aquaculture industry through SySAAF.