Despite the fact that vaccine use in poultry is greater than in any other farmed species, the mechanisms by which they induce protection, particularly at mucosal surfaces, are poorly understood. Many diseases constraining avian productivity and welfare affect the respiratory tract and are multi-factorial. A better understanding of responses in the respiratory tract to bacterial and viral infections, co-infections and vaccines is needed to control endemic production diseases. Avian pathogenic Escherichia coli (APEC) cause severe respiratory and systemic disease, threatening food security and avian welfare at a time of increasing global demand. Infections frequently involve sepsis, inflammation of visceral organs and reduced egg yield/quality, with losses through early mortality, reduced productivity and product condemnation. The expansion of free-range production systems will increase the incidence of colibacillosis through greater exposure of birds to environmental pathogens, stress and injury associated with forming a social hierarchy. Importantly, APEC infections are frequently associated with respiratory viral infections. The nature and consequences of host-pathogen interactions during APEC (co-)infections are poorly understood. Virulence factors of APEC, antagonistic or synergistic effects of co-infection and the basis of immunity and resistance are ill-defined. The EC-wide ban on prophylactic antibiotic use and transmissible resistance render poultry susceptible to APEC infection. Existing vaccines confer limited serogroup-specific protection. This project will advance understanding of mucosal immune responses in the avian respiratory tract. It will provide a comprehensive description of the respiratory tract immune system, leading to new tools to study immune responses and improved understanding of the mechanism and site of antigen presentation in the lung. We will thereby identify correlates of resistance and susceptibility to, and the impact of viral infections on the outcome of, APEC infection. Using transgenic chickens we will further characterise the role of antigen-presenting cells and humoral immunity during APEC infection and vaccination, for example by using our unique MacRed chickens (in which all cells of the mononuclear phagocyte lineage (macrophages, monocytes and dendritic cells) express a fluorescent protein driven by the chicken CSF-1 receptor), and immunoglobulin knock-out chickens (which lack the B cell receptor and thus antibody).

Antibiotic resistance is a significant and increasing problem in many bacterial pathogens that infect animals and humans. Escherichia coli is among the most important of these pathogens, because of its role in intestinal, urinary tract and respiratory disease, and septicaemia in a variety of livestock species, including poultry; and also because many serotypes of E. coli that are associated with extra-intestinal infections in animals and humans are closely related. Antibiotic resistance in E. coli strains is increasing worldwide and this resistance can be maintained even after reducing or withdrawing antibiotic use (Tadesse, 2012). Treatment of E. coli infections in animals and humans thus requires a new and sustainable approach. This consortium will isolate viruses which infect bacteria (bacteriophages, or 'phages') which specifically target surface bacterial determinants of virulence and/or antibiotic resistance transfer. We will isolate phages from the environment, surface water, farms, drains and sewage which are able to infect a range of Avian Pathogenic Escherichia coli (APEC) serotypes. These will be characterised in vitro, and bacteriophage biocontrol candidates will be selected for evaluation in an E. coli septicaemia model in chickens. Selection of the phage will be based on the ability to infect a wide range of pathogenic E. coli strains, in vitro phage replication kinetics, and lack of/minimal host resistance. The potential issue of E. coli resistance to phage infection will be addressed by (i) targeting surface receptors which are important for virulence and/or antibiotic resistance, (ii) the use of cocktails of phages which target different receptors, and (iii) studying the CRISPR-Cas system of wild strains of E. coli to determine its role in phage resistance and its epidemiology and evolution during phage infection. The phage therapy company Ampliphibio is a partner and has collaborated with consortium members for more than 15 years through its UK subsidiary Biocontrol Ltd. This approach can synergise with the development of new drugs and has the potential to provide a sustainable platform for control of antibiotic-resistant pathogens which could easily be extrapolated to many other animal pathogens.

Processing can induce contaminants in food, especially when high temperature is reached. This is the case of bakery, whose products can contain neoformed contaminants (NFC) from inoffensive precursors in the dough and exogenous contaminants (EC) transferred from the support coating at the interface. EU regulations do not appropriately cover these fields and industrials are missing the tools and protocols to produce breads safely. In particular the existing food simulants and migration tests are not adapted to baking supports. SATIN will focus on Pan Bread and Rusk baked most of the time with Perfluorinated (PFC) coated pans. These two cases represent the main utilization of these coating with effective sticking and ageing problems. SATIN aims at developing technologies and knowhow which will allow the production of pan (tin) bread and rusk with (i) a reduced energy demand for baking by exploring ways to reduce oven temperature with even sensorial qualities and (ii) a better control of the chemical risks associated to perfluorinated antistick coating. One of the challenges lies in the assessment of the ageing of antistick coating in industry and in correlating the ageing with either the baking practices (pan temperature) or the risk of release of EC in the product. SATIN will concomitantly look at both NFC and EC and related their formation to various parameters influenced by food processing. Key objectives are (i) to assess the exposure of EC in particular PFC, (ii) to develop ageing tests in the case of baking support, (iii) to develop testing equipment(s) to monitor the ageing of the coating and to assess the conditions of an anti-stick coating to detect its end of life by analysing the crust condition and the volatiles in the baking oven and (iv) to develop innovative pan coating structure which will permit to mitigate the risk of transfer of PFC in the products. This will be supported by a transversal approach based on a reduction of the baking temperature and by the way of the baking energy. SATIN proposes a “win-win” strategy to reduce the EC and NFC while extending the shelf life of the coating; in turns, it will result in a reduction of the baking energy and a reduction of chemical waste generated when refurbishing used coating. SATIN will contribute to the improvement of the French and European regulation on Food Contact Material (FCM). SATIN will alsoinvestigate vacuum baking to reduce the baking temperature and baking energy with the objective of extending the life span of the antistick coating.

Climate change affects mountain forests by increasing the intensity and frequency of disturbances such as drought, insect and pathogen outbreaks, fire, wind and ice storms. As a result widespread tree mortality has been reported in recent decades. Most mountain forests support a rich community of organisms, so the loss or replacement of any tree species implies a change in species composition and a financial and economic cost. Understanding which species are lost and which are resilient to these environmental changes is crucial in order to take reasoned management decisions for mitigation. In addition, the presence of large numbers of dead trees and the replacement of dying native trees by exotic species have an impact on human inhabitants, tourists, and forest owners and can lead to local social conflicts over whether resources should be expended on maintaining traditional landscapes. To study the impact of climate change and forest management on the biodiversity of highland forests, we will quantify changes in species richness and composition of a wide range of terrestrial and freshwater organisms, along tree-dieback gradients of four highland conifers in European and Chinese mountains, using cutting-edge molecular technology. We will also measure changes in functional diversity for several focal groups recognized as regulators and indicators of key water and soil processes and ecosystem services. To study the perception of climate change by local populations and the socioeconomic impact of climate-induced mountain forest diebacks and tree replacement strategies on local communities we will carry out both qualitative and quantitative surveys in Europe and China. This project involves a multidisciplinary team of ecologists, sociologists, economists, geographers, forest entomologists, limnologists, mycologists, molecular biologists, forest managers and policy makers. We will work with stakeholders to disseminate the results of the project and facilitate the adoption of newly generated tools and indicators by policy makers.