Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 19 (COVID-19) with symptoms ranging from mild respiratory illness to severe lung injury, multi-organ failure and ultimately death. Although SARS-CoV-2 primarily infects the lungs, gastrointestinal symptoms are frequently observed and are associated with worse COVID-19 outcomes, underlying the need to also study the infection of the intestinal mucosa. New recently identified SARS-CoV-2 variants raised particular concerns worldwide due to their high transmissibility rates. They all bear mutations in the Spike protein that binds to host cells and allows virus entry. The rapid emergence of such variants highlights the urgent need to develop highly relevant and standardized experimental models to study critical aspects of SARS-CoV-2 variant infection and replication but also to screen therapeutic candidates and assess whether drugs known to affect SARS-CoV-2 parental strain entry and replication are still efficient on these variants. Our proposal aims to monitor the ability of SARS-CoV-2 variants of concern, including South Africa, United Kingdom and Brazil ones, to infect human colonic organoid-derived cell monolayers, a model of choice to study host pathogen interaction in a standardized and reproducible way closely mimicking the in vivo situation. Our proposal also aims to study the immune response of the colonic epithelium to these variants and the impact of this response on the infection process. Finally, our project will be useful to perform a first drug screening of therapeutic candidates known to interfere with infection by the SARS-CoV-2 parental strain. In conclusion, our project will help to understand how the SARS-CoV-2 mutations affect entry and replication of the virus, and defence mechanisms of the intestinal epithelium as well as virus resistance to therapeutic candidates or to interferons. In addition, our experimental model will allow to quickly investigate other potential therapeutic candidates for other types of enteric infections, which is crucial in case of rapidly spreading pathogens, such as SARS-CoV-2.

Southeast Asia (SEA) is considered to be a hotspot for infectious diseases and antimicrobial resistance(AMR). The alarming prevalence of extended-spectrum beta-lactamases producing enterobacteria (ESBL-E)and the emergence and the rapid dissemination of plasmids carrying the mcr-1 gene conferring resistance tocolistin (polymixin E) in Thailand is therefore a global health concern. The abuse of antibiotic in human issuggested to be the cause of this very high prevalence in community. However, other factors could also beresponsible, in particular, occupational or direct contact with farm’s animals could be a risk factor ofacquiring genes of resistance from zoonotic bacteria. For example, colistin has been extensively used inanimal production, often as growth promoters and clonal transmission of colistin-resistant E. coli from adomesticated pig to a human was demonstrated in Laos (Olaitan et al. 2015). Colistin is re-introduced as thelast resort antibiotics to cure multidrug resistant Gram-negative infection in human setting and thereforeresistance to colistin is worldwide, one of the most worried concern. Therefore it is urgent to elucidate therole of farm animals in the spread of AMR in the community and to assess the risk factors for animals andhumans to be colonized with AMR. Therefore, the main objective of this proposal is to assess, with a OneHealth approach, the occupational risk for pig and poultry farmers to be colonised with animal-associatedESBL-E and colistin-resistant Gram-negative Enterobacteria. The second objective is to look at theassociation between farm parameters and prevalence of AMR. In particular: a) the type of animal production(extensive vs intensive), b) the antimicrobial usage (type and quantity) and c) the role of the other animalspresent on the farm with a special focus on rodents. The third objective is to study the influence of faecalcarriage of ESBL-E or colistin resistant bacteria on the faecal microbiota of farmers. Finally, the fourthobjective is to transfer the analytical methods (microbiota analysis) to a Thai PhD student and to proposeefficient preventive measure to reduce the prevalence of resistance in animal farms and to avoid thetransmission to the farmers.

HYPOTHESIS Multiplexed analysis of the diversity and targets of fungal exposome-induced sensitization enables risk modeling and long-term prediction, at the population and individual levels, of lung function, a correlate of longevity and quality of life. OBJECTIVES Main objective: To establish a biomarker pattern of multiplex sensitization to the environmental fungal exposome and allergic inflammation associated with lung function temporal trajectories in asthmatic and healthy adults from the French part of the ECRHS cohort (discovery cohort). The selected biomarkers will address allergic sensitization as revealed by specific antifungal antibodies of isotype E, hereafter denoted as immunoglobulin (Ig) E, using a custom multiplex allergen platform featuring all currently known allergenic fungal genera, and allergic inflammation based on eosinophil activation-related molecules. FUNGIPLEX involves and is coordinated by the French ECRHS clinical and scientific PIs: Pr P. Demoly (FUNGIPLEX coordinator and ECRHS clinical PI, Montpellier), Dr I. Pin (ECRHS clinical PI, Grenoble), Dr C. Neukirch (ECRHS clinical PI, Paris), Pr C. Raherison (ECRHS clinical PI, Bordeaux), Dr B. Leynaert (scientific coordinator of ECRHS France, Paris). FUNGIPLEX study design addressing the endpoint of allergic sensitization to environmental allergens is in compliance with ECRHS ethical and regulatory requirements. Secondary objectives: 1. To test the discovery cohort results in two distinct replication cohorts: a. Pediatric replication of adult findings: Replication in pediatric asthma. This replication arm will test the influence of age, assuming climate and genetic factors are comparable to ECRHS France. It will also add pathophysiological insight into the natural history of fungal sensitization during childhood. It will be performed with the French SAMP cohort comprising 424 preschool and school patients. Pr J. Just (Paris), the clinical PI of SAMP, is involved in FUNGIPLEX as scientific team leader. b. Swedish ECRHS replication of French ECRHS findings. This replication arm will test the influence of climate and genetic variation, assuming demographic and lung function characteristics are comparable to ECRHS France. ECRHS Sweden was designed and conducted similarly to ECRHS France. ECRHS Uppsala comprises 302 patients assessed at the 3 time points. FUNGIPLEX involves the clinical PIs of ECRHS Uppsala: Pr C. Janson and Pr A. Malinovschi. 2. To improve detection of susceptibility to long-term lung and health outcomes at the individual level: FUNGIPLEX will bridge mold exposure questionnaires with corresponding multiplex mold immune sensitization. ORIGINALITY A translational hub from epidemiological data to personalized medicine in the context of fungal exposome. EXPECTED RESULTS In terms of new knowledge, FUNGIPLEX will provide the description of the evolution of the fungal sensitization in relation to clinical outcomes at various times of life and taking different regions into account at the general population level. Of note, some of the fungi have never been considered in population studies. Determinants of this evolution will be investigated taking an EnvWAS approach into account. This information will be used for personal prevention. Clinically, FUNGIPLEX will provide an extensive fungal multiplex assay to be used in other cohorts (COBRA, EGEA, etc.) as well as in clinical routine. FINAL PRODUCT DEVELOPED The multiplex assay developed in the FUNGIPLEX study will help identify the most informative fungal allergens and serve as a basis for tailored multiplex tools. Such tools are needed for the extended or focused investigation of other fungal-related diseases involving IgE, IgG, or IgA in serum or local samples (nasal fluid, sputum), e. g. hypersensitivity pneumonitis, allergic bronchopulmonary mycoses and allergic fungal rhinosinusitis.