Short Bowel Syndrome (SBS) results from an extensive intestinal resection and is the leading cause of intestinal failure. In addition to parenteral nutrition, an effective pharmacological treatment with a great heterogeneity of response in patients with SBS is used today. This very expensive treatment ( 250,000€/patient/year) prompts the search for other therapeutic targets. Our hypothesis is that the specific microbiota or "lactobiota» of subjects with SBS is a potential reservoir of target signals contributing to the improvement of intestinal absorption capacities. The objective of the project is to study the role of this particular microbiota by identifying the signal factors improving intestinal absorption in SBS. The perspectives are to identify bacterial species and / or metabolites from this « lactobiota » that could serve as targets to develop therapeutic strategies for the management of patients with SBS.

The epidemic due to the Sars-CoV2 virus is spreading in France with an increasing number of affected patients. The medical and paramedical staff of the front-line departments for the care of patients infected with Covid-19 are potentially exposed to the risk of occupational contamination due to the large number of patients treated. Therefore, and despite the application of standard protective measures, it is possible that a certain number of caregivers already have or will contract Covid-19 infection, including in its asymptomatic form, which could represent 50% of cases. The main objective of the SEROCOV project is to assess the proportion of caregivers with documented Sars-CoV2 infection among the medical and paramedical staff of the front-line departments for the care of patients infected with Covid-19 at the end of epidemic of Sars-CoV2. The documented Sars-CoV2 infection is defined by Sars-CoV2 seroconversion and / or a positive Sars-CoV2 PCR on nasopharyngeal sample during follow-up. The secondary objectives are 1) to study the risk factors for documented infection, 2) to describe the type of infection presented in particular the proportion of asymptomatic and severe infections, 3) to assess whether there is viremia in asymptomatic infections, 4) to assess the number of different strains among infected caregivers in the same department. To meet these objectives, we are setting up a multicenter prospective cohort of caregivers working in 12 Ile de France departments on the front line for the care of patients infected with Covid-19. Eligible caregivers who have signed consent will have Sars-CoV2 serology at inclusion. Their socio-demographic data will also be collected. A weekly self-monitoring booklet will be given to the caregiver to collect any symptoms of the infection during the follow-up period. In case of acute respiratory or digestive clinical viral syndrome, serology and PCR will be performed. At 3 months, a new serology will be performed again. The proportion of documented infection will be estimated and its 95% confidence interval calculated. The risk factors for documented infection will be identified in participants whose serology is negative at inclusion, with a logistic model. It is expected to include approximately 1,300 caregivers over a period of one month.

Systemic lupus erythematosus (SLE) is the most common chronic systemic autoimmune disorder, with 30000 patients followed in France. SLE patients are at increased risk of infections which are more frequent and severe both because of SLE disease itself and immunosuppressive drugs. A specific vaccination policy has been applied in such patients, in particular with pneumococcal vaccination. The vaccine response is however highly variable with > 50% of SLE patients who fail to reach immune protection after pneumococcal vaccination. In the current SARS Cov-2 pandemic context, vaccination using mRNA Covid-19 vaccine has started in France in January 2021. It is unclear whether and how SLE patients will develop protective and enduring immunity following SARS-CoV-2 vaccination. Major questions are indeed currently unanswered for patients with chronic autoimmune disease such as SLE who will receive mRNA Covid-19 vaccine: do they develop a humoral and cellular immune response comparable to the general population? How long will be the protective immune response in SLE patients? Can viral mRNA vaccine promote lupus flares? COVALUS project aims to study the humoral and cellular response following SARS Cov-2 vaccination in patients with systemic lupus erythematosus. Accurate knowledge of the immune response induced by Covid-19 vaccine in patients with autoimmune disease who receive immunosuppressive treatments will be essential for the epidemiological control of Covid-19 in this population.

Azole resistance in Aspergillus is one of the emerging public health concerns, listed as a WHO priority and suited to an integrated One Health approach. Selective pressure due to the use of azole pesticides in agriculture being incriminated, identification of clinical and environmental resistance patterns, and a greater understanding of the factors driving this resistance are urgently needed in order to issue recommendations to the stakeholders. The multidisciplinary AspergillusOne-health project strengthened with model and innovative methodologies (WGS, genotyping, MALDI typing, metabarcoding, AI) aims to identify hotspots as possible sources for selection of azole-resistance in the environment, after the detection of azole-resistant Aspergillus in patients and patiens's home, avian facilities, the environment (farming and sawmills), and detection of the azole fungicides in soil and air. The role of resistance trait on Aspergillus fitness cost will be investigated, using environmental strains and mutants selected after fungicide pressure, to assess its clinical involvement.

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.