For several years, Campylobacter has remained the leading cause of foodborne zoonosis in Europe. The main route of Campylobacter transmission to humans is the ingestion of contaminated poultry meat. Controlling the contamination of poultry meat by Campylobacter represents a major public health issue but also an economic issue due to the application of a new process hygiene criterion to the broiler carcasses. To date, the risk assessments relating to Campylobacter have been based on studying the behaviour of the pathogen without taking into account the microbiota also present on meat. However, it is known that the bacterial interactions that take place within the microbiota influence the behaviour of pathogens to the consumer's plate and that the composition of the microbiota depends on the conditions encountered along the food chain. In recent studies, network analysis of significant taxon co-occurrence patterns, combining multivariate statistical techniques and high-throughput DNA sequencing technologies, was used to investigate potential interactions between microbial taxa. This method may help to decipher the structure of complex microbial communities across spatial or temporal gradients and offers valuable insights to investigate taxonomic interactions and ecological niche associations in complex microbiota in which pathogens evolve. In this context, ESCAPE project aims to: (i) quantitatively assess the effect of the rearing method, chilling and packaging/storage of broiler carcasses on the composition of the microbiota and the level of Campylobacter contamination in the broiler carcasses, (ii) to determine whether certain bacterial species within the microbiota of the carcass promote or deter the persistence of Campylobacter using network analysis and box tools used in microbial ecology, and thus identify potential bacterial indicators predicting the presence of Campylobacter on the carcass, (iii)and to understand how and why Campylobacter survives on meat, by studying the mechanisms relating to the pathogen response in interaction with these bacterial indicators. ESCAPE is part of an approach to improving meat safety by considering new risk mitigation strategies and assessing risk exposure taking into account the microbiota of the food concerned. The results of the project will make it possible to obtain a better knowledge of the behavior of Campylobacter, in particular by considering the influence of biotic factors (microbiota) on the presence and survival of Campylobacter on meat, for a possible integration of these factors in quantitative microbial risk assessment. The identification of microbial indicators facilitated the monitoring of the presence of Campylobacter within the framework of quality monitoring. In the longer term, the investigation of other control strategies with the use of inhibitory bacteria will allow better control of the risks and thus reduce the impact of campylobacteriosis.

The objectives of the FLUOPATH project are 1) to find new biomarkers (promoeters that induce the expression of genes of interest) coupled to a fluorescent biosensor allowing to acquire new knowledge in bacterial cell physiology related to the impact of technological disturbances inducing stresses. The study will be focused on the growth, survival and virulence of two pathogens in dairy products (milk, diluted cheese and if possible solid cheese) and 2) to use this knowledge combined with the knowledge present in the scientific literature to improve the models for predicting the microbiological risk in dairy products. The pathogens considered will be L. monocytogenes and B. cereus. The matrices considered will be liquid milk as well as model diluted and undiluted cheese (gelified matrix). New models based on the use at the scale of the single cell and the whole population of biomarkers will be developed to predict growth, resistance and virulence (invasive capacity for L. monocytogenes and entry into sporulation and toxin production for B. cereus) to stress while taking into account cellular variability. A precise quantification of the impact of stressful industrial conditions will be carried out on bacterial responses at the cellular level: probability of single cell / whole poulation growth, survival, toxin production, spore formation, invasive capacity. The challenge is to design and validate in food matrices bacterial biomarkers of phenotypes of interest in risk assessment in order to incorporate the intensity of biomarker response into exposure assessment models.

In France and worldwide, during COVID-19 pandemic workers in the agri-food sector are considered part of the essential workforce of critical infrastructures, and this concerns farmers as well as employees in processing plants, truck drivers who make deliveries as well as hypermarket cashiers. In addition, in some countries such as the US, by presidential decree, meat and poultry processing plants must continue to operate to avoid disruption to the food supply chain. The workers in these industries may be more exposed to coronaviruses because telework is not possible, and many face increased risks due to the proximity of their work environment. There is a need to carefully address the issue of virus circulation in meat processing plants in France from three perspectives: (i) protection of workers and avoidance of these premises becoming hotspots of virus circulation in the communities; (ii) prevention of the closure of these processing plants and ensuring supplies; and (iii) prevention of contamination of food in order to avoid the export of this virus to other locations. The main goal of this project is to gain insights on the circulation of SARS-CoV-2 in meat processing plants in order to provide preventive or risk mitigation measures for workers and consumers. We are planning to gather/collect the data necessary to understand the circulation of the virus in this type of workplace and to use them to build a simulation model of the propagation of the SARS-CoV-2. The present project will be organized into four work packages. First, the SARS-CoV-2 transmission and persistence factors in meat processing plants will be studied. The objectives of WP1 is to carry out an extensive literature review on SARS-CoV-2 transmission factors/parameters in order to extract relevant data for studying the circulation of the virus in meat processing plants and to define protocols to be conducted under laboratory conditions to overcome data gaps or uncertainties on certain virus transmission parameters/factors. In the second work package, a description of the conditions and environmental factors of work in meat processing plants will be done, through questionnaires and interviews (face to face) as well as observations, to be carried out in authentic food processing plants. The data collected will be used to provide directions and clarifications for the laboratory work carried out in WP1, and to populate the simulation model. The objective of WP3 is to construct a mathematical model to simulate the spread of the virus in a meat-processing plant in order to assess the impact of certain prevention or mitigation measures on the probability of transmission of the virus to employees and the contamination of products and the environment. This model will also allow us to explore the transmission of the virus outside the plants. The objective of the WP4 is to provide different critical communication mechanisms to engage employees in an effective safety management policy, gain cooperation and support, and maintain a positive safety culture. The impacts of this project will be 1) to increase the knowledge about how the virus is transmitted in a professional setting; 2) provide solutions to companies to better calibrate their preventive measures and mitigate the risks in the event of the introduction of the virus into their premises; 3)provide tangible data on transmission modalities and simulate the circulation of the virus according to different scenarios and 4) provide a decision support for business and government based on science and available data. The approach is extendable to other situations: processing plants, offices, universities, public places, etc.