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 The PhD project is included in the inter-region Bretagne - pays de la Loire project, i.e. Biomics, coordinated by the Pôle Agronomique Ouest, which began the 1st of march, 2016. The scientific objective of the PhD project is to develop an innovative methodology of identification of adaptation biomarkers, combining molecular methods such as transcriptomics, and very robust statistical methods (probabilistic methods, differential analysis of gene expression), in order to evaluate the capacity of bacteria to survive stress encountered during food processing. 
The PhD thesis will more specifically focus on poultry and on the foodborne pathogen Campylobacter jejuni responsible for campylobacteriosis, the foodborne outbreak most likely due to consumption of undercooked chicken meat  or to cross-contaminations (EFSA, 2015). The PhD thesis aims at studying the influence of chicken slaughtering conditions on adaptation and survival of C. jejuni in processed poultry meat producst during refrigerated storage.

The project comprises several steps:
-    The first one is dedicated to the selection of representative strains of  C. jejuni in poultry and to characterization and transposition of slaghter conditions to laboratory.
-    In a second step, the influence of slaughter conditions will be evaluated on the survival of C. jejuni according to two approaches, a phenotypic approach (survival of C. jejuni to stress conditions) and a transcriptomic approach expression of preselectionned genes after application of adaptations steps). A quantitative analysis will enable to establish a link and develop a mathematical model between C. jejuni survival and biomarker genes expression.
-    Lastly, the third step will aim at developping a probabilistic model to calculate the contamination level of  C. jejuni in the consumer's plate and estimate the probability to exceed a security (FSO) or performance (PO) objective as  a function of process and storage conditions. Recommendations on microbiological criteria to be set will follow.

 Valorisation:

• Duqué, B., J. Canon, N. Haddad, S. Guillou and J.-M. Membré 2021. Quantitative approach to assess the compliance to a performance objective (PO) of Campylobacter jejuni in poultry meat in France. International Journal of Food Microbiology 336: 108916. Ranking du JCR: Q1 (JCR® 2019). https://doi.org/10.1016/j.ijfoodmicro.2020.108916.
• Duqué, B., S. Rezé, A. Rossero, J.-M. Membré, S. Guillou and N. Haddad 2021. Quantification of Campylobacter jejuni gene expression after successive stresses mimicking poultry slaughtering steps. Food Microbiology: 103795. https://doi.org/10.1016/j.fm.2021.103795.
• Duqué, B., N. Haddad, A. Rossero, J.-M. Membré and S. Guillou 2019. Influence of cell history on the subsequent inactivation of Campylobacter jejuni during cold storage under modified atmosphere. Food Microbiology 84: 103263. Ranking du JCR: Q1. https://doi.org/10.1016/j.fm.2019.103263.
• Duqué, B., S. Daviaud, S. Guillou, N. Haddad and J.-M. Membré 2018. Quantification of Campylobacter jejuni contamination on chicken carcasses in France. Food Research International 106: 1077-1085. Ranking du JCR: Q1. https://doi.org/10.1016/j.foodres.2017.12.017.