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This thesis is the result of a collaboration between the OPAALE research unit of INRAE and the SEL unit of ANSES. The scientific objective is to describe the genomic diversity and soil fitness of Listeria monocytogenes strains isolated from the livestock manure recovery sector, in order to evaluate the possible impact of this sector on the flows of this pathogen in the agricultural environment.
This study is a follow-up to previous collaborative projects between INRAE and ANSES (Fedelilas, CloDia, PathoGaz) and benefits from their complementary expertise. It will consist in:

• the genomic characterization of these strains, using bio-informatics tools, and the comparison of the diversity with the one observed in the food processing industry.
• the study of their survival in soil and several matrices simulating different steps of the manure recovery chain, using methods developed by the OPAALE unit.
• The identification of genetic markers linked to soil survival, followed by in silico prediction of this phenotypic trait using machine learning.

This thesis will broaden the spectrum of pathogens considered in the assessment of the health impact due to the recycling of waste and organic effluents, a thematic supported by the OPAALE unit.