Mots-Clés
Genomic epidemiology, Phylogeny, One-Health, Pangenome
Description
A genomic approach to the epidemiological and phylogeographic characterisation of human Salmonella enterica subsp. enterica serotype Veneziana infections in France
This internship is part of an ongoing project within the unit aiming to evaluate the epidemiological risks associated with the emergence of environmental non-typhoidal Salmonella (NTS) in the context of climate change in France. The main tasks of the candidate will be to:
1. Further characterise the epidemiology of human infections caused by Salmonella enterica subsp. enterica serotype Veneziana in France.
2. Describe the population genetic structure of the Veneziana serotype in France, and compare this structure to that described for another emerging environmental serotype in Western Europe, S. Napoli.
3. Determine the antibiotic resistance gene content of S. Veneziana.
4. If time allows, compare the gene content (pan-genome analysis) of bacterial isolates and potentially identify genes specific to certain sub-lineages, geographic regions, or isolation sources (human vs non-human).
For this study, the candidate will have access to surveillance data on human salmonellosis collected by the French National Reference Centre for Escherichia coli, Shigella and Salmonella (CNR-ESS) since 1992 (>900 records of S. Veneziana, including date, biological source, location, patient age, and travel history), as well as more than 400 complete genomes (Illumina WGS and complete reference genome) associated with these metadata. This dataset may be supplemented by isolates from historical and current collections, of human or environmental origin. The candidate will handle a subset of these strains.
Although the proposed topic has a strong component of epidemiological and genomic data analysis, candidates with no prior experience in these areas are welcome to apply.
This project will be carried out within a structure combining surveillance and research activities, with recognised expertise in microbiology, antimicrobial resistance (AMR), epidemiology, genomics, and the evolutionary history of enterobacteria (in particular Salmonella, E. coli, Shigella and Vibrio).
Recent publications from the laboratory related to the project:
Frézal et al. Phylogeographic structure and evidence of genetic introgression in Salmonella enterica
serotype Napoli: a genomic epidemiology study. 2026. Lancet Microbe (In press)
[PREPRINT available at Research Square [https://doi.org/10.21203/rs.3.rs-8608855/v1].