Postdoc génomic and evolutionary microbiology

Name of the project: Enrichment of emerging antibiotic resistance of public health concern in the hydric environment: toward a genomic, phenotypic and evolutionary-based proxy of exposition risk in a territory.

The postdoc will work in the context of the WATERISK project, funded by the ExposUM Institute (University of Montpellier). The aim of this project is to identify genomic and phenotypic characteristics determining the enrichment of emerging AMR genes of public health concern in hydric environments. WATERISK focuses on emerging resistances to β- lactams in Gram-negative bacteria and is designed at the local scale (drainage basin of a coastal river and hospitals from the Montpellier area). This project is composed of three main parts: (1) building a resistant isolates collection, (2) obtaining and analysing the genomes of the isolates of the collection and (3) characterizing the phenotype and evolutionary potential of associations of plasmid and strains from the collection.

Main mission and activities:

The postdoc will be in charge of the second part and will conduct the genome sequencing analysis of a collection of 500 Enterobacteriacea isolates collected at Montpellier University Hospitals and at different points along the coastal river. The goal of this analysis will be to identify the association of antibiotic resistance genes with strains, species, mobile genetic elements and other resistance genes across environments to better understand the circulation of antibiotic resistance genes.

The postdoc will also participate in the characterization of the evolutionary potential of strain-plasmid associations by designing and implementing an experimental evolution approach and contributing to the phenotypic and genomic characterization of the evolved lines.

Genomic analysis: de novo genome assembly, annotation, strain identification, antibiotic resistance gene screening, mobile genetic element search.

Large dataset management.

Basic techniques in microbiology.

Experimental evolution.

Articles writing.

Presentation of the results in national and international conferences.