Mots-Clés
Metagénomique.
Antibiorésistance
Pathogène
Connectivité
Aquaculture
Une seule santé
Description
Offer Description
Project title : HealTH and food security Risks associated to marinE Aquaculture practices and their influence on the circulation of anTibiotic microbial reSistances and pathogens in floating farm socio-ecosystems.
Project description : The postdoctoral researcher will work within the framework of the THREATS project, funded by the ExposUM Institute (University of Montpellier). Adopting an interdisciplinary approach to address key One Health questions, the THREATS project aims to better understand the health risks associated with aquaculture practices and their influence on the circulation and spread of antimicrobial resistance and pathogens in the socio-ecosystems of floating farms in Vietnam.
Main mission : Most emergences of infectious diseases and the spread of antimicrobial resistance (AMR) begin with exposure to pathogens or antibiotic resistance genes (ARGs) that naturally circulate in environmental or animal reservoirs. The postdoctoral researcher will be responsible for analyzing metagenome sequencing data from a collection of 200 human, environmental, and animal samples collected from 40 floating aquaculture farms in the Nha Trang region of Vietnam. The objective of this task is to decipher the diversity and key drivers of potential marine pathogenic bacteria (PPB), ARGs, and potentially antibiotic-resistant pathogenic bacteria (PARB), as well as the effectiveness of their circulation between the three compartments.
Activities :
• Metagenomic data analysis: Characterization of the functional repertoire of microbial communities, with a focus on the resistome, virulome, and mobilome.
• Comparative analysis of connectivity between compartments
• Identification of antibiotic resistance determinants
• Quantification of health risks associated with the resistome, virulome, and mobilome
• Ensuring traceability and reproducibility of bioinformatics analyses
• Presentation of results and writing of publications
Requirements
Research Field : Biological sciences
Education Level: PhD or equivalent
Skills/Qualifications
Initial Training: PhD in Bioinformatics/Microbiology/Molecular Biology, with advanced experience in microbial bioinformatics preferred. PhD obtained within the last three years.
Technical Skills:
- Proficiency in Python, Shell, and R programming languages
- Strong expertise in bioinformatics analysis of (meta)genomic data applied to antibiotic resistance (assembly, gene annotation, script and pipeline design/implementation, use of a computing cluster)
- Good practices in bioinformatics
- Mastery of basic NGS analysis tools
- Proficiency in written and spoken English
- Publications in high-impact journals (A-rank)
Personal Qualities:
- Ability to work in a team and engage in interdisciplinary research
- Strong interpersonal and communication skills
- Autonomy in work organization
- Scientific rigor and analytical thinking
- Excellent writing skills