CBS - Postdoctoral Research Fellow in Antimicrobial Resistance and Resistome Mapping

Institution/Department

Mohammed VI Polytechnic University
Chemical & biochemical sciences.green process engineering
Research Unit on Microbiome and Host-Pathogen Interactions

Project Overview:

We are looking for a highly motivated Postdoctoral Research Fellow to join our interdisciplinary team focused on antimicrobial resistance (AMR). The selected candidate will have a vital role in an innovative project that aims to map the resistome and clarify the mechanisms of multidrug resistance across diverse microbiomes—comprising clinical, environmental, and host-associated microbial communities. This project seeks to comprehend how antimicrobial resistance genes (ARGs) disseminate within microbial populations via horizontal gene transfer (HGT) and mobile genetic elements (MGEs) and how these processes affect human health, particularly regarding colorectal cancer (CRC).

Key Responsibilities:

• Perform shotgun metagenomics and whole-genome sequencing (WGS) on microbial samples from various environments (clinical, environmental, tumor-associated microbiomes).
• Develop and implement bioinformatics pipelines for resistome, mobilome, and virulome profiling using tools such as MEGARes, CARD, VFDB, and PlasmidFinder.
• Investigate horizontal gene transfer (HGT) dynamics and plasmid-mediated dissemination of ARGs across microbial communities.
• Conduct phylogenetic and comparative genomic analyses to uncover the evolution of multidrug resistance in pathogenic bacteria.
• Analyze co-occurrence networks between resistance genes, virulence factors, and mobile elements in microbiome datasets.
• Collaborate with clinical partners and microbiome researchers to integrate multi-omics data for comprehensive resistome analysis.
• Publish high-quality research articles and present findings at international conferences.
• Contribute to grant writing and development of new research proposals.

Required Qualifications:

• PhD in Microbial Genomics, Bioinformatics, Molecular Microbiology, Infectious Disease Biology, or a related field.
• Proven experience with high-throughput sequencing technologies (Illumina, Nanopore) and metagenomic analyses.
• Strong background in bioinformatics tools for microbiome analysis (QIIME2, Kraken2, MetaPhlAn) and AMR gene identification (MEGARes, CARD, ResFinder).
• Proficiency in Python, R, or Perl, with experience in Linux/Unix environments.
• Solid understanding of antimicrobial resistance mechanisms, horizontal gene transfer, and mobile genetic elements.
• Evidence of scientific publications in peer-reviewed journals.
• Excellent communication and teamwork skills.

Preferred Qualifications:

• Experience in clinical microbiome research, oncology microbiomes, or environmental resistome surveillance.
• Familiarity with spatial metagenomics, single-cell microbiome analysis, or multi-omics data integration.
• Knowledge of machine learning approaches for resistome prediction or biomarker discovery is a plus.

Why Join Us?

• Access to cutting-edge technologies (mass spectrometry, next-gen sequencing, high-performance computing).
• Work on high-impact research addressing one of the urgent challenges in global health—antimicrobial resistance.
• Collaborate with a multidisciplinary team of microbiologists, bioinformaticians, clinicians, and data scientists.
• Opportunity to lead high-profile publications and contribute to international consortia.
• Career development support, including grant writing, conference funding, and training opportunities.

Application Process:

Applicants should submit the following in a single PDF file:

1. A Cover Letter explaining their interest and fit for the position
2. A detailed Curriculum Vitae (CV)
3. Names and contact details of 2–3 references
4. Up to three key publications (optional)