Missions

Development of a meta-pangenomic method to determine the abundance of strains of bacterial species of interest, as well as the presence of mobile genetic elements carrying antibiotic resistance genes.

Activities

•  Develop a meta-pangenomic method that will include a sequencing read mapping step on pangenome graphs and a deconvolution step to quantify strains and identify their variable genomic regions
• Validate the method on simulated and reference data sets
• Apply the method to several metagenomic projects to study the spread of antibiotic resistance
• Ensure a technological and scientific watch
• Publication of the method and participation in its integration into the ABRomics platform

Skills

• Experience
  PhD in bioinformatics with a focus on methodological development for massive data analysis
• Knowledge
  On graph algorithms and unsupervised classification methods 
  In (meta)genomics and related bioinformatics analyses
  In microbiology (wished)
• Operational skills
  Proficiency in several programming languages, including Python
  Software project management
  Use of computing clusters in the Linux environment
• Behavorial skills
  Ability to work in a team, both face-to-face and remotely
  Good oral and written communication skills in English
  Autonomy, rigor, integrity
  Be a driving force

Context

The ABRomics project (PPR antibiorésistance funding) aims to develop a digital platform to collect, analyze, organize and make accessible (meta)genomic data on bacterial infectious diseases and their metadata for research and surveillance of antibiotic resistance. This project is led by the Institut Français de Bioinformatique (IFB; france-bioinformatique.fr) and the Institut Pasteur (IP; www.pasteur.fr) and relies on a network of researchers from 44 teams including epidemiologists, clinical microbiologists, bioinformaticians, mathematicians and the wider research community. ABRomics will provide a unique data storage and analysis infrastructure, developed by a team with expertise in DevOps, database and software development, data management and data analysis.

The development of the ABRomics platform is based on several use cases. As part of Use Case 3, which aims to propose new strategies for monitoring antibiotic resistance using environmental or clinical samples (i.e. mainly gut microbiota), we propose to develop an analysis method that will use pangenome graphs, reconstructed by the PPanGGOLiN software (github.com/labgem/ppanggolin), as a reference. This meta-pangenomic method will make it possible to quantify, from sequencing data (i.e. short and long metagenomic reads), the abundance of strains of bacterial species of interest (i.e. ESKAPEE) as well as the presence of mobile genetic elements (MGEs, e.g. plasmids, integrative and conjugative elements) carrying antibiotic resistance genes.

To this end, the IFB is recruiting a post-doctoral fellow to develop this new method, validate it and apply it to several datasets to study the spread of antibiotic resistance. The person will be recruited within the LABGeM team and will work in close collaboration with an engineer in charge of building up the reference pangenome resource, as well as with the ABRomics platform stakeholders involved in Use Case 3.

For more information: https://www.abromics.fr/use-case/meta-pan-genomics-for-tracking-amr/