Mots-Clés

Bacterial genomics antibiotic resistance mobile elements horizontal transfers

Description

Context

In the framework of the ResisTrack project we are seeking for a highly motivated postdoc to work on the annotation and the comparative genomics of antibiotic resistance-conferring genes (ARGs) and mobile genetic elements (MGEs) involved in enterobacterial antibiotic resistance. ResisTrack is a collaborative effort between the CIRI (Centre International de Recherche en Infectiologie), the LBBE (Laboratoire de Biométrie et Biologie Évolutive) and the ISYEB (Institut de Systématique, Évolution, Biodiversité), funded by ANR (Agence Nationale de la Recherche).

Goals

In order to fight antibiotic resistance with efficient antibiotic stewardship and infection control (AS/IC) strategies, we must gain a deeper understanding of the eco-evolutionary phenomena that govern the dynamics of resistant bacteria. For that purpose, the ResisTrack project aims at building a holistic, multiscale model of the dissemination of ARGs, MGEs, enterobacteria and patients at the scale of the 5,400-bed HCL (Hospices Civils de Lyon) teaching hospital group.

To inform the model, we will jointly analyse the resistomes and mobilomes of a carefully selected subset of bacterial isolates, along with exhaustive contextual data on patient movements and antibiotic consumption. Through simulations of this bacterial ecosystem, we will investigate the impact on resistance of an extensive set of AS/IC interventions, allowing to select candidate optimal strategies against resistance.

The LBBE partner will annotate a stream of bacterial genomes sequenced during the project, with a special focus on the ARGs and the MGEs. A database of integrases and transposases will be developed and curated, and submitted to phylogenetic clustering before human curation. Other elements such as phages and plasmids will also be considered as they might be involved in the dissemination of resistance in pathogenic enterobacteria.

Skills

The candidate must:

• Be skilled in bacterial genomics.
• Have some knowledge in bacterial ecology and evolution.
• Be familiar with genome annotation tools.
• Be familiar with Unix/Linux working environment and cluster computing.
• Have good experience in writing papers and communicating research in conferences.

Work environment

This part of the project will take place at LBBE. This laboratory is located in the Mendel building on the La Doua campus of University Claude Bernard – Lyon 1 (UCBL), Villeurbanne, France. The LBBE is hosting teams active in population genetics, evolutionary ecology, molecular evolution, ecotoxicology, medicine and bioinformatics. It has always been home to scientists with very different backgrounds such as evolutionary ecology, molecular genetics, mathematics, computer science and medicine.