We are looking for a postdoctoral researcher who will decipher the relationships between strain genotype and its antibiotic resistance phenotype, in E. coli and K. pneumoniae. He or she will combine computing and experimental approaches to (i) characterize the evolutionary trajectories of drug resistant bacteria, (ii) identify loci and polymorphisms contributing to the acquisition of antibiotic resistance and their epistatic interactions and (iii) provide mechanistic bases for their contribution to resistance. The project eventually aims to improve and rationalize our capacity to predict the antibiotic resistance phenotype of an isolate based on its whole genome sequence.
The researcher will join the Ecology and Evolution of Antibiotic Resistance (EERA) Unit at the Institut Pasteur, in Paris, France (https://research.pasteur.fr/fr/team/ecology-and-evolution-of-antibiotics-resistance/). The project is embedded in the Seq2Diag project funded by the National Priority Research Plan antibiotic resistance. Seq2Diag overarching objective is to provide a proof of concept of the use of artificial intelligence to predict the antibiotic susceptibility phenotype of an isolate in the clinic. It gathers a consortium of nine teams (https://research.pasteur.fr/fr/project/whole-genome-sequencing-and-artificial-intelligence-to-characterise-and-diagnose-antibiotic-resistance-and-capacity-to-escape-treatment/) with a broad range of expertise: from clinical microbiologists, expert in human and animal health, to bioinformatics and machine learning experts specialized in genomics and evolution.
The EERA unit combines experimental and bioinformatic studies to characterize the ecology and the evolution of antibiotic resistance from modelling dissemination to the characterization of the underlying molecular mechanisms. It collaborates with clinicians, modelers and bioinformaticians and has access to the state-of-the-art technological platforms from the Institut Pasteur.
We are seeking a candidate motivated by the urgent issue of antibiotic resistance. He or she will hold a PhD degree in microbial bioinformatics or microbiology. Expertise in bioanalysis and sequence analysis is needed. The balance between experimental and in silico work will depend upon the recruited candidate expertise and interest.
The funding for this position is available for two years with a salary set on the experience of the candidate. Applications including a CV, motivation letter and reference letters must be addressed to: pglaser@pasteur.fr. Expected starting date is from June 1st to October 1st.