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    Opportunity: Post-doctoral in microbial genomics @ University of Nice -- Nice, France
    Submitted by croce; posted on Tuesday, June 04, 2019


    Genomic and virulence analysis of a collection of Bacillus cereus strains causing bacteremia in preterm neonates

    Bacillus cereus is an environmental bacterium that is the second most common pathogen found in food-borne outbreaks in France. The use of routine identification techniques by mass spectrometry of this species does not allow it to be precisely discriminated against among 15 other Bacillus species. When isolated from clinical samples, it is often considered as a contaminant. However, we and others have also recently shown the lethal potential of this bacterium in premature infants.

    Recently, we collected clinical data and blood culture isolates of B. cereus from 55 premature infants in 16 French cities. The mortality rate was 23%.

    In this project we propose to perform a genomic study of these 55 strains after sequencing their entire genomes. We want to obtain high quality genomes by combining sequencing Illumina and Nanopore long reads technology. The objective is to accurately characterize the strains studied at the species level and to analyze their resistance to antibiotics and virulome. We will also compare these genomes with those already available in public databases. The genome analysis will be carried out in collaboration with Raymond Ruimy, researcher and professor of microbiology at the Nice University hospital and Olivier Croce, head of the Bioinformatics department at IRCAN in Nice. In addition, this project will be in collaboration with the Professor Edouard Fournier of the IHU in Marseille.


    • Good experience in genomics: assembly, sequences curation, annotations, SNP analysis, orthologs, inter-genomes comparison, ...
    • Have knowledge in evolution and phylogeny
    • Knowledge of at least 2 programming languages, including Python preferably
    • Be comfortable under Linux system
    • Knowledge of microbiology is recommended.
    • Fluent English, French is appreciated.
    • Communication skills


    This contract is reserved for students who (i) have NOT done their PhD in France; (ii) are for people from "Southern countries" (compared to France), ie. all Africa, southern Europe, Asia, ...

    The contract could start from now to September.


    The candidate will be mainly located in the Bioinformatics service of the IRCAN institute (Faculty of Medicine - Pasteur tower - 5th floor 28, av. Valombrose, 06107 Nice) and sometimes in Bacteriology Laboratory Nice. Some missions will be at the IHU of Marseille.


    Basic salary is 1500€ per month – 2 years contract.


    Please, send you CV and letter to croce[at] and ruimy.r[at] including contacts of 2 referents.

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