Job description
In the context of the collaborative project KLEB-GAP – “Klebsiella pneumoniae, a key driver in the global spread of antimicrobial resistance and a target for new approaches in diagnostics, surveillance and alternative therapeutics”, we seek a post-doc with strong experience in microbial genomics to implement, disseminate and benchmark the LIN codes nomenclature system for genomic taxonomy of bacterial strains. We offer a 1-year contract (possibly extensible); the position is available from August 2023. The selected candidate will work in the group of Sylvain Brisse at Institut Pasteur and in collaboration with the BIGSdb-Pasteur project coordination (Federica Palma).
The research project builds on our recent work on the innovative strain genomic taxonomy system based on the core genome MLST Life Identification Number (LIN) approach (Hennart et al. 2022, https://doi.org/10.1093/molbev/msac135) implemented within the BIGSdb-Pasteur platform (https://bigsdb.pasteur.fr/klebsiella/cgmlst-lincodes/). We are looking for someone with strong expertise in genomic data handling but also with a strong interest in communication, dissemination and teaching, to: (i) Disseminate the LIN codes approach towards international surveillance networks and leading public health agencies; (ii) Help with analysis of large collections of genomes; (iii) Help develop novel LIN code taxonomies for novel bacterial or eukaryotic pathogens; and (iv) Contribute to a project to compare the LIN codes-based taxonomies with alternative classification systems.
The selected candidate will also contribute to genomic analyses of Kp genomes and the curation of the isolate and sequences database hosted in the BIGSdb-Pasteur platform in view of extending the LIN code taxonomic databases. He/she may also take part in a project aiming at benchmarking the cgLIN code approach with previously developed systems such as HierCC (https://enterobase.readthedocs.io/en/latest/features/clustering.html). He/she will work closely with the BIGSdb-Pasteur project manager to outreach and raise awareness in the scientific community on the suitability of this new method for surveillance of bacterial pathogens.
Missions
– Analyse microbial genome population structures and large genomic datasets to develop novel cgLIN code systems (bacteria, fungi, parasites), and contribute to scientific valorization of such projects
– Contribute to disseminate the LIN codes approach by reaching out to the international epidemiological surveillance community, including by developing training or demonstration material
– Curate and analyse genome and metadata in BIGSdb-Pasteur
– Compare the cgLIN code classifications with alternative approaches such as Hierarchical clustering (HierCC) implemented in EnteroBase
– Participate in the design and writing of scientific documentation and publications
– Participate to the Brisse group activities (lab meetings and other interactions)
Profile
– PhD in microbial genomics or equivalent with strong expertise in genomic data handling
– Excellent communication skills in written and oral English
– Autonomy in project management
– Strong interest for scientific dissemination and public health applications of microbial genomics such as genomic epidemiology and surveillance
– Experience with cgMLST and strain taxonomic approaches will be appreciated but is not required
Environment
The Biodiversity and Epidemiology of Bacterial Pathogens (BEBP) unit is a young and dynamic research lab focused on the diversity, evolution and epidemiology of bacterial pathogens of high public health importance: Klebsiella pneumoniae (Kp), which causes various types of infections including urinary tract, respiratory and blood infections; Bordetella pertussis, the agent of whooping cough; and Corynebacterium diphtheriae, the agent of diphtheria. We also host national reference laboratories. We study the links between the genotypic and phenotypic (ecology, colonization, transmission, virulence, antibiotic resistance, immune response) diversity of the strains within particular species and combine epidemiological surveillance, microbiology, genomics, proteomics, bioinformatics and immunological approaches as well as in-vivo and in-vitro models of infection.
This Brisse lab also develops and maintains widely used genomic libraries of bacterial isolates and strain nomenclatures that facilitate global collaborative surveillance and population biology of bacterial pathogens (https://bigsdb.pasteur.fr/). The extension of such activities is the focus of the present role.
Applications (a motivation letter, a full CV and references) should be sent to Sylvain Brisse (sylvain.brisse@pasteur.fr). Please apply at the latest on June 30 th, 2023.