Post-doc in Genomic Taxonomy of Bacterial Pathogens and Genomics of Outbreaks

Job description

We seek a post-doc or bioinformatician with experience in microbial population genomics to develop and benchmark novel strain subtyping schemes and nomenclature systems for genomic subtyping of bacterial pathogens. We offer a 1-year contract (possibly extensible); the position is available from July 2024. The selected candidate will work in the group of Sylvain Brisse and at the Biological Resources Center of Institut Pasteur (CRBIP), within the BIGSdb-Pasteur project team and with external collaborators of the project CENTAUR – “Creating and refining whole-genome and core-genome typing schemes for pathogen surveillance”, coordinated by Mario Ramirez (University of Lisbon, Portugal; https://imm.medicina.ulisboa.pt/people/mario-ramirez/#intro). This project is funded via the ISIDORe European infrastructure project (https://isidore-project.eu/) aiming at developing integrated services to fight against infectious disease outbreaks.

Scientific background and purposes

Surveillance, epidemiological tracking and outbreak investigation of microbial pathogens was revolutionized by the power of genomics, allowing the identification of chains of transmission or of new variants with altered virulence or transmissibility. The project aims at addressing remaining analytical challenges in the use of bacterial genomics, by automatizing the development of genotyping methods, tools and databases. Gene-by-gene approaches, such as whole- or core-genome multilocus sequence typing (wg/cgMLST), leverage genomic information while building on MLST, the standard for microbial typing in most bacterial species. Public repositories allow a common nomenclature, continuous distributed surveillance and pandemic or multi-country outbreak responses, leading international agencies to adopt wg/cgMLST for surveillance. Still, developing new, high-quality genotyping schemes (i.e., dedicated wg/cgMLST methods) for emerging bacterial pathogens, and integrating their usage in nomenclature platforms, remains a challenging barrier. CENTAUR gathers leading groups in wg/cgMLST development and application to develop tools that will facilitate the creation and adoption of genotyping tools, readily applicable to a bacterial pathogen X. By leveraging coding sequences, these tools will also provide a potential link to expressed antigens and possible clues into specific phenotypes of any emerging clones, which may in turn contribute to design prevention or therapeutic strategies. We will select diverse key priority bacterial models: Klebsiella pneumoniae (a prominent multidrug resistant hospital pathogen), Bordetella pertussis (agent of whooping cough) and Neisseria gonorrhoeae (agent of gonorrhoea). The outputs of CENTAUR will allow ISIDORe to offer services to quickly detect and track emerging bacterial pathogens.

Missions

We are looking for someone with expertise in genomic data handling, to: (i) Use and/or develop bioinformatics tools to create schemes, i.e., lists of gene loci carefully selected for genotyping purposes; (ii) Implement the genotyping schemes in international genotyping platforms, including BIGSdb-Pasteur (https://bigsdb.pasteur.fr/) and Chewie-NS (https://pubmed.ncbi.nlm.nih.gov/33068420/ ); and (iii) Benchmark these tools for outbreak investigations and strain nomenclature purposes. This work will involve the analysis of large collections of bacterial genomes, the comparison and integration of different systems to genotype bacterial strains, and further implementation of life identification number (LIN) codes-based strain taxonomies (https://bigsdb.pasteur.fr/klebsiella/cgmlst-lincodes/).

In addition, the position role may also:

– Contribute to disseminate the LIN codes approach by reaching out to the international epidemiological surveillance community

– Curate and analyse genome and metadata in BIGSdb-Pasteur

– 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, or Masters in bioinformatics with experience in genomics

– Good 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 and its collaborative BIGSdb-Pasteur group in the CRBIP focus on the diversity, evolution and epidemiology of bacterial pathogens of high public health importance, including: Klebsiella pneumoniae (Kp), which causes various types of multidrug resistant infections; Bordetella pertussis, the agent of whooping cough; and Corynebacterium diphtheriae, the agent of diphtheria. We study the links between the genotypic and phenotypic (ecology, colonization, transmission, virulence, antibiotic resistance, immune response) diversity of the strains within species and combine epidemiological surveillance, microbiology, genomics and bioinformatics.

The group 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.

Contact: Applications (a motivation letter, a full CV and references) should be sent to Sylvain Brisse (sylvain.brisse@pasteur.fr). The selected candidate could start as early as July, 2024. Deadline for application is end of June, but please apply as soon as possible, as the selection process may begin before the deadline.