Genotyping of Pathogens and Public Health


  HEADDr BRISSE Sylvain / sbrisse@pasteur.fr
  MEMBERSBERTHET Nicolas / DELANNOY-VIEILLARD Anne-Sophie / DIANCOURT Laure
Dr FOURNIER Bénédicte / GUIGON Ghislaine / Dr ITEMAN Isabelle / REINHARDT Anita


  Annual Report

Created in January 2005, the platform Genotyping of Pathogens and Public Health (PF8) collaborates with microbial surveillance laboratories such as National Reference Centers (CNR), World Health Organization Collaborative Centers and hospitals, in the domains of genotyping, population genetics, and pathogen microevolution. The platform also provides support in cases of bio-emergency. All pathogens, as well as their vectors, are considered: bacteria, viruses, parasites, fungi.

Our missions are (1) Sequencing and genotyping services, including high reactivity in case of major epidemics or bio-emergency; (2) Collaborative research projects in the field of population genetics and strain microevolution; (3) Technology-oriented research projects aiming at developing or evaluating new genotyping technologies.

SERVICES AND BIO-EMERGENCY

Approx. 20,000 sequences of PCR products from CNRs are realized each year for strain identification or antibiotic resistance/virulence characterization. The platform has also set up a minisatellite (VNTR/MLVA) system for fine strain typing.

Preparedness for H5N1 influenza virus pandemic has been set-up (coll. CNR Influenzae, Institut Pasteur, Paris). In the context of an unprecedented Chikungunya outbreak in the French island La Réunion, six complete genome sequences of Chikungunya virus were determined (coll. CNR Arbovirus, Institut Pasteur, Lyon; see PLoS Medicine, July 2006).

COLLABORATIVE RESEARCH PROJECTS

Twelve collaborative projects were established either through the first PF8-specific call for proposals in July 2006 or through external granting, e.g.: Escherichia coli antibiotic resistance from natural reservoirs; Salmonella enterica strain tracking; artesunate resistance surveillance in Plasmodium; Genotyping of C. neoformans. Microarray projects are developed for strain evolution and identification, e.g. for whooping cough strains or respiratory viruses.

TECHNOLOGICAL RESEARCH AND BIOINFORMATICS

An Affymetrix resequencing DNA array is being designed and validated for detection of pathogens and genetic elements involved in pathogenicity (NIH grant). The platform is evaluating the xMAP technology for SNP genotyping in bacteria. Bioinformatics developments include DNA array and sequence data analysis.

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  Web Site

More informations on our web site


  Publications

Publications 2006 of the unit on Pasteur's references database




Activity Reports 2006 - Institut Pasteur
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