Genotyping of Pathogens and Public Health  

  HEADBRISSE Sylvain CARO Valérie /
  MEMBERSDIANCOURT Laure (Engineer) / GUIGON Ghislaine (Biostatistician) / THIBERGE Jean-Michel (Engineer) / TRAN Coralie (Technician)

  Annual Report

Created in January 2005, the main mission of platform Genotyping of Pathogens and Public Health (PF8) is to supply a scientific and technical support for the laboratories of surveillance or microbiological expertise. This support concerns the domains of the infectious diseases, in particular in the help to the molecular identification and to the molecular typing of the pathogenic agents in cause. The PF8 brings to laboratories addressed a simple access to the genomics thanks to varied technologies. PF8 then collaborates with national microbial surveillance laboratories such as French National Reference Centers (NRC), the Laboratory for Urgent Response to Biological Threats, called in French Cellule d’Intervention Biologique d’Urgence (CIBU), World Health Organization Collaborative Centers and hospitals, in the domains of genotyping, population genetics, and pathogen microevolution. The platform provides support in cases of bio-emergency, and gives an ability to react (of the order of one in some working days) with an expertise, accepting streams of very variable samples in term of number. 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 (through a PF8-specific call for public health oriented research program) of in the field of genotyping, population genetics and strain microevolution; (3) support in terms of analysis and management of the data of sequences generated (creation of database for example), by the way notably of its expertise of the software BioNumerics, and data repositories (MLST interface and MLVA net); (4) support in bio-statistical and bio-informatic with the presence of an engineer bio-statistician and bio-informatician within the team (5) Technology-oriented research projects aiming at developing or evaluating new genotyping technologies.


Approx. 24,000 sequences of PCR products from NRC are realized in 2007 for help in molecular identification and molecular typing of the different isolates analyzed by the NRC. The platform has also set up a minisatellite (VNTR/MLVA) system for highly discriminative strain typing, representing around 5,000 sequences. The platform is also prepared in case of H5N1 influenza virus pandemic with tested protocols for sequencing viral strains (coll. NRC Influenzae, Institut Pasteur, Paris).


Twenty collaborative projects were established either through the two PF8-specific calls for proposals (2006-07 and 2007-2008) or through external granting, e.g.: Escherichia coli antibiotic resistance from natural reservoirs; genotyping of Neisseria gonorrhoae; genetic exchanges analysis in Human Enterovirus. Around 50,000 sequences were performed in the context of the different collaborative projects in 2007. Collaborative microarray projects are also developed for strain evolution and identification, or through bioinformatic development in comparative genomic studies.


The platform presents activities of research and development directed to new less expensive, more successful, faster, innovative technologies of identification and molecular characterization of the microbial pathogenic agents (e.g. evaluation of the xMAP technology for SNP genotyping in bacteria, validation of Affymetrix resequencing DNA array for detection of pathogens).

PF8 receives financial support from Institut Pasteur and InVS (Institut de Veille Sanitaire, French agency in charge-among other missions- of microbiological surveillance)

Keywords: pathogens, genotyping, public health



- Lecoeur, H., Buffet, P., Morizot, G., Goyard, S., Guigon, G., Milon, G., Lang, T. 2007. Optimization of Topical Therapy for Leishmania major Localized Cutaneous Leishmaniasis Using a Reliable C57BL/6 Model. PLoS Negl Trop Dis 1(2): e34.

- Schuffenecker, I., I. Iteman, A. Michault, S. Murri , L. Frangeul, M.-C. Vaney, R. Lavenir, N. Pardigon, J.-M. Reynes, F. Pettinelli, L. Biscornet, L. Diancourt, S. Michel, S. Duquerroy, G. Guigon, M.-C. Frenkiel, A.-C. Bréhin, N. Cubito, P. Desprès, F. Kunst, F. A. Rey, H. Zeller, and S. Brisse. 2006. Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak. PLoS Med 3:e263.

- V. Caro, D. Hot, G. Guigon, C. Hubans, M. Arrivé, G. Soubigou, G. Renauld-Mongénie, R. Antoine, C. Locht, Y. Lemoine, N. Guiso. 2006. Temporal analysis of French Bordetella pertussis isolates by comparative whole-genome hybridization.Microbes Infect. Jun 6.

- Weber, C., G. Guigon, C. Bouchier, L. Frangeul, S. Moreira, O. Sismeiro, C. Gouyette, D. Mirelman, J. Y. Coppee, and N. Guillen. 2006. Stress by Heat Shock Induces Massive Down Regulation of Genes and Allows Differential Allelic Expression of the Gal/GalNAc Lectin in Entamoeba histolytica. Eukaryot Cell 5:871-5.

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Activity Reports 2007 - Institut Pasteur
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