Genotyping of Pathogens and Public Health  

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

  Annual Report

The missions of platform Genotyping of Pathogens and Public Health (PF8) are (i) to provide scientific and technological support to microbiological surveillance laboratories and (ii) to perform research on the diversity and evolution of microbial pathogens (bacteria, viruses, parasites, fungi, and their vectors). Innovative genomics-based methods are developed and applied at large scales for molecular identification, strain tracking and evolution of pathogenic agents. PF8 collaborates mainly with national surveillance laboratories such as National Reference Centers (NRC) or hospital labs, and can be quickly mobilized for genotyping of large strain collections in case of epidemics.

Platform PF8 deploys four main types of activities: (1) Sequencing and genotyping services, including high reactivity in case of bio-emergency; (2) Collaborative research projects in the field of genotyping and population genetics of pathogens; (3) Technology-oriented research; (4) Research in microbial population biology.


Approx. 85,000 sequences and minisatellite (VNTR/MLVA) analyses were realized in 2009. PF8 is partner of numerous scientific teams and of more than 20 NRCs. Since April 2009, PF8 has been strongly mobilized for the genetic analysis of the novel reassortant swine-origin H1N1 influenzavirus (H1N1pdm), in collaboration with the two French National Reference Centers for Influenza.


Around thirty collaborative projects are currently running. These are funded by Institut Pasteur and by Institut de Veille Sanitaire (the French agency in charge of microbiological surveillance), or by external grants. Projects are selected through a call for proposals, open all year. Examples of projects are sequence-based genotyping of Clostridium difficile strains from French hospitals, analysis of Dengue viruses on several continents, or H. pylori worldwide diversity.


The platform performs R&D on innovative diagnostic and genotyping technologies, e.g. resequencing DNA arrays for detection of pathogens, and is involved in several projects using ‘next-generation’ sequencing for discovery of yet-unknown pathogens or genome-wide comparisons.

We develop bioinformatics tools, sequence and DNA arrays data analysis methods and statistical expertise. Web tools (;, beta-lactamase databases) allow global standardization of strain tracking.


We conduct research into the species and strain-level biodiversity and evolution of the bacterial pathogens Salmonella, Listeria, Klebsiella and Acinetobacter.

Keywords: pathogens, genotyping, public health, population genetics


Multilocus sequence typing databases provide a common language for strain tracking and evolutionary studies.


Brisse, S., C. Fevre, V. Passet, S. Issenhuth-Jeanjean, R. Tournebize, L. Diancourt, and P. Grimont. 2009. Virulent clones of Klebsiella pneumoniae: identification and evolutionary scenario based on genomic and phenotypic characterization. PLoS ONE 4:e4982.

Monfort, L., V. Caro, Z. Devaux, A. S. Delannoy, S. Brisse, and P. Sednaoui. 2009. First Neisseria gonorrhoeae genotyping analysis in france: identification of a strain cluster with reduced susceptibility to Ceftriaxone. J Clin Microbiol 47:3540-5.

Moodley, Y., B. Linz, Y. Yamaoka, H. M. Windsor, S. Breurec, J. Y. Wu, A. Maady, S. Bernhoft, J. M. Thiberge, S. Phuanukoonnon, G. Jobb, P. Siba, D. Y. Graham, B. J. Marshall, and M. Achtman. 2009. The peopling of the Pacific from a bacterial perspective. Science 323:527-30.

Ragon, M., T. Wirth, F. Hollandt, R. Lavenir, M. Lecuit, A. Le Monnier, and S. Brisse. 2008. A new perspective on Listeria monocytogenes evolution. PLoS Pathogens 4:e1000146.

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.

  Web Site

More informations on our web site

Activity Reports 2009 - Institut Pasteur
If you have problems with this Web page, please write to