Genotyping of Pathogens and Public Health  

  HEADBRISSE Sylvain, CARO Valérie /,
  MEMBERSDELANNOY-VIEILLARD Anne-Sophie (Engineer) / DIANCOURT Laure (Engineer) / GUIGON Ghislaine (Biostatistician) / PASSET Virginie (Technician) / THIBERGE Jean-Michel (Engineer)

  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. Innovative genomics-based methods are developed and applied at large scales for molecular identification, pathogen discovery, 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. 100,000 sequences and minisatellite (VNTR/MLVA) analyses were realized in 2010. PF8 is partner of numerous scientific teams and of > 20 NRC. In 2010, PF8 has been strongly mobilized for the genetic analysis of Chikungunya and Dengue in collaboration with the French National Reference Centers for Arboviruses.


Approximately twenty collaborative projects are currently running. Examples are sequence-based genotyping of antibiotic-resistant Escherichia coli and Staphylococcus epidermidis isolates, Listeria monocytogenes worldwide diversity, and analysis of emerging Dengue and Influenza viruses on several continents.


The platform performs R&D on innovative diagnostic and genotyping technologies, e.g. resequencing DNA arrays for detection of pathogens. Several projects for discovery of novel pathogenic agents, genome-wide characterization of pathogens, and population genomics of viruses and bacteria, have started since the acquisition in 2010 of our second-generation sequencer, Illuminas HiSEQ-2000.

We develop bioinformatics tools and data analysis methods and statistical expertise. Our web-accessible databases (;, 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, high throughput sequencing


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


  1. Berthet, N., A. Deletoile, V. Passet, G. C. Kennedy, J. C. Manuguerra, S. T. Cole, and S. Brisse. 2010. Reconstructed ancestral sequences improve pathogen identification using resequencing DNA microarrays. PLoS One 5:e15243.

  2. Dacheux, L., N. Berthet, G. Dissard, E. C. Holmes, O. Delmas, F. Larrous, G. Guigon, P. Dickinson, O. Faye, A. A. Sall, I. G. Old, K. Kong, G. C. Kennedy, J. C. Manuguerra, S. T. Cole, V. Caro, A. Gessain, and H. Bourhy. 2010. Application of broad-spectrum resequencing microarray for genotyping rhabdoviruses. J Virol 84:9557-74.

  3. 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.

  4. 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.

  5. 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.

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Activity Reports 2010 - Institut Pasteur
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