Unit: Public Health (Platform)
Director: BRISSE Sylvain
The platform Genotyping of Pathogens and Public Health (PF8) collaborates with microbial surveillance laboratories (National Reference Centers - CNR, World Health Organization Collaborative Centers - WHOCC, hospitals) in the domains of genotyping, populations 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.
Creation and missions
The Platform was created in January 2005 and its laboratories were installed in October 2005. Its mission is to provide scientific and technological support in the domain of pathogen genotyping to French laboratories involved in microbial surveillance or with expertise on specific pathogens.
Access to our platform can take the form of (1) Paying service; (2) Direct scientific collaboration or (3) Collaborative projects selected through our calls for proposals.
Activities and expertise of the platform include:
DNA sequencing service;
Molecular typing of strains by standardized multilocus methods (MLST; VNTR-MLVA);
Comparative genomics or molecular identification of pathogenic strains using DNA array technologies;
Bio-statistics and bio-informatics support (conception of experiments to data analysis);
Scientific expertise in the domains of population genetics, phylogenetics, and evolution of infectious agents.
The platform Genotyping of Pathogens and Public Health has specific expertise and fast-reaction capacity, and benefits from technological infrastructure available in other platforms (see Pasteur Genopole platforms PF1, PF2, PF4, PF7).
Sequencing service (I. Iteman, R. Lavenir, A.-S. Delannoy, S. Brisse)
In 2005, 15,000 samples were sequenced for several CNR and other laboratories. The process ranging from reception of biological material (PCR or RT-PCR products) to result delivery takes 48 hours (24 h in case of extreme emergency). The service accepts small number of samples and is thus not meant to be a high throughput service. A robotized service is currently being created in parallel for higher throughput.
Influenza pandemic preparedness (I. Iteman, R. Lavenir, A.-S. Delannoy, S. Brisse)
Anticipating the possible need to test high numbers of samples, we have collaborated with the CNR for influenza for Northern France (S. van der Werf and J.T. Aubin) in order to adapt RT-PCR and sequencing protocols of eight genomic segments for H5N1 viral identification and typing.
Expertise in biostatistics and DNA arrays (G. Guigon)
We have finalized the statistical analysis of comparative genomics data of isolates of Bordetella pertussis, the agent of whooping cough. This project aimed to determine the temporal and spatial evolution of strains at the genomic level, after 50 years of intensive vaccination coverage in France. In parallel, we contributed to the development of a DNA array for the molecular identification of strains of the genus Bordetella (B. bronchiseptica, B. parapertussis et B. pertussis) associated with human respiratory infections. We contributed to the statistical and bioinformatics analysis of Plasmodium falciparum and Entamoeba histolytica transcriptomes. We also contributed to data analysis within several projects.
Affymetrix Resequencing DNA array for detection of pathogens and genetic elements involved in pathogenicity (I. Filliol, N. Berthet)
The goal of this project is to allow rapid identification of viral and bacterial pathogens and determination of their virulence and resistance gene content. A very high density (2.4 million spots per square cm) DNA array is developed and used. The array includes specific nucleotide sequences from 42 viral and 28 bacterial pathogens, and genetic elements (resistance and virulence genes, toxins). A universal extraction protocol from biological samples and whole genome amplification procedures are being developed.
Genome sequencing of serotype 1 Streptococcus pneumoniae (B. Fournier)
This project is conducted in collaboration with CNR for pneumococci at Hôpital Européen Georges Pompidou (L. Gutmann, E. Varon) and Pasteur Genopole Genomics Platform (PF1). DNA libraries are currently being constructed.
Data analysis software (S. Brisse)
A centralized network was created to give access to laboratories of the Pasteur campus to BioNumerics version 4.5 (Applied-Maths, Belgium, www.applied-maths.com). This software allows data storage and analysis of diverse types of genotyping information (sequences, VNTR/minisatellites, banding profiles, biochemical data, spoligotypes, ). A users group was created.
Keywords: Genotyping, Population genetics, Comparative genomics, Biostatistics, Pathogen