Project #2417
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#2417 : Whole-genome sequencing of microbial agents for disease surveillance, outbreak investigation, epidemiology and population biology
Topics :
Organisms :
Group :
Name of Applicant : Sylvain Brisse
Date of application : 03-11-2014
Unit : Microbial Evolutionary Genomics
Location : Jacob 5eme
Phone : 1040613658
@ Mail :

Project context and summary :

The PIBnet initiative is a joint effort by the above laboratories to modernize their activities, including collection management and microbial characterization approaches and technologies. Within this large concerted effort, a priority is to promote WGS as the major characterization approach of microbial agents for surveillance and outbreak investigation. Our ambition is to have shifted to WGS as a routine strain characterization method for epidemiological surveillance and outbreak investigation in the Institut Pasteur NRCs at the end of 2016. The target volume is 10 000 genomes a year. On the bioinformatics level, this requires implementing (1) fast data treatment tools and (2) Genotyping/classification schemes and methods to extract medically relevant information from genomic sequences (resistome, virulome).

Related team publications :
Bialek-Davenet et al 2014 Emerging inf Diseases Genomic definition of K. pneumoniae clonal groups
Vaux S, Criscuolo A, Desnos-Ollivier M, Diancourt L, Tarnaud C, Vandenbogaert M, Brisse S, Coignard B, Dromer F, Geotrichum Investigation G. 2014. Multicenter outbreak of infections by Saprochaete clavata, an unrecognized opportunistic fungal pathogen. mBio 5.
Fabre L, Zhang J, Guigon G, Le Hello S, Guibert V, Accou-Demartin M, de Romans S, Lim C, Roux C, Passet V, Diancourt L, Guibourdenche M, Issenhuth-Jeanjean S, Achtman M, Brisse S, Sola C, Weill FX. 2012. CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections. PloS one 7:e36995
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Project Type : Long
Status : Closed

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