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Project #2760
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#2760 : Pasteur International Bioresources Network (PIBnet) bioinformatics: whole-genome sequencing of microbial agents for disease surveillance, outbreak investigation, epidemiology and population biology
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Name of Applicant : Sylvain BRISSE
Date of application : 13-11-2015
Unit : Microbial Evolutionary Genomics
Location : Jacob – 5 – 10a
Phone : 3658
@ Mail : sbrisse@pasteur.fr

Project context and summary :

The PIBnet initiative is a joint effort by 15 National Reference Centers (NRC), 8 Collaborative Centers of World Health Organization, the Collection de l’Institut Pasteur & Cyanobacteria collection and the CIBU to modernize their activities, including collection management and microbial characterization approaches and technologies. Within this large concerted effort, a priority is to promote whole genome sequencing (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 at the end of 2016. The target volume is 10,000 genomes a year. On the bioinformatics level, this requires implementing fast data treatment tools, databases, genotyping schemes and methods to extract medically relevant information from genomic sequences (resistome, virulome).


Related team publications :
Bialek-Davenet S, Criscuolo A, Passet V, Delannoy-Vieillard A-S, Garin B, Le Hello S, Arlet G, Nicolas-Chanoine M-H, Decre D, Brisse S. 2014. Genomic definition of Klebsiella pneumoniae clonal groups reveals emergence of dual-risk hypervirulent and multiresistant strains. Emerging Infectious Diseases 20:1812-1820
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:e02309-14.
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.
Service Delivery
Project Manager : alexis.criscuolo@pasteur.fr
Project Type : Embedded
Status : In Progress
Publication : 10.1038/ng.3501;10.1038/srep30379;10.1038/nmicrobiol.2016.185;10.1038/ncomms15483;10.1016/j.syapm.2017.07.002;10.1099/ijsem.0.002065;10.1007/s10482-017-0926-3;10.3201/eid2309.170336;10.1128/genomeA.00222-18


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