Forces et Faiblesses de la recherche en microbiologie à Marseille

Transcription

1 Forces et Faiblesses de la recherche en microbiologie à Marseille Michel Drancourt / Jean-Louis Mège URMITE CNRS UMR 6236, IRD198, IFR 48 IHU POLMIT Marseille Conseil Scientifique Infectiopole SUD Arles, octobre 2011

2 Contexte: création de l IHU Marseille IBISA IRT, Lyon Drug screening IHU BUILDING HIA Laveran, Marseille Morphology Proteomic IRD Montpellier P3A3 Lab cell culture arthopods Structural Genomics IBiSA MicroBioGenomic SOUTH NETWORK SENEGAL Immunophenomics ALGERIA CHU, Nice Immunomonitoring

3 Contexte: Creation of RTRS, 2007 Government, regional public administration EPST private partners NICE MONTPELLIER MARSEILLE Budget: 1.6 m Grants: Master, PhD and Postdocs: 0.9 m Platforms: 0.6 m Other : 0.8 m Infectiopôle Sud

4 Contexte: IFR48 «Infectiopole: de la molécule au malade» Hôpital Instruction d des Armé es A. Laveran: - Unité 7 Campus Saint -Charles - Unité 5:Equipe EBM, UMR 6632 CampusPharo - Unité3 :Institut de la M édecine Tropicale du Service de Santé des Armées (IMTSSA) UMR MD3 CampusTimone -Unité1 :URMITE, UMR Unité4 :Unitédes Virus Emergents UMR 190 -Unité6 :Assistance Publique Hôpitaux de Marseille CampusLuminy -Unité 2:Architecture et Fonction des Macromol écules Biologiques, AFMB UMR 6098

5 Plateformes IFR 48 : Culturomics Platform, Collection de souches de l Unité des Rickettsies CSUR (PE. Fournier), World Data Centers for Microorganism WDCM875 2 NSB3 laboratories housing, 14 working hoods and 2 boxes (animals) Shell-vial technique Cells: Cells lines (embryonic, cancerous,..) Fibroblasts, Endothelial Macrophages unknown Origin: human, animals, insects, Amoebae Legionella sp. (including LLAPs) Bosea sp., Afipia sp. The shell vial technique: Inoculation Centrifugation Washing Unique cell lines : human, mamal, insect,

6 Plateformes IFR 48 Plateform MicroBioGénomique : Sequencing & Genomic Sequencing Technologies Available Sanger Sequencing Next-Generation Sequencing STAFF Permanent C. Robert IR (Aix-Marseille II) T. NGuyen Tech (AP-HM) R. Rivet Tech (Aix-Marseille II) Applera ABI 3130 LifeTechnologies GS FLX Titanium SOLiD Roche LifeTechnologies Activities Genome Finishing Sanger Genome Sequencing Metagenomic NGS Bacterial 16S Diversity RNAseq (in developpment) Non-Permanent Q. Leroy IE (Aix-Marseille II) S. Fontaine Stagiaire (ESIL) Production Bacteria Virus MetaGenomes 16S diversity 15* NGS Since Total Sanger (Collaboration Genoscope*)

7 Plateformes IFR 48 :Plateform MicroBioGénomique : Transcriptomic & Microarray Transcriptomic & Microarray technologies Available Microarray QPCR RNA Quality Control STAFF Non-Permanent Q. Leroy IE (Aix-M II) A. Ben Amara Thesard Microarray Solution Agilent ABI prism 7900HT LifeTechnologies Activities Host transcriptomic Pathogen transcriptomic Pathogen comparative genomic Bacterial exploration (in developpment) RNAseq (in developpment) Nanodrop Bioanalyzer Thermo Agilent Production (in arrays) Mouse Human Bacteria Transcriptomic Genomic

8 teformes IFR 48 : Proteomics plateform Image Acquisition Spot cutter Staff Mass spectrometry Gel-based approches S. AZZA IR (Aix-Marseille II) M. KOWALCZEWSKA IE (AixMarseille II) B. AMPHOUX Tech (APHM) MALDI-TOF Autoflex nanolc MS/MS Ultimate LTQ XL ETD Intens. [a.u.] Typhoon FLA 9000 EXQuest Spot Cutter Mass spectrometry P. DECLOQUEMENT Ingénieur (APHM) C. FLAUDROPS Ingénieur (APHM) C. COUDERC Ingénieur (APHM) N. ANDERSON Ingénieur (APHM) m/z Activities Bacteria Viruses Protein map Rickettsiae, Nanon, T. whipplei, C. Burnetii, B. henselae Mimivirus, Marseillevirus Immunoproteomics Rickettsiae, Nanon, T. whipplei, B. henselae, C. burnetii, Mimivirus, Spoutnik, D. massiliae, F. tularensis, Marseillevirus Comparative proteomics (DIGE) R. prowazekii, C. burnetii, B. henselae, Borrelia, Nanon, Y. pestis Mimivirus Posttransionnal modifications (PTMs) Rickettsiae, Nanon Mimivirus, Marseillevirus Biotyping The data base of 4500 bacteria, 300 eucaryotes infériors, 200 eucaryotes superiors, 24

9 Plateformes IFR 48 : Plateform MicroBioGénomique : BioInformatics Analysis Power available Current Server 8 servers unix Dell Apple Futur Server Altix UV 100: cores Go Memory -48 To Hard Drive SGI Assembling Server STAFF Permanent GS FLX Titanium Cluster 454 Roche G. Fournous K. El Karkouri M II) G. Gimenez S. Buffet A. El Filali Genome Assembly / Annotation Phylogeny Metagenomics Primer and Probe Design Transcriptomics / Microarray Comparative Genomics IR (CNRS) IE (AP-HM) IE (CNRS) Non-Permanent F. Armougom Activities IR (AP-HM) IR-Dr (Aix- IR (IRD)

10 Insectarium : ticks lice - fleas 5 TICK species including infected colonies feedingon 6th floor Animal Room. 130 m2 Scientific coordinator Pr Ph Parola HDR (team 5) C Socolovschi (Autorisation Experimentation Animale) 2 techniciens LICE: human body louse Pediculus humanus humanus FLEAS: Ct. felis felis s feeding through membranes

11 demiological clinical cohorts of 700,000 people in Sene URMITE, UMR IRD 198/CNRS 6236)

12 Travaux communs IFR total : UMR UMR 6632 UMR UMR 6098 AP-HM UMR 190, UMR 6236, 3 AP-HM

13 Séminaires IFR 48 :

14 IFR 48 et Ecole Doctorale Organigramme : J.L MEGE dirige une équipe de recherche dans l UMR 6236, est membre du Bureau IFR 48 et Co-Directeur de l Ecole Doctorale des Sciences de la Vie et de La Santé (62) Les séminaires IFR48 sont intégrés dans le parcours des PhD Les séminaires IFR48 juniors sont le lieu du Comité de Thése

15 Bilan recherche Classification en France Période Nice Montpellier Tropical medicine Nîmes Marseille France % de Marseille ,46 HIV and AIDS ,28 Microbiology ,71 Virology ,37 Antibiotics ,23 Parasitology, Mycology ,79 Vaccine ,16 Entomology , Health-care-associated infections ,00

16 Bilan, recherche Classification of the first 10 European cities : publications in ID&TM Rank City Volume of publications from 2008-to London Paris Madrid Geneva Barcelona Oxford Amsterdam Copenhagen Liverpool Marseille Munich 375

17 Bilan, recherche Classification of the first 10 European cities : publications in Microbiology and Virology Rank City Volume of publications from 2008-to Paris London Madrid Berlin Barcelona Amsterdam Copenhagen Munich Oxford Marseille Geneva 778

18 Bilan, recherche Classification of the first 10 European cities: publications in parasitology, mycology and entomology Rank City Volume London Paris Madrid Geneva Oxford Berlin Barcelona Copenhagen Amsterdam Marseille 113 of publications from 2008-to

19 13 leaders IH 30 Impact Factor sur 2010-year to date Directeurs Unités 1RAOULT Didier URMITE - UMR D198 2HENRISSAT Bernard 3MALISSEN Bernard 4CAMBILLAU Christian 5FOUNIER PierreEdouard 6DRANCOURT Total Publi h-index total CIML Michel BOURNE Yves AFMB Inserm UMR MEGE Jean-Louis LA SCOLA Bernard UMR S912 - ORS UMR-IRD ROGIER Christophe 11MOATTI Jean-Paul 12De Xavier LAMBALLERIE 13PONTAROTTI Pierre LATP UMR - CNRS 6632

20 Valorisation Brevets : 22 (Montpellier 11, Nice 0, Nîmes 0) Une PME: InoDiag (Groupe Elitech) Une start-up: Amikana Biologics

21 Bilan, recherche Analyse des forces/faiblesses FORCES: Science: Infectious diseases, microbiology, virology Leaders: 10 out of 50 highest publishers in France in the domains Tools & platformes: Culture outstanding Tools & platformes: Genomic: very good (1 ERC Grant) Sampling/cohorts: Cohorts, largest in Africa, many series (world largest), travellers (soldiers!) Sampling/cohorts: Kits Physiopathology: Good question, rising from physicians Physiopathology: Large cohort of single diseases (WD, Q fever) Social sciences: Anthropology (Paleomicrobiology), Ethics, Economy FAIBLESSES: Parasitology, mycology Entomology Health-care associated infections Translation vers l entreprise

22 Objectifs, recherche 1 Infectious Diseases, Microbiology: Goal going from 9-10th to 7-8th rank in Europe 2 Parasitology, Mycology, Entomology: Goal going to the 15th 20th rank in Europe 3 Health-care associated infections: Ranking 20th in Europe 4 Valorisation: 10 patents a year and 5-10 products in 10 years

23 Politique incitative domaine de la parasitologie 1 Création d un poste en mycologie recherche : niveau international. 2 Création d un poste en parasitologie diagnostic en parasitologie diagnostic : annonces Lancet / NEJM. 3 Création d un poste en épidémiologie des maladies parasitaires et en métagénomique virale (partenariat EFS). 4 Accueil jeunes équipes : ATIP/Avenir ou chaires d excellence.

24 Citation reports Raoult D. 81 Malissen B. 64

25 Cambillau C. 53 Fournier PE. 45

26 Henrissat B. 43 Drancourt M. 40

27 Gorvel JP. 40 Bourne Y. 38

28 Brouqui P. 36 Mège JL. 34

29 La Scola B. 32 Moatti JP. 32

30 De Lamballerie X. 31