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, 28 29 octobre 2011
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
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
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 6236 -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
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,
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 4 454 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* 1 - - NGS 28 31 36 4 Since 2011 6 7 16 - Total 42 32 36 4 Sanger (Collaboration Genoscope*)
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 10002100 Bioanalyzer Thermo Agilent Production (in arrays) Mouse Human Bacteria Transcriptomic 35 350 150 Genomic - - 150
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 3000 + LTQ XL ETD 5385.3238 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) 4368.3748 5100.3707 5000 2837.5608 6260.0803 4000 3000 5000 7000 9000 10475.6408 9235.3366 8883.2166 8333.9548 9546.4330 9072.7371 8000 9750.3232 7164.0489 6000 7877.6343 6417.6725 5757.2420 5236.5759 4535.7432 4771.6593 4000 4873.4760 4187.7715 3939.3056 2693.2360 1000 0 2000 3582.1413 2411.8066 2000 3130.1487 3000 10000 11000 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
Plateformes IFR 48 : Plateform MicroBioGénomique : BioInformatics Analysis Power available Current Server 8 servers unix Dell Apple Futur Server Altix UV 100: - 144 cores - 768 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)
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
demiological clinical cohorts of 700,000 people in Sene URMITE, UMR IRD 198/CNRS 6236)
Travaux communs IFR48 2008-2011 total : 71 18 1 16 UMR 190 1 9 11 2 4 UMR 6632 UMR 6236 1 3 1 UMR 6098 AP-HM UMR 190, UMR 6236, 3 AP-HM
Séminaires IFR 48 :2008-2009-20102011
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
Bilan recherche Classification en France Période 2008-2011 Nice Montpellier Tropical medicine Nîmes Marseille France % de Marseille 2 168 3 100 743 13,46 HIV and AIDS 32 54 6 85 640 13,28 Microbiology 88 360 25 572 5 343 10,71 Virology 32 270 5 232 2 475 9,37 Antibiotics 62 76 21 100 1 215 8,23 Parasitology, Mycology 12 273 3 98 1 258 7,79 Vaccine 28 137 4 101 1 957 5,16 Entomology 13 171 0 0 787 0,00 3 10 Health-care-associated infections 0 0 0 30,00
Bilan, recherche Classification of the first 10 European cities : publications in ID&TM Rank City Volume of publications from 2008-to 2011 1 London 4278 2 Paris 2018 3 Madrid 1229 4 Geneva 1040 5 Barcelona 976 6 Oxford 946 7 Amsterdam 946 8 Copenhagen 810 9 Liverpool 800 10 Marseille 631 11 Munich 375
Bilan, recherche Classification of the first 10 European cities : publications in Microbiology and Virology Rank City Volume of publications from 2008-to 2011 1 Paris 3029 2 London 2665 3 Madrid 2015 4 Berlin 1363 5 Barcelona 1299 6 Amsterdam 1280 7 Copenhagen 1028 8 Munich 987 9 Oxford 934 10 Marseille 793 11 Geneva 778
Bilan, recherche Classification of the first 10 European cities: publications in parasitology, mycology and entomology Rank City Volume 2011 1 London 804 2 Paris 660 3 Madrid 470 4 Geneva 383 5 Oxford 375 6 Berlin 345 7 Barcelona 321 8 Copenhagen 319 9 Amsterdam 216 27 Marseille 113 of publications from 2008-to
13 leaders IH 30 Impact Factor sur 2010-year to date Directeurs Unités 1RAOULT Didier URMITE - UMR 6236 - D198 2HENRISSAT Bernard 3MALISSEN Bernard 4CAMBILLAU Christian 5FOUNIER PierreEdouard 6DRANCOURT Total Publi h-index total 160 81 41 68 CIML 33 65 18 53 13 45 Michel 37 40 7BOURNE Yves AFMB Inserm UMR 891 9 38 8MEGE Jean-Louis 22 34 9LA SCOLA Bernard 23 32 35 32 UMR S912 - ORS 16 32 UMR-IRD 190 43 31 9 31 10ROGIER Christophe 11MOATTI Jean-Paul 12De Xavier LAMBALLERIE 13PONTAROTTI Pierre LATP UMR - CNRS 6632
Valorisation Brevets 2008-2011 : 22 (Montpellier 11, Nice 0, Nîmes 0) Une PME: InoDiag (Groupe Elitech) Une start-up: Amikana Biologics
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
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
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.
Citation reports Raoult D. 81 Malissen B. 64
Cambillau C. 53 Fournier PE. 45
Henrissat B. 43 Drancourt M. 40
Gorvel JP. 40 Bourne Y. 38
Brouqui P. 36 Mège JL. 34
La Scola B. 32 Moatti JP. 32
De Lamballerie X. 31