1. WP3 Strategic analysis of the future perspectives for cooperation and coordination Summary of the expert workshop on the European Research Agenda (WP 3)

2. Objectives of WP3 WP 3 and 4 are designed to lay the strategic foundations of joint and transnational activities. With regard to the scientific and technological issues, WP 3 Strategic analysis of the future perspectives for cooperation and coordination analyses the complementarity between the partner countries´ programmes (or programme areas), topics of common interest, new ideas for potential future cooperations, new demands/opportunities in the field, as well as overlaps/redundancies and gaps. To implement this step of networking, strategically oriented workshops of programme makers with leading scientists will be organised. Based on the outcome of these workshops, selected “rapporteurs” will formulate a European research agenda for pathogenomics-related research.

3. Annex I Pathogenomics: A Proposed European Research AGENDA The development of genomic technologies and bioinformatics to provide novel opportunities for studying life-threatening human pathogens with great potential of enhancing human health A: The microbes 1.Microbial ecology and populations 2.Metabolism and signalling 3.Evolution of microbial virulence and antibiotic resistance 4.Biofilm formation 5.Genome plasticity and gene pools 6.Antigenic diversity and variation 7.Unculturable microorganisms 8.Relation between pathogenic and non pathogenic related species 9.Environmental reservoir

4. B: Host-microbe interactions 1.In vivo pathogenesis of infections caused by bacterial and fungal microorganisms with the capacity of affecting human health 2.Mechanisms underlying breakage of epithelial and endothelial barriers (blood-brain; gut epithelium; pulmonary epithelium; placenta...) a.Receptors and cell surface structures of the host cell b.Bacterial cell surface structures c.Cell-cell communication 2.2 Metabolic interactions and adaptations of host cells and bacteria 3.Evasion of the host immune defences 4.Commensalism and nosocomial infections 5.Secondary pathologies (eg cancer and autoimmune diseases) induced in the host 6.Probiotics, role of the resident flora

5. C: Development and improvement of tools 1.Development of new bioassays for the identification of novel targets for therapy and vaccination 2.Novel diagnostic approaches 3.Metagenomics of microbial communities 4.New in vitro screening techniques 5.Bioluminescence (and other) imaging techniques to follow infections in vivo 6.Microarrays and proteomics of infected tissues 7.Animal models by transgene techniques 8.Establishment of strain and tissue collections 9.Databases and data analysis techniques

6. Priorities for the first call (Bonn April 05) What is pathogenomics? The application of global methods and genome based approaches to study + Bacterial and fungal human pathogens + Related non-pathogenic species + Host response to the pathogen Pathogenomics is not The study of viruses or parasites Random screening for antimicrobial compounds Research topics should include: Microbial community ecology, reservoirs, asymptomatic infections Commensalism / virulence transition Manipulation and exploitation of the host by the pathogen Evolution of microbial virulence, fitness and antibiotic resistance Regulatory networks and metabolism of the pathogen in the host

7. Objectives of the meeting Prospective discussion between leading scientists in the field of Pathogenomics Define what is Pathogenomics To identify major trends in the field of pathogenomics To publish the conclusion as a research agenda To refine priorities for the first call

8. Divining the Future of Microbiology A committe convened to puzzle out where trends in microbiology may lead provides some intriguing projections By Christon J. Hurst ASM News June 2005 Understanding microbial interrelationships and interactions: microbial ecology communities & metagenome Health of humans and of the world: infectious dose response, agricultural use of antibiotics, new vaccines, interaction between humans and microbes, infections and cancer, evolution and emergence of pathogens, survival of pathogens in the environment. Microbiology as a whole: … microbial life beyond our planet. Biology as a whole: co-evolution and its immunological significance (horizontal gene transfer)

9. Organization of the meeting Section 1: Host-microbe interaction (7 speakers) Section 2: technological developments (4 speakers) Section 3: The microbes (8 speakers) Section 4: Industries and Pathogenomics (3 speakers) Section 5: Transversal activity (3 speakers) Group discussion on each theme

10. The subject of the talks Description of the research activity in the country with examples related to Pathogenomics High quality of the talks with interesting highlights on specific projects Difficulty to define priorities Better definition of new fields through new technological approaches

11. Priority in pathogenomics Need to improve interactions with other disciplines –Mathematics : system biology –Physics : in vivo imaging, fluorescent methods, single cell and single molecule studies –Chemistry : identification of (new) functions of “unknown” proteins Need for technological innovation (example in proteomics) Importance of animal models : –Alternative model to the mouse model of infection –Use of RNAi to study gene function –Transgenic mice (humanized) and xenografts

12. Outcomes of the meeting Interesting but not exhaustive view on the research activity in the field of Pathogenomics in the ten participating countries Several new themes, which deserved to be considered in the future calls. Some ambitious goals which will require cooperation at the European level Importance of the cooperation with the industry Difficulty to define the specificity of Pathogenomics, in a context where study of infectious diseases integrates focused and global approaches Difficulty to go behind these general statements in the frame of a meeting of 25 scientists

13. The next step To constitute a smaller discussion group of 6 to 8 participants to prepare the final agenda To better define the specificity of Pathogenomics To combine discussion with WP4 “analyses the complementarity between the partner countries´ programmes (or programme areas), topics of common interest, new ideas for potential future cooperations, new demands/opportunities in the field, as well as overlaps/redundancies and gaps“.  Need to extend the duration of wp3 to 24 months