WP3 Strategic analysis of the future perspectives for cooperation and coordination

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• WP3 Strategic analysis of the future perspectives
  for cooperation and coordination

Summary of the expert workshop on the European
Research Agenda (WP 3)
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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.

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• 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
• 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
• Antigenic diversity and variation
• Unculturable microorganisms
• Relation between pathogenic and non pathogenic
  related species
• Environmental reservoir

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• 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
• Secondary pathologies (eg cancer and autoimmune
  diseases) induced in the host
• Probiotics, role of the resident flora

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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
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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

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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

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Divining the Future of MicrobiologyA committe
convened to puzzle out where trends in
microbiology may lead provides some intriguing
projectionsBy 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)

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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

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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

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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

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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

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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