FORESIGHT STUDY Future Trends and Challenges in Pathogenomics

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FORESIGHT STUDYFuture Trends and Challenges in
Pathogenomics

• JUDITH SIMON SVEN POMPE
• PROGRAMME GROUP MUT

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OBJECTIVES

• Overview on future trends and challenges in
  research on human-pathogenic microorganisms
  (bacteria fungi)
• Developments in basic research
• Diagnostics therapy
• Public health
• Research co-operations
• Technology transfer market development

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STRUCTURE

• Methods
• Literature internet research
• Preliminary assessment
• Expert survey
• Results
• Research foci
• Methods, diagnostics therapeutics
• Challenges for research
• Public health
• Co-operations
• Market development technology transfer
• Recommendations
• Discussion

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METHODS

• Triangulation combination of literature and
  internet research with expert survey interviews
• "Triangulation ... reduces the risk of
  systematic distortions inherent in the use of
  only one method.

Maxwell 1998
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METHODS Literature Research

• Databases
• PubMed
• Medline
• Important scientific journals
• Keywords combinations
• pathogenomics, infectious disease, public health,
  bacteria, fungi, bioweapons, bioterrorism and/or
  human-pathogenic
• Focus on reviews
• Specialised articles on particular
  micro-organisms were excluded

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METHODS Internet Research

• Internet research on national international
• Surveys
• Experts
• Institutions
• Networks

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METHODS Preliminary Assessment

• Addressee
• 62 members of the ERA-NET PathoGenoMics from 17
  countries
• Questions
• Contact partners and national institutions
• National main foci in microbiological research
• National newly emerging hot topics in
  pathogenomics
• Existing foresight studies on pathogenomics or
  related subjects

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METHODS Expert Survey

• Development and application of questionnaires
  with questions on
• Basic research
• Future prospects in diagnostics therapy
• Strengths and weaknesses in research
• Important cooperations and projects
• Technology transfer market development
• Public health

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METHODS Expert Survey
A total of 329 experts was selected and contacted.
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METHODS Expert Survey
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RESULTS Research Foci

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RESULTS Trends in Methodology

• Improvement of conventional methods
• Microscopy
• Serology
• Novel technologies
• High-throughput analyses
• Real time approaches
• Bioinformatics
• Omics

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RESULTS Trends in Omics

• Systemic approach

Proteomics
Genomics
Transcriptomics
Metabolomics
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RESULTS Trends in Omics

• Understanding of
• Infection
• Pathogenesis

Genomics Transcriptomics Proteomics Metabolomics
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RESULTS Trends in Diagnostics

• Use of novel technologies
• PCR
• Sequence-based identification
• Molecular strain typing

• But tools need to be more ...
• rapid
• sensitive
• specific
• robust
• affordable

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RESULTS Challenges for Therapeutics

• Extension of databases discovery of molecular
  strategies
• In order to ...
• enable comprehensive statistical and comparative
  analyses
• standardise validate diagnostics
• find novel targets
• develop new vaccines
• innovate antibiotic intervention
• individualise therapy

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RESULTS Challenges for Research

• Multidisciplinary research on
• Ecology environment
• Population dynamics
• Evolution taxonomy
• Epidemiology
• Risk assessment

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RESULTS Challenges for Research

• Basic research on infection pathogenesis
• Analysis of host-pathogen-interaction
• Identification of signaling pathways
• Analysis of metabolic interactions
• Identification of virulence factors
• Target identification
• ...

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RESULTS Public Health - Risks

• Major risks are
• Multidrug resistance (cf. tuberculosis)
• Nosocomial infections
• Bioterrorism

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RESULTS Public Health Measures

• Surveillance systems
• Action plans for emergencies
• Vaccination strategies
• Rapid and early diagnostics

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RESULTS Co-operations

What are the most important research partners for
scientists in pathogenomics?
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RESULTS Market Development Technology
Transfer

• Barriers
• High RD costs
• Limited market size for vaccines and antibiotic
  products compared to the market for diseases of
  civilisation

• Opportunities
• Public-private partnerships
• Subcontracting with SMEs for preclinical studies
• Public funding for orphan drugs

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RECOMMENDATIONS

• 1. Establish a European surveillance system
• 2. Reduce the misuse of pesticides in
  agriculture and animal technology
• 3. Create a European Competence Center for
  epidemiological research and modelling
• 4. Create an RD programme that is specifically
  tailored to support public-private partnerships
• 5. Create structures for early warning and rapid
  response to emergencies

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RECOMMENDATIONS

• 6. Develop comparative risk assessment
  strategies for setting national health
  priorities
• 7. Reconsider work-sharing between research
  institutes and universities
• 8. Foster cooperations between microbiological
  researchers and clinicians
• 9. Foster inclusion of ecological aspects into
  microbiology
• 10. Improve transparency about the function of
  different networks on pathogenomics
• 11. Conduct a study on industrial research
  objectives and economic interests

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• THANK YOU VERY MUCH
• FOR YOUR ATTENTION!
• The complete report on
• FUTURE TRENDS AND CHALLENGES
• IN PATHOGENOMICS
• will soon be available at
• http//www.pathogenomics-era.net

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RECOMMENDATIONS

• 1. Establish a European surveillance system
• 2. Reduce the misuse of pesticides in
  agriculture and animal technology
• 3. Create a European Competence Center for
  epidemiological research and modelling
• 4. Create an RD programme that is specifically
  tailored to support public-private partnerships
• 5. Create structures for early warning and rapid
  response to emergencies
• 6. Develop comparative risk assessment
  strategies for setting national health
  priorities
• 7. Reconsider work-sharing between research
  institutes and universities
• 8. Foster cooperations between microbiological
  researchers and clinicians
• 9. Foster inclusion of ecological aspects into
  microbiology
• 10. Improve transparency about the function of
  different networks on pathogenomics
• 11. Conduct a study on industrial research
  objectives and economic interests