FORESIGHT STUDY Future Trends and Challenges in Pathogenomics JUDITH SIMON & SVEN POMPE PROGRAMME GROUP MUT

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 OBJECTIVES

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 STRUCTURE

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.“ METHODS Maxwell 1998

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 METHODS: Literature Research

Internet research on national & international –Surveys –Experts –Institutions –Networks METHODS: Internet Research

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 METHODS: Preliminary Assessment

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 METHODS: Expert Survey

A total of 329 experts was selected and contacted.

METHODS: Expert Survey Table 1: Reply & return rates

RESULTS: Research Foci

RESULTS: Trends in Methodology Improvement of conventional methods – Microscopy – Serology Novel technologies – High-throughput analyses – Real time approaches – Bioinformatics – Omic‘s

RESULTS: Trends in Omic`s Systemic approach Genomics Proteomics Transcriptomics Metabolomics

RESULTS: Trends in Omic`s Genomics Transcriptomics Proteomics Metabolomics Understanding of: Infection Pathogenesis

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

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

RESULTS: Challenges for Research Multidisciplinary research on –Ecology & environment –Population dynamics –Evolution & taxonomy –Epidemiology –Risk assessment

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 –...

Major risks are –Multidrug resistance (cf. tuberculosis) –Nosocomial infections –Bioterrorism RESULTS: Public Health - Risks „ Infectious diseases account for [...] 25 % of global deaths (over 14 million deaths annually)“ (WHO 2000)

Surveillance systems Action plans for emergencies Vaccination strategies Rapid and early diagnostics RESULTS: Public Health Measures

RESULTS: Co-operations What are the most important research partners for scientists in pathogenomics? Table 2: Co-operations and global players (N=30)

Barriers –High R&D costs –Limited market size for vaccines and antibiotic products compared to the market for diseases of civilisation Opportunities –Public-private partnerships –Subcontracting with SME`s for preclinical studies –Public funding for orphan drugs RESULTS: Market Development & Technology Transfer

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 R&D programme that is specifically tailored to support public-private partnerships 5. Create structures for early warning and rapid response to emergencies 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 RECOMMENDATIONS

THANK YOU VERY MUCH FOR YOUR ATTENTION! The complete report on FUTURE TRENDS AND CHALLENGES IN PATHOGENOMICS will soon be available at

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 R&D 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 RECOMMENDATIONS