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

METHODS: Expert Survey

ERA-Net19%

International Scientists

48%

German Scientists

20%

Industry and Biotechnolgy

13%

Figure 1: Contacts

A total of 329 experts was selected and contacted.

METHODS: Expert Survey

Table 1: Reply & return rates

Contacted Replies Filled-out questionnaires

n n [%] n [%]

ERA-NET 62 15 24,19 9 14,52 International Scientists 158 22 13,92 16 10,13 German Scientists 66 20 30,30 14 21,21 Industry and Biotechnolgy 43 8 18,60 1 2,33 International/German 224 42 18,75 30 13,39 Total 329 65 19,76 40 12,16

RESULTS: Research Foci

Diagnostics Identification and Detection

Omic`s Pathogenese and Infection

Therapeutics Molecular Strategies

Methods Novel Technologies

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

GenomicsTranscriptomicsProteomicsMetabolomics

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)

I. European Cooperation II. International Cooperation III. Future Global Player nation rate [%] nation rate [%] nation rate [%]

UK 56 USA 78 USA 74 France 52 Japan 37 UK 63 Germany 52 Canada 22 Germany 56 Sweden 22 China 15 France 44 Holland 19 Australia 7 Japan 26 EU 19 India 7 EU 19 Switzerland 15 Russia 7 China 19 Spain 11 EU 7 Spain 15

• 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 system2. Reduce the misuse of pesticides in

agriculture and animal technology3. Create a European Competence Center

for epidemiological research and modelling4. Create an R&D programme that is

specifically tailored to support public-private partnerships5. Create structures for early warning and rapid

response to emergencies

RECOMMENDATIONS

6. Develop comparative risk assessment strategies for setting national health priorities7. Reconsider work-sharing between research

institutes and universities8. Foster cooperations between microbiological

researchers and clinicians9. Foster inclusion of ecological aspects into

microbiology10. Improve transparency about the function of

different networks on pathogenomics11. 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

http://www.pathogenomics-era.net

1. Establish a European surveillance system2. Reduce the misuse of pesticides in agriculture and animal technology3. Create a European Competence Center for epidemiological research

and modelling4. Create an R&D programme that is specifically tailored to support

public-private partnerships5. Create structures for early warning and rapid response to emergencies6. Develop comparative risk assessment strategies for setting national

health priorities7. Reconsider work-sharing between research institutes and universities8. Foster cooperations between microbiological researchers and clinicians9. Foster inclusion of ecological aspects into microbiology10. Improve transparency about the function of different networks on

pathogenomics11. Conduct a study on industrial research objectives and economic

interests

RECOMMENDATIONS