wp2* study on the programmes in third countries and existing international cooperations

ERA-NET PathoGenoMics

I.Keutmann, FZJ PTJ-BIOBonn, April 7th 2005

WP2*

Study on the programmes in third countries and existing international cooperations

Inventory of pathogenomics-related programmes

*Ina KeutmannProject Management Jülich



Results Task 2.1

• Who was included in the inquiry?

• Methodology

• Responses

ERA-NET Partners/ Third Countries

• Results sorted by Categories of national funding

• Transnational Funding/ Cooperations

• Summary



Investigation in and outside Europe

Inquiry through questionnaire sent via E-mail

• 10 ERA-NET partner countries

• 21 Third European countries

• 16 Third countries outside Europe

Questionnaire was sent to approx. 150 contacts* in approx. 40 countries (Feedback rate 8%)*(ministries, foundations, national institutes, academies, EU contacts (Cordis))

• Additional Identification of programmes and contacts by internet research• Collaboration of the International bureau, Bonn



Questionnaire was sent to ERA-NET Partners on December 8th ´04

Questionnaire concerning (inter-)national programmes:

A1: General Programme InformationA2: History and Road Map of the ProgrammeA3: Programme / Project statisticsA4: Research Content

The ERA-NET Partners were kindly asked to send the completed questionnaire back until February 5th 2005

Answers from 4 Countries are still missing…



Returned Questionnaires

Country Answer Returned

National programmes

Transnational programmes

Austria Yes - -

Finland Yes - Sweden

France No

Germany Yes * -

Hungary No

Israel Yes * -

Latvia No

Portugal No

Slovenia Yes * -

Spain Yes * -



Countries included in this survey: + Programmes, Projects or Grants identified

Austria France Liechtenstein Singapore Australia + Germany + Lithuania Slovenia +Belgium Greece Luxembourg Spain Brazil + Hungary Malta + South Africa Bulgaria India Mexico Sweden +Canada + Ireland + Netherlands + Switzerland +Chile Iceland New Zeeland + Taiwan +

China + Israel + Norway + Turkey Cyprus Italy Poland UK +Denmark Japan + Portugal Vietnam +Estonia Korea + Rumania USA +Finland Latvia Russia



Categories of national funding

1. (Genome-)Programmes that, among other topics, cover pathogenomic projects

2. National programmes, with pathogenomic related programme parts and larger projects that are part of a more general funding programme

3. Grants and Funds that cover pathogenomics related projects



Results

e.g. Canada

(Genome-)Programmes that, among other topics, cover pathogenomic projects and larger projects as part of a more general funding programme

1. Genome Canada

2. Genomics of Human Pathogens and their Host Interactions

3. Immunochemistry Program



Genome Canada

• Established by the federal government in April 2000

• A not-for-profit corporation leading a national strategy on genomics and proteomics with $375 Mio in funding from the Government of Canada

• Dedicated to developing and implementing a national strategy in genomics and proteomics research

• Genome Canada has established 5 Genome Centres across the country

• 2 running programmes focused on human pathogens



Genome CanadaProjects

1. Comparative and Functional Genomics of the Human Pathogen Cryptococcus neoformans

Funding: Genome Canada (50%)Genome British Columbia (50%)

Funding Envelope: total value : $ 2.158.557 (€ 1.322.040)

Project goal: to identify the virulence mechanisms by which Cryptococcus causes disease in humans



Genome CanadaProjects

2. Genome wide Essential Gene Identification in Candida albicans and Applications to Antifungal Drug Discovery

Funding: Genome Canada (50%)Genome Québec (50%)

Funding Envelope: Total value: $ 5.740.927 (€ 3.516.114)

Project Goal: to genetically dissect the organism

to identify all essential genes

to identify all drug targets



2. Canadian Programme: Genomics of Human Pathogens and their Host Interactions

The programme is part of the Genomics and Health Initiative (GHI)

Funding: Provided by the Canadian Federal Government through the National Research Council (NRC)

Duration of the programme: Original program (Genome Sciences in Infectious Diseases) 1999 to 2002

renewed in 2002 as the Genomics of Human Pathogens and their Host Interactions continued until March 2005

Funding Envelope: Budget from 1999 to 2005: $ 26 Mio (€ 15.924.077)

Content: The objective was to apply new genomics tools to three human pathogens, Candida albicans, Francisella tularensis and Campylobacter jejuni.

8 running projects focused on human pathogens



3. Canadian Programme: Immunochemistry Program

Funding Organization: Canadian federal Government

Running since 1929, with changing of the current foci of the research

Actually 2 running projects focused on human pathogens:

1. Project Title: Molecular Pathogenesis2. Project Title: Pathogen Genomics

Details see report



(Genome-)Programmes that, among other topics, cover pathogenomic projects and larger projects as part of a

more general funding programme

e.g. USA:

1. Microbiology and Microbial Pathogenesis Programme

2. Large Scale Genome Sequencing Program

includes “Pathogen Genomics”



1. USA Programme:Microbiology and Microbial Pathogenesis Programme

Programme Owner:

The National Institute for Dental and Craniofacial Research (NIDCR) (National Institute of Health, Department of Health and Human Services)

Sequencing support since 1995

Funding Envelope: The goal is a success rate of 25%(by the end of the fiscal year NIDCR will have funded 25% of the research grant applications assigned to the institute)

Actually 13 running sequencing projects focused on human pathogens



2. USA Programme: “Pathogen Genomics” within the

“Large Scale Genome Sequencing Program”Programme Owner: National Institute of Allergy and Infectious Diseases NIAID/ National Institute of Dental and Craniofacial Diseases NIDCR

Running since September 1999

An Addendum to this programme has been released in 2000 by the NIAID together with the Defence Advance Research Project Agency. This addendum complemented the “Large Scale Genome Sequencing Program” by focussing on pathogens as pathogen agents for bioterrorism.

40 running sequencing projects focused on human pathogensestimated 10 additional projects in the field of pathogenomics

No detailed information was available in concerning the funding envelope



National programmes, with pathogenomic related programme parts and larger projects that are part of a more

general funding programme e.g.:

Australia: Medical Bioinformatics, Genomics and Proteomics ProgrammeChina: Gene Manipulation ProgrammeGermany: Infection and Inflammation NetworkJapan: National BioResource Project Pathogenic Microorganisms

Research for the Future ProgrammeKorea: 21st Century R&D ProgrammeMalta: National RTDI ProgrammeRomania: VIASAN – National programme of Biomedical researchSweden: Functional analysis of the vag-gen family-a constitute of conserved

genes among bacterial pathogens Switzerland: Antibiotic ResistanceTaiwan: National Research Programme for Genomic MedicineUK: Plant and Microbial Science Programme/ Agri-Food ProgrammeVietnam: National Programme on Biotechnology



GermanyInfection and Inflammation Network of the National Genome Research Network

Programme Owner: German Federal Ministry for Education and Research

First Phase started 2001, actual programme runs from 2004 to 2007

Funding: 15.991.668 € for the whole network6.539.584 € (14 microbial pathogens projects)

Content: The Infection and Inflammation Network of the NGFN has assembled scientific and clinical investigators of different backgrounds and comprises 9 work packages; 3 WPs are concerned with human pathogenic bacteria

WP 1 Sepsis WP 2 Gastrointestinal infections WP 5 Tuberculosis

The objective is to develop functional and comparative studies, into a molecular understanding of the human inflammatory response system in health and disease, thereby improving diagnostic and therapeutic options.

14 running projects focused on human pathogens (49 in total )



Switzerland “Antibiotic resistance” NRP49

Programme Owner: Swiss National Science Foundation

Duration of the programme: 1999–2006

Funding Envelope: CHF 12 million (7.763.473 €) over a 5- year period

Content : - Scientific strategies of resistance monitoring

- Survey of the current resistance situation

- Determination of the degree of mobility of resistant bacteria and genes

- Molecular studies on bacterial resistance

- Social, legal, ethical and economic aspects

~ 5-10 running projects focused on human pathogens (21 total)



RomaniaThe National Programme of Bio-medical research and

Development “Life and Health” (VIASAN)

Programme Owner: The Ministry of Education and Research (MEdC)

Running from 2001-2006

Funding Envelope: About 2,7 million € for the projects in the Genomics and Proteomics field, including both clinical and fundamental research

Content: The VIASAN Programme includes four thematic fields of research: Immunology & Organ Transplant, Neuroscience, Cellular and Molecular Medicine and Genomics and Proteomics.

63 running projects for Genomics and Proteomics field



Grants and Funds that cover pathogenomics related projects e.g.

Ireland: Science Foundation Ireland grants

Israel: Israel Scientific Foundation grants

U.K.: The Wellcome Trust

New Zeeland: Marsden Fund grants



United Kingdom

Funding Organization: The Wellcome Trust (WT)

1. 1995 Set up of the Pathogen Sequencing Unit (PSU) to sequence the genomes of organisms relevant to human and animal health

• PSU is now funded through the Sanger Institute

• Main budget provided by the WT

• Funding support of the Institute: 300 Mio £ (432 Mio € ) from 2001 to 2006



United Kingdom

Funding Organization: The Wellcome Trust (WT)

2. Ad hoc applications are accepted in all areas of pathogen research

e.g.

Project grants: 3 year-project grant awards £150 000 to £300.000 (218.277 - 436.554 €)

Programme grants:5 year programme grant awards up to £1 200. 000 (1.746.217 €)



Transnational FundingEurope

Only one binational programme:MICMAN

Partner countries: Finland – Sweden

Organizations: Acadamy of Finland Swedish Foundation for Strategic Research (SSF)

Duration of the programme: 01.01.2003 – 31.12.2005

Main objective: -to increase the understanding and knowledge of the interaction between host and microbes

- to apply this knowledge to the maintenance of health and to prevention and treatment of diseases



MICMAN

Funding Envelope (1/2003 – 12/2005):

The total budget of the programme: 5,4 Mio €Academy of Finland: 4,1 Mio € Swedish Foundation for Strategic Research: 1,3 Mio €

15 research projects or consortia: 5 Finnish-Swedish consortia 2 Finnish consortia 8 individual Finnish projects.

Altogether 26 research groups are funded in these projects/consortia



Transnational Funding

Special Programme for Research and Training in Tropical Diseases (TDR) Global Collaborative research grant

“Pathogenesis and Applied Genomics”

TDR is an independent global programme of scientific collaboration co-sponsored by

United Nations Children's Fund (UNICEF)United Nations Development Programme (UNDP)World BankWorld Health Organization (WHO)

TDR depends on voluntary contributions from donors for most of its income. In 2004, contributing partners consisted of:

4 co-sponsors 23 governments9 other (foundations, agencies etc.)

Total Budget for 2004: US$ 6.614.992,00 (5.122.738 €)



Special Programme for Research and Training in Tropical Diseases (TDR)“Pathogenesis and Applied Genomics”

Duration: Established in 1975

The aim is to help coordinate, support and influence global efforts to combat a portfolio of major diseases of the poor and disadvantaged

TDR supported international efforts to unravel the genomes of tropical parasites through five genome networks.

FundingResearch projects: up to US$ 35 000 per year for 2 years

one-time renewal possible (27.105 €)

Multicentre projects: up to a total of US$ 70 000 per annum and for a 2 years (54.210 €)The project must involve endemic country researchers (South-South or South-North collaborations)



Transnational Cooperations European results

Finland/ MICMANSweden

Norway: The national functional genomics research programme in Norway (FUGE)Cooperation with Norwegian and foreign research groups

Ireland: The Health Research Board works closely with partners in Northern Ireland, the United States and Europe .



Transnational CooperationsResults Outside Europe

Canada: Genomics of Human Pathogens and their Host Interactions formal collaborations with institutes and research groups in Europe and USA. The GHI Coordination Office considered this information confidential.- Immunochemistry Program

“…international research collaborations are too numerous to list.“

Israel: German Israel foundation for Scientific Research and DevelopmentUS Israel binational Science fund (BSF)

Korea: “The 21st Century Frontier R&D Program” includes foreign collaboration due to the problem of the shortage of home-grown talents

Vietnam: National Program on Biotechnology Cooperations with Japan, UK, Australia, Germany



USA International Collaborations in Infectious Disease

Research ProgramProjects in Cooperation with Universities of:

• Bangladesh

• Brazil

• Chile

• Tanzania

• Colombia

• Egypt

• Gabon

• Gambia

• Ghana

• Kenya

• New Mexico

• Papua New Guinea

• Peru

• Salvador

• Shanghai

• South Africa

• Venezuela



Summary

•Pathogenomic related projects covered by unspecific programmes

•Obviously most focused countries outside Europe: Canada and USA

•Transnational pathogenomic activities on programme level are rare:

In Europe only Finland and Sweden

•Most mentioned scientific contents have been questions on- The host pathogen interaction

- The problem of resistance

- Genome sequencing for further applications



Relativ division of the most mentioned microorganisms(69 of 124 mentioned species sorted by genus)

Bacillus

Candida

E.coli

Helicobacter pylori

Mycobacterium tuberculosis

Staphylococcus

Yersinia

Francisella tullarensis

Mycoplasma

Salmonella

Pseudomonas

Staphylococcus

Streptococcus



Summary

•Pathogenomic related projects covered by unspecific programmes

•Obviously most focused countries outside Europe: Canada and USA

•Transnational pathogenomic activities on programme level are rare:

In Europe only Finland and Sweden

•Most mentioned scientific contents have been questions on- The host pathogen interaction- The problem of resistance- Genome sequencing for further applications

There is a big need for coordination activities!



Thank you for your kind attention!

Any Questions!



Some Coffee or thee after the dry sheets?



JapanNational BioRsource Project "Pathogenic Microorganisms (Bacteria,

Fungi and Protozoa)“ Part of the "Research Revolution 2002 (RR2002)

Programme Owner: Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT)

Running from 2003-2008

No information on funding budget available

Content: - research in infections and microorganisms- education of students in the control of infections- basic research for countermeasures against bioterrorism- providing of a systematic accumulation, storage and provision structure for nationally recognized bio resources

~ 24 central resource centres and an information centre are involved

wp2* study on the programmes in third countries and existing international cooperations

Documents