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  • AMR Research Infrastructures: biobanking,

    database and handling

    Opportunities for the JPI AMR

    February 2016

  • 2 Research Infrastructures, data sharing and data re-use Opportunities for the JPI AMR

    Contents

    Introduction ................................................................................................................... 3

    Methods ........................................................................................................................ 4

    Surveys ..................................................................................................................... 4

    Strategy meeting ....................................................................................................... 4

    SAB advice ............................................................................................................... 4

    Results ......................................................................................................................... 5

    Survey, Spring 2015 ................................................................................................. 5

    Survey, autumn 2015 ................................................................................................ 5

    Strategy meeting ....................................................................................................... 6

    Remarks SAB ............................................................................................................ 7

    Conclusions and advice ................................................................................................ 8

    Appendices ................................................................................................................. 11

    Annex 1: Report survey spring 2015 ....................................................................... 12

    Annex 2: Presentation survey autumn 2015 ............................................................ 47

    Annex 3: Minutes Strategy Meeting October 28th 2015 ........................................ 4850

  • 3 Research Infrastructures, data sharing and data re-use Opportunities for the JPI AMR

    Introduction Since 2011 the Joint Programming Initiative on Antimicrobial Resistance, JPI AMR

    (http://www.jpiamr.eu/), aims to develop integrated approaches to pursue unique world-class

    research in the AMR-field. It strives to promote open-access to data, research results, and

    materials. Furthermore, JPI AMR aims to reduce research duplication, enhance coordination of

    research efforts, and advance collaboration between parties, e.g. between scientists and

    Research Infrastructures (RIs).

    The European Commission uses the following definition of Research Infrastructures in relation

    to its Framework Programme (FP): RIs are ”facilities, resources and related services used by

    the scientific community to conduct top-level research in their respective fields, ranging from

    social sciences to astronomy, genomics to nanotechnologies”.

    Examples include singular large-scale research installations, collections, special habitats,

    libraries, databases, biological archives, clean rooms, integrated arrays of small research

    installations, high-capacity/high speed communication networks, highly distributed capacity

    and capability computing facilities, data infrastructure, research vessels, satellite and aircraft

    observation facilities, coastal observatories, telescopes, synchrotrons and accelerators,

    networks of computing facilities, as well as infrastructural centres of competence which

    provide a service for the wider research community based on an assembly of techniques and

    know-how.” (http://ec.europa.eu/research/infrastructures/index_en.cfm?pg=what)

    RIs may be ‘single-sited’ (a single resource at a single location), ‘distributed’ (a network of

    distributed resources), or ‘virtual’ (the service is provided electronically). Examples of RIs

    include the CERN (www.home.web.cern.ch/), which is the world's largest particle physics

    laboratory, as an example of a single-sited European RI. The European Mouse Mutant Archive

    (EMMA) (https://www.infrafrontier.eu/) is a typical example of a so-called distributed

    infrastructure, consisting of a large scale repository of mouse lines, with nodes in six different

    countries yet appearing as one unique centre to the users, via a single web interface. Finally

    the GÉANT high-speed network (https://www.geant.net/) is one example of an e-

    Infrastructure initiative launched to facilitate cooperation among researchers.

    Apart from the above mentioned European RIs, other research infrastructures also exist which

    are located in and operated by (European) countries at a national level. JPI-AMR is interested

    in collaborations with these infrastructures as well.

    http://www.jpiamr.eu/ http://ec.europa.eu/research/infrastructures/index_en.cfm?pg=what http://www.home.web.cern.ch/ https://www.infrafrontier.eu/ https://www.geant.net/

  • 4 Research Infrastructures, data sharing and data re-use Opportunities for the JPI AMR

    In this report when the expression ‘research infrastructure’ is used, we mean a distributed

    infrastructure; which is a network of databases or collections made available to the research

    community.

    In order to advise the Management Board of the JPI AMR on next steps concerning sharing and

    re-using data, strains and samples two surveys were conducted and a strategy meeting was

    organized. The draft advise was commented on by the Scientific Advisory Board of the JPI AMR

    before it was finalised.

    Methods

    Surveys

    In the spring of 2015 and in September 2015 two surveys were held via SurveyMonkey. The

    first survey aimed to gain some insight into existing research infrastructures that are known

    and used in the AMR research community. The second one aimed to get an impression of the

    numbers of strains, samples and associated data that are being collected within research

    projects funded with European money.

    Strategy meeting

    On October 28th 2016, a strategy meeting with 14 experts in the field was organized. On the

    one hand experts in the field of data sharing, biobanks and datamanagement in relation to

    databases were present. On the other hand expertise in the AMR research field was invited.

    The combination of the different expertise led to insights that are meaningful for further steps

    of the JPI AMR

    SAB advice

    At the meeting of the Scientific Advisory Board of the JPIAMR, which took place at the

    beginning of February 2016, the draft advice was commented on by the members.

  • 5 Research Infrastructures, data sharing and data re-use Opportunities for the JPI AMR

    Results

    Survey, Spring 2015

    Via email and twitter, experts in the AMR (research) field were invited to answer four

    questions on research infrastructures, databases and the possible role of JPI AMR in

    connecting the two.

    82 responses were received, yielding 88 research infrastructures and 51 databases/collections.

    Only a few of those were mentioned by more than one participant. Of the 51 databases, 23

    were also mentioned as research infrastructure. From the comments one can conclude that

    knowledge of, use of, awareness of, and access to research infrastructures and databases is

    limited and scattered.

    Several roles for JPI AMR were suggested: providing information on existing research

    infrastructures and databases. This could – in part – be tackled by the mapping exercise,

    carried out by Infect-ERA. Enhancing collaboration and stimulating database/biobank use were

    runner ups.

    All the results of the survey are presented in Annex 1

    Survey, autumn 2015

    Via email, 168 project leaders of FP6 en FP7 projects were invited to fill in a survey on the

    amount of data, strains and samples that was collected in their project. Of course a lot of the

    projects did not concern AMR related research but still 11 people responded.

    In four projects, 1000-10.000 or even over 10.000 samples (blood, urine, stool, respiratory)

    were collected.

    Respondents reported large collections (1000 – 10.000 strains) of MRSA, ESBL producing

    Enterobacteriaceae and carbapenem resistant Enterobacteriaceae. Most of the time there was

    additional information available (clinical data, antibiogram, molecular confirmation of

    resistance)

    Regarding the sharing of those strains, samples and data: Most respondents reported that they

    do share strains, samples or data with consortium members, which makes sense because often

    that is part of the project. Sharing also takes place with non-consortium academic institutions.

  • 6 Research Infrastructures, data sharing and data re-use Opportunities for the JPI AMR

    Samples are least shared, data the most. Sharing with commercial institutions outside the

    consortium hardly ever takes place.

    Of the 10 projects that reported they shared samples, strains or data, three of them didn’t

    have a formal procedure and one did not ans

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