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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


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/


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.


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.


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 answer that question.

Therefore, the survey confirmed the conjecture that large collections and databases are being

collected. Sharing them is, however, often not very well organised.

Annex 2 contains a presentation with the results of this survey.

Strategy meeting

During the strategy meeting, fourteen experts with different backgrounds discussed the issues

concerning and conditions necessary for successfully sharing data, strains and samples.

Experts representing the European Virus Archive (EVAg), ELIXIR, TRANSLOCATION and BBMRI-

ERIC gave short presentations about their research infrastructure and what they think makes it

work. Their experiences were discussed and in the afternoon the participating experts

formulated an advice to the Management Board concerning how to move on the subject of

data sharing and data re-use. The full minutes of this meeting are attached as Annex 3

In the afternoon pitch the participating experts formulated the following recommendations

regarding the development of an AMR infrastructure:

● Do not start something entirely new. There are existing infrastructures; do not create something completely new, but build on what is already there. Pick the best structures and try to avoid the mistakes that were made in the past. Learn from what has already been done.

● To decide on which ones are most suitable for the AMR field, interviews with the large infrastructures will be needed.

● Which issues do you want to retrieve from your infrastructure? A really good catalogue will be needed in order to be able to find relevant databases for AMR, and support on legal issues that occur when sharing data with other countries.

● The reusability of data was also discussed: how to judge the relevance and usefulness of existing data, and what can be learned from that for new databases?

● Determine the quality of data, strains or samples. In order to do so, one can learn from how this was accomplished in other fields.

● Publicly funded data should be publicly available. There are no rules on that yet and it will be very difficult to start requiring physicians and researchers to share their data. Something should be developed to ensure this will happen for forthcoming grants and how. The actual situation is actually a unique opportunity for JPIAMR to do this.


● A decentralised approach is what most existing infrastructures use; a connection across Europe. This seems most suitable and will also be less expensive than actually having a physical location.

● The patent period is a difficult issue. It is probably a good idea to give researchers a certain period of time to finalise their work, but after that the data should be available to others. Legal issues are very important and should of course be worked out.

Remarks SAB

The members of the Scientific Advisory Board of the JPIAMR subscribe the need for

coordination in sharing collections in the AMR research field. Collections can be strains,

samples and data. The JPIAMR can play a pivotal role in providing a standard operating

procedure for access to these collections that should be used in research projects funded by

the JPIAMR and beyond.

Dissemination of such a tool should be part of countries’ strategies for AMR. This is of great

importance due to high costs of maintaining collections. The SAB feels this must be country-

funded and that these collections are made freely available to the research community.

Industry should be able to buy into this system.

The SAB advises the MB to look at implementing an EU-wide scheme and endorses the advice

to make use of the existing infrastructures.


Conclusions and advice

Use existing experience for creating an AMR related infrastructure

Based on the web-based survey, it is was concluded that major financial and scientific

investments have been committed and thousands of citizens have voluntarily contributed data

and bio-specimens to biobanks and databases, but there is no financial sustainable EC funded

AMR infrastructure. Limited sharing and linkage of samples, strains and data is a key barrier for

AMR research.

Several member states and existing research infrastructures that provide services for sharing

data, strains or collections have experience with data management and regulations concerning

data sharing. Don’t re-invent the wheel but use what is available.

Also one has to be clear if it is worthwhile to store data, strains or samples. Data related to

very rare situations or unique strains are hard to duplicate or find. Data about common

situations or common strains/samples might easier (and cheaper) be recollected than stored.

Learn from existing databases how to judge the relevance and usefulness of new databases.

Data worthwhile sharing need to be managed properly to make sharing possible. Make sure

researchers are advised about data management; often it is not their area of expertise.

Possible role for the JPIAMR:

● A JPI AMR infrastucture should be developed that can be used for clinical care, personalised medicine and translational research. This infrastructure should build on existing infrastructures, resources and technologies, and be properly embedded into European ethical, legal and societal frameworks.

● This infrastructure should harmonize the databases and biobanks to ensure effective interchange of valid information and samples and to maximise public health benefits.

● A coherent framework and sustainable governance mechanism should be created to operate successfully, to better coordinate and collaborate between existing biobanks, and to engage with stakeholders

● This governance mechanism should connect to existing EC funded infrastructures to ensure that the research infrastructure is in conformity with all relevant regulation. As an example, the infrastructure can connect to BbMRI for biobanking and to ELIXIR for data management.


Collections (strains, samples as well as data) need users

Only data, strains or samples that are being used are worth keeping. This means that proper

attention not only has to be given to data management but also to finding users for the data.

Besides storing interesting information, this means that potential users need to be actively

approached. The infrastructures present at the strategy meeting all have a policy for finding

users. EVAg, ELIXIR and BBMRI-ERIC all actively approach potential users and promote their

initiative. TRANSLOCATION is part of the big Bad Bugs for New Drugs (BB4ND) initiative. All the

participants in this IMI initiative form a big amount of potential users. When researchers are

interested in using (or adding) data a follow up on data management is organized. The JPI AMR

should play a role in making the possibilities of research infrastructures available to the AMR

research community. Criteria could be set to make biobanks and databases eligible for

sustainability. Actual use of those research infrastructures should be one of those criteria.


● A dissemination strategy should be developed so that Europeans can understand and obtain the benefits from biobank and database AMR research

● Develop criteria to assess if biobanks and databases are sustainable

Generate more information on available information

During the discussion the participants of the strategy meeting expressed their appreciation for

the performed surveys. The process of mapping generates awareness of the existence of

research infrastructures for sharing data, strains and samples. As one of the surveys showed,

knowledge about them is very scattered. An up to date mapping of research infrastructures

relevant for the AMR research community helps people finding the way to those RI’s. It is

probably a good thing to go through this stage of making inventories at a very decentralized

level. Such inventories should be made available to the whole community, to see if there are

actually points of connection. Mapping is also part of bringing (potential) users and research

infrastructures together


● To complete the picture of the survey, to obtain missing knowledge on the extent of AMR database and biobanking in Europe, to analyse challenges for networking and harmonization, more information should be gathered through qualitative research and expert interviews on the AMR database and biobanking activities, that have been supported by the EC, Member States, national/regional agencies, hospitals, and universities.


● A central registry describing the content of these collections of samples, strains and data, should be developed.

Promote the sharing and re-using of data

Funders and publishers are in a position to contribute to sharing and re-using data, strains and

samples. JPI AMR for instance reaches a lot of AMR researchers through the joint actions. In

the call text information on possibilities for sharing and re-using data can be provided. Results

of research previously funded by the JPI AMR has to be published in open access publications.

As a final instrument JPI AMR could make sharing and re-using of data, strains and samples

mandatory in its joint actions. If so, the proper infrastructures must be available for the

scientists.

● Spread information on AMR related research infrastructures. Use the JPIAMR

communication network to bring users and providers of data/strains/samples together

● Use the joint actions to bring researchers and existing research

infrastructures/biobanks/collections togehter; make sharing and/or re-using of

data/strains/samples mandatory unless one can explain why that does not add value.


Appendices


Annex 1: Report survey spring 2015

Report on Research Infrastructures Survey In preparation of Strategy Meeting on access to and re-use of data, collections and

biobanks

Version 0.2

Dunja Dreesens, ZonMw, work package 3


Summary

In order to prepare a workshop on Research Infrastructures and AMR which was tuned

to the needs and wishes of the particular target group, a survey was conducted. 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 JPIAMR 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 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 infrastructure and databases is limited, scattered.

Several roles for JPIAMR 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.

With regard to the aim of the workshop: participants thought exchanging knowledge

and expertise would be most worthwhile, followed by getting acquainted.

Even though it was not a scientific survey, it shows and confirms that there is room for

improvement in this area. And that JPIAMR could have a role in this. Discussing the

results with the SAB chair and the JPIAMR secretariat, and subsequently with the chair

of the workshop, it was decided to organise a strategy meeting on data sharing and re-

use which will lead to a strategy/approach how to tackle this issue, what we would like

to, need to achieve, whom we need as partners, which lessons can be learned from

other initiatives, what possible barriers we will encounter and how to circumvent these.

Members and observers of JPIAMR were asked to nominate participants. The strategy

meeting will take place on 28th October and the results will be presented to the

Management Board.


Content

Summary 2

Research Infrastructures and JPIAMR – introduction 3

Survey 4

- Set up

- Participants

- Results

- Conclusions

Event on Research Infrastructures/Data and AMR 10

- What, how en when

- Who

- Intended results

Infect-ERA 11

Annexes 12

- Survey questions

- Survey results

- Draft programme strategy meeting


Research infrastructures and JPIAMR - introduction

The Joint Programming Initiative on Antimicrobial Resistance, JPIAMR

(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, JPIAMR 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: 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.

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/


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.

JPIAMR is also interested in collaborations with these infrastructures as well.


Survey

In order to define in which way JPIAMR would advance collaboration between the AMR

domain and research infrastructures, it was decided to organise a workshop. However,

when organising a workshop it is necessary to know what the current state of affairs is

and what needs and/or wishes the AMR (research) community has. Otherwise, there is

no match between content, aim and participants. It was therefore decided to sent out a

survey to gain insight thereof.

Setup

A short survey was developed together with Spain, UK and Sweden. As platform

Survey Monkey was used. The survey focused not only on RIs, but also on data.

Regarding RIs, JPIAMR more specifically would like to gain insight into:

- The current collaborations with existing research infrastructures;

- The desired/needed collaboration with existing research infrastructures;

- The necessity to facilitate access to specific RIs; and/or

- The need to create or contribute to the creation of new RIs.

The question on data was added on behalf of the Scientific Advisory Board (SAB) of

JPIAMR. The SAB has indicated that the access to and re-use of data (i.e. data sharing

and open access to data) produced from AMR/ Bacterial Infection/ Bacterial Host-

Pathogen research could be improved. Furthermore, the knowledge of the existence of

AMR-databases and bio-banks created during research is limited, according the

Scientific Advisory Board, and could be enhanced.

The survey consisted of 4 questions (see annex 1), and was discussed extensively

before it was approved and sent out.

Participants

The JPIAMR secretariat has a list of experts which have been consulted during the last

years of the initiative. All the persons (approx. 600) on this list were sent an email with

an invitation to participate in the survey. The members of SAB and the Management


Board were sent an invitation as well. As an extra impetus for response tweets on the

survey were twittered (by Israel on the official JPIAMR account). Next to that Laura

Piddock, vice chair of the SAB, re-tweeted the tweets as she has more than 2,000

followers on Twitter.

The survey was open from March 3rd 2015 up and until March 29th 2015. The deadline

was moved once, to: April 15th 2015 in order to collect more responses. The

participants were reminded via email and also reminder-tweets were sent during the

response period.

Results

In the end we received 82 responses. Unfortunately, we forgot to add a question in the

survey to inquire after country and/or background of the participants. The ‘nationality’ of

the mentioned RIs and data collections, however, can be seen as an indication of the

countries from which respondents participated.

Regarding research infrastructures:

- 85 research infrastructures were mentioned, of which:

- 44 were mentioned as known by the participants; only 4 RIs were mentioned by 4 or

more participants (EARS-NET, EMBARC, NCIMB and NCTC)

- 47 RIs were mentioned as being used by the participants; only 2 of those were used by 5

or more participants (ATCC and NCTC)

- 20 RIs were mentioned by the participants for wishing to be used

- 5 RIs were mentioned as couldn’t be used, due to several reasons, such as insufficient

resources.

One question concerned RIs of which the participants thought these were missing.

Several suggestion were brought forward, such as: focused specialist hubs, directory of

active labs, a global hit finding initiative and an open access data of industry research.

Looking at the suggested RIs, there seems to be none or only a few that have use of

antibiotics and/or behavioural change as topic.


Comparing the list with RIs yielded by the survey with the overview prepared for the

SAB in October 2014 by ZonMw, no obvious research infrastructure seems te be

missing. Nonetheless, looking at the origins of the mentioned RIs, and for that matter

the databases as well, there seems to be an overrepresentation of RIs and databases

in Europe and North-America.

It was not checked if all the mentioned RIs fall within the definition of research

infrastructures by the EU. The purpose was to unveil what the participants consider an

RI.

Regarding databases, collections and biobanks:

- 51 data collections, databases and/or biobanks in total were mentioned, of which:

- 47 were mentioned as known by the participants; however only 4 of these were

mentioned by 5 or more respondents (ATCC, DSMZ, GenBank and NCBI)

- 28 were mentioned as used by the participants; and now only 3 of these were used by 3

or more respondents (ATCC, DSMZ and GenBank).

Between RIs and databases exists an overlap. 23 databases that were mentioned,

were also mentioned as RI.

Also with this question, participants could make suggestions, especially concerning

using data collections, and the conditions for better (re-)use of data.

For using databases, collections and biobanks, the themes were:

- Access and open access (10): more publicly available information on databases, collections

and biobanks, but also grant criteria with regards to open access to data generated.

- Availability and location (8): a single repository was proposed, and a one platform website,

next to centralisation and visibility.

- Infrastructure (11): Establishment of new and improved accessible repositories and data and

biobanks that can be accessed by AMR researchers, or a website devoted to AMR related

data.

- Funding (criteria) (3): Support/funding of data maintenance, funding for a EU archive.

- Other (16), e.g.: unify and modify legislations, advertising/communication


With regard to (pre-)conditions for (re-)using the suggestions could be divided into

mainly the same themes, but perhaps with a slightly different emphasis or focus:

- Open access (6): publishing in open access journals (and include this in funding decisions).

- Location (2): all publications that use data from a particular data set should be

hosted/accessible from the bio-bank website.

- Regulatory (2): definitions of data warehouse (definitions of variables, dictionaries, etc.),

loosening of data safety and patient data protection

- Role JPIAMR (3): to take the lead in creating awareness, and set publishing in open access

journals as funding criterion.

- Funding (1): Public funding means open access.

- Ownership and IP (3): clear rules on ownership, use and IP issues, and involvement of the

originator of data in any (re-)use.

- Other (12), e.g.: provision of Ethics Approvals, requirement for deposition of data in suitable

repositories, rules for use.

Another question asked which role JPIAMR should assume with regard to RIs and the

collaboration between RIs and the AMR domain. The participants replied as follows:

- No role for JPIAMR: 3

- Contact details RIs on JPIAMR website: 61

- FAQ RIs on JPIAMR website: 38

- Enhance collaboration between RIs and AMR: 59

- Stimulate biobank and/or database use: 45

The participants could tick more than box when answering this question.

Other suggestions on the role of JPIAMR that were put forward, were:

- Determine what the community needs new or continuing support for to make progress in key

areas of active research in priority areas, e.g. provision of tools and reagents to the

community;

- Have a joint workshop on funded progress;

- More efforts on developing novel antibiotics;

- Open more calls for young researchers;

- Create curated databases for researchers;

- Increase the awareness of the local existing repositories of clinical isolates, clinical research

on AMR, bridging basic and clinical research in AMR;


- Joint resources for animal-based research to efficiently gain important preclinical data

without duplication for ethical and economic reasons;

- Promote the establishment of the necessary open access research infrastructure;

- Please consider the antimicrobial stewardship topic, the antibiotic use data and the social

sciences aspects.

The participants were also asked to indicate whether they deemed a workshop

necessary and if so, what the aim of the workshop should be.

- No workshop: 28

- Get acquainted: 32

- Exchange knowledge, expertise: 41

- Learn (from each other): 30

The participants could tick more than box when answering this question.

At the end of the survey, participants could put forward additional suggestions to

JPIAMR in order to increase the collaboration between RIs and the AMR community.

These suggestions could be categorised into the following areas: funding (5),

information (5), research areas/proposals (4), over-arching infrastructure (6), and

conferences (3) (others (4)).

See annex 2 for a detailed overview of the survey results.

Conclusions

The survey is not a scientific one, so interpreting the results should be done with care.

It seems, however, that there are a lot of RIs, databases, data collections and biobanks

out there. The use and knowledge thereof, however, is limited. Also, there appear to be

some gaps in what’s out there and needed. Databases on behaviour and other

qualitative research are not mentioned at all. Furthermore, an overview of existing

databases, collections and biobanks seems to be lacking, just as the coordination of all

these resources. Possibly, that the Infect-ERA database on Research Infrastructures

can address some of the awareness issues.

These findings coincide with the workgroup AMR resources at the Diagnostics

workshop in London (11th May 2015). For good use of resources in AMR, and data,


samples and material are considered essential resources, databases, procedures,

ease of access, consistency of data and awareness of which data, collections and

biobanks are available.

The challenge of sharing and re-use of data is not unique to the AMR domain, so in

trying to address this, JPIAMR should make use of experiences and lessons learned

elsewhere.


Event on Research Infrastructures/Data and AMR

What, how (format): the participants will be divided into small groups who will act on the

fact that:

- several months ago, they have been given the task to advice on the strategy;

- in this period, they have had several meetings, access to all relevant documents and key

persons;

- now they have one hour left to conclude, summarise their findings and after that hour, to

present a short summary of their findings and recommendations.

The method tends to raise the motivation and the ambition level of participants. The

precise focus of the task can be adapted based on the outcome of the morning

session. Afterwards each group has 5-7 minutes to present their findings and

recommendations (see annex 3 for draft programme).

When: 28th October 2015, Amsterdam/Schiphol, Netherlands

The topics are the following:

- What is our vision – the optimal one, and the ”must have” on how to enable sharing and re-

using data, collections and bio-bank materials in the AMR domain?

- At this stage, do we need to deal with the difference between human and veterinary and

environment, and the respective relevant databases and collections ? If so, how, if not (yet),

why?

- What would be a pragmatic – and as comprehensive as possible way of capturing the

various data collections related to AMR, taking into account available but limited resources

(such as costs and time)?

- Do we need to set up (inter) national databases with clear and easy-to-followprocedures to

facilitate the storage of data ? Or can we use existing databases and bio-banks for this

purpose?

- If so, what needs to be done, and by whom ? – with what skills and competencies ?

- What are potential obstaceles for achieving this, and how can we circumvent these ?

- What procedures should be in place to enhance data sharing and/or re-use of data ?

- What needs to be done to ensure and enhance the ease of access to data ?

- What hurdles are there, who needs to be involved ?

- What needs to be done to ensure and enhance the consistency of the data ?


- What hurdles exist, who needs to be involved to put the measures in place and maintain

them?

- How can we increase the awareness of what databases and data collections are available?

Again, taking into account the limited means available and the dispresed, fragmented field

we currently find ourselves in.

Who

Experts nominated by MB members, plus speakers on data, regulatory affairs, JPND

invited by ZonMw and Laura Piddock, plus representatives from COMPARE, ESFRI

and IMI projects.

Intended results

A report with recommendations or a strategy on data sharing and re-use within the

AMR domain, including the role JPIAMR could, or should take; other parties needed to

execute the strategy, necessary means, description of contributing factors and how to

use these to the fullest, and barriers and how to circumvent these.


Infect-ERA

Human infectious diseases (ID) research challenges require distributed health

observation sites, very efficient data and information exchange systems, as well as

high security laboratory centres for molecular analysis, strain collection and common

databases for molecular genetic data (Report of the expert group on infrastructures,

European Union, 2010).

Infect-ERA “Through this initiative, Infect-ERA partners aim to understand all basic

aspects of complex human infection biology questions such as co-infection that are not

limited to specific pathogens, the cross-talk between host and pathogens, as well as

the relationship between microbes’ environment and infection.” (http://www.infect-

era.eu/mission)

Taking the above into consideration and in order to assist and maximize the Infect-ERA

scientific community’s capacities to face the global challenges, awareness of all

existing infrastructures and available funding programmes is necessary. Therefore, a

task dedicated to the mapping of European and International Infrastructures and

Programmes central for the Infect-ERA scientific community was undertaken. The final

goal of this task is to deliver a database to researchers with all the information on

infrastructures and funding programmes clustered. This database will be made public

through Infect-ERA website (http://www.infect-era.eu/). (source: Deliverable D2.3 Update report on

infrastructures, funding programmes and research expectation in ID).

As there exists an overlap with the AMR domain, it was discussed between Infect-ERA

and JPIAMR and decided to include the JPIAMR countries in the second phase of

mapping that were missing in the first mapping phase. By collaborating, JPIAMR can

realise one of the aims/suggestions of the participants of the survey: awareness of RIs

and make information on RIs available. How to do this will be part of the strategy

meeting in October 2015.

http://www.infect-era.eu/mission

http://www.infect-era.eu/mission

http://www.infect-era.eu/


Annexes

Annex 1 – Survey questions

Annex 2 – Survey results

Annex 3 – Draft programme strategy meeting


Annex 1 – Survey questions

1. Research Infrastructures relevant to antimicrobial resistance

Besides the examples of RI’s mentioned above, there are RIs that are more relevant to

antimicrobial resistance; such as EMBARC (European Consortium for Microbial Resource

Centres) and BBMRI (European Biobanking and Biomolecular Resources Research

Infrastructure), among others.

a. What RI(s) – on an international and/or national level – do you know of?

...........................................................................................................................

........

b. What RI(s) – on an international and/or national level – do you use or have

used previously?

...........................................................................................................................

...................................

c. What existing RI(s) – on an international and/or national level – would you

like to use? Please indicate the importance and/or urgency of this need.

...........................................................................................................................

....................................

d. What existing RI(s) – on an international, and/or national level – would you

like to use, but you can’t or haven’t? Why? Please indicate the importance

and/or urgency of this need.

...........................................................................................................................

......

e. In your opinion, what RI would be beneficial in addressing the AMR

(research) issues, but is missing? Why? Please indicate the importance

and/or urgency of this need.

...........................................................................................................................

...................................

2. AMR domain, RIs and JPIAMR


JPIAMR strives to promote open-access to data, research results and materials. It also

encourages the re-use of data and materials collected throughout AMR research

projects/ programmes. It also aims to reduce research duplication, enhance

coordination of research efforts, and advance collaboration between parties, e.g.

between scientists and RIs.

How do you think the JPIAMR could help or support the AMR community to access

existing RIs, and/or establish new ones? Please tick the appropriate boxes.

- There is no role for the JPIAMR;

- Provide the contact details of RIs on the JPIAMR website;

- Provide FAQ on RIs on the JPIAMR website;

- Encourage collaborations with RI in grant proposals submitted to JPIAMR joint calls and/or

joint actions;

- Determine if an AMR database and/or bio-bank would be beneficial;

- Organise a workshop for those working on AMR and those managing RIs mainly to: (more

than one answer possible)

o Get acquainted;

o Exchange knowledge, expertise;

o Learn from one another;

- Other suggestions:

..............................................................................................................................................

3. Data

Most of the research projects/programmes generate data, databases and/or (bio-)

materials. After the project is finished this data could be re-used. However, the

impression of the Scientific Advisory Board of the JPIAMR is that these collections are

not fully known to others, and as a result the data is not fully utilised.

- What data collections, databases, collections of (bio-) materials and bio-banks do you know?

...................................................................................................................................................

...........

- What data collections, databases, collections of (bio-) materials and bio-banks do you use or

have used previously?

...................................................................................................................................................

...........


- What is needed to enable the use of data, databases, (bio-) materials and bio-banks

generated by AMR related research projects/programmes to be re-used?

...................................................................................................................................................

...........

- What (pre)conditions should be in place for a better (re-)use of AMR data?

...................................................................................................................................................

...........

4. Suggestions

In order to address the AMR issues that society face:

- What other suggestions do you want to propose to the JPIAMR in order to increase the

collaboration between RIs and the AMR community??

My suggestion(s)/idea(s):

...................................................................................................................................................

...................................................................................................................................................

...................................................................................................................................................

.................................


Annex 2 – Survey results


NAMED RESEARCH INFRASTRUCTURES (85) # resp's known used like to use can't use

ACCESS (at EFPL) 1 known - - -

ALBA (Synchroton Light Source) - - 1 1 -

ANR (Agence Nationale de la Recherche) - - - 1 -

ATCC - - 5 - -

ATTIKON (4th Dept of Intern Med University Hospital Athens) - - 1 - -

BACWAN 1 known 1 - -

BESSY - - 1 - -

BBMRI 3 known - 1 -

Caesar (Central Asian and Eastern European Surveillance on AMR) 1 known - - -

CARD (Comprehensive Antibiotic Resistance Database) 1 known 1 - -

CDC 1 known 2 1 1

Center for Genomic Epidemiology - - 1 - -

Central Laboratory of Sera and Vaccines 1 known 1 - -

CERN 1 known - - -

CIPARS (Canadian Integrated Program for AMR Surveillance) 1 known - - -

Clin-Net - - - - -

COMBACTE (Clinical trial network, CLIN-Net) 1 known 1 1 -

COMBACTE (laboratory surveillance network, LAB-Net) 1 known 1 1 -

CPNDB (A Chaperonin Database) 1 known - - -

CCUG - - - 1 -

DESY - - 1 - -

DIAMOND - - 1 - -

DLS - - 1 - -

DSMZ 1 known - - -

DZIF (German Center for Infection Research) 1 known 1 - -

EARS-NET 6 known 2 1 -

EATRIS 2 known - - -

ECDC 2 known 1 - -

E-Infrastructure Reflection Group 1 known - - -

EMBARC (European Consortium of Microbial Resources Centres) 4 known 2 1 1

EMBL - - 1 - -

EMBO 3 known 1 - -

ERIC - - - - -

ESGI - - 1 - -

ESRF (European Synchroton Radiation Facility) - - 3 - -

EUCAST 1 known 1 - -

European Molecular Biology Laboratory-Deutsches Elektronen Synchrotron - - 1 - -

EVA (european virus archive) 1 known - - -

Fundacion Centro de excelencia en investigacion de medicamentos innovadores en andalucia (Fundacion Medina)- - 1 - -

GAFFI (Global Action Fund for Fungal Infections) 1 known - 1 -

GARP (Global Antibiotic Resistance Partnership) 1 known - 1 -

GBB (Groninger Biomolecular and Biotechn Institute) - - 1 - -

GBI (Department of Genetics and Biotechnology (Aarhus)) 1 known - - -

GRACE (Genomics to combat Resistance against Antibiotics in Community-Acquired LRTI in Europe)1 known - 1 -

IATRIS (ERIC) - - 1 - -

IMI (ND4BB) 1 known 1 - -

Institut Pasteur 2 known 3 - -

INSTRUCT (Integrating Structural Biology) 2 known - 1 1

INTEGRALL (integron database) - - 1 - -

ISDAGBB (10x20 initiative of …) 1 known - - -

IS-finder - - 1 - -

ISIS-AR (Infectieziekten Surveillance Informatie Systeem - Antibiotica Resistentie)1 known - - -

ITMO ADVISAN 1 known - - 1

JPIAMR - - - 3 -

JPGAC - - - 1 -

Keio Collection - - 1 - -

Lab-Net - - - - -


MAX IV Laboratory - - 1 - -

Microbial Pathogenesis team - Resistance Determinants - - 1 - -

MLST database (whole genome …) - - 1 - -

MIRRI (Microbial Resource Research Infrastructure) 2 known 1 1 -

NADIR (The Network of Animal Disease Infectiology Research Facilities) 1 known - - -

Nanobiosis - - - - -

NARSA (Network on Antimicrobial Resistance in Staph Aur) 1 known - - -

NCBI (National Center for Biotechn Info) - - 1 - -

NCIMB (National Collection of Type Cultures) 8 known - - -

NCTC (National Collection of Type Cultures) 8 known 5 - -

NIAID (National Institute of Allergy and Infectious Diseases) - - 1 - -

NIH BEI - - 1 - -

NORM 1 known - - -

Number Registry - - 1 - -

ONERBA (Observatoire National de l'Epidemiologie de la Resistance Bacterienne aux Antibiotiques)1 known - - -

OPIC (Cryoelectronmicroscope at …) - - - 1 -

PCUBE (Infrastructure for Protein Production Platforms) - - - 1 -

Prime-XS (European Research Infrastructure on Protomics) 1 known - - -

REA-RAISIN / Surveillance des infections en reanimation adulte - - 1 - -

REIPI 1 known 1 1 -

RESFINDER - - 2 - -

SGI 1 known - - -

SLING 1 known - - -

SLS - - 1 - -

SWEDSTRUCT - - 1 - -

TRANSVAC 1 known - - -

TGAC - - - - 1

Wellcome Sanger Centre 2 known 1 1 -

- -

None 17 - 29 10 13

Not sure/unclear - - 1 - 7

Other:

Bacterial identification by Malditof - - 1 - -

Whole Genome Sequencing - - 1 1 1

Biobank of bacteria with resistence genes of interest - - 1 - -

NMR, mass spec fac's - - 1 - -

Divers compound collections including natural products - - - 1 -

an RI that has biological and spectroscopical infrastructure under one roof - - - 1 -

animal model facility - - - 1 -

curated databases amr - - - 1 -

national level RIs + cooperation with groups from other countries - - - 1 -

bioinformatic tools for whole genomic sequencing - - - 1 1

plasmid bank - - - 1 -

protein production structural biology - - - 1 1

chemical biology and screening - - - 1 -

HTS screening based RI(s) - - - 1 -

small molecule screening at BSL3 - - - - 1

Resistance and antibiotic use data - - - - 1

antimicrobial resistance national institute - - - - 1

next generation sequencing - - - - 1

in vivo infection models - - - - 1

friendly software/platform for resistance surveillance (data management, analysis)- - - - 1

clinical trials for novel antibiotics - - - - 1


NAMED DATA COLLECTIONS - DATABASES (51) # resp's known used

AddGene 2 known 2

ARG-ANOT 1 known -

ARPCARD (Comprehensive Antibiotic Resistance Database) 1 known 1

ATCC (American Type Culture Collection) 10 known 9

Bacteriology biobank at the centro nacional de microbiologia 1 known -

BACWAN (Bacterial Cell Wall Network) 1 known -

BBMRI (Biobanking and Biomolecular Research Infrastructure) 4 known 1

BCCm (Belgian Co-ordinated Collections of Micro-organisms) - - 1

CECT (Spanish Type Culture Collection) 1 known -

Central Laboratory of Sera and Vaccines 1 known 1

CCUG (Culture Collection, University of Goteborg) - - 1

Department of Biobank Research (Umea) 1 known 1

DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH) 7 known 4

EARS-net 1 known 1

EATRIS Biomarkers platform 1 known -

EECMID (European Society of Clinical Microbiology and Infectious Diseases) 1 known 1

EMBL (European Molecular Biology Laboratory) 2 known -

ErasmusMC Biobank - - 1

ESBL gene classification - - 1

EUCAST (European Committee on Antimicrobial Susceptibility Testing ) 1 known 1

Genbank (National Genetic Sequence Database) 5 known 4

GEO ( Gene Expression Omnibus) 1 known 1

Hellenic Sepsis Study Group 1 known -

EMBL - - 1

Institut Pasteur Collection 2 known 2

INTEGRALL (integron database) 1 known -

KEGG (Kyoto Encyclopedia of Genes and Genomes) 1 known -

Keio Collection (Yale collections) 3 known 3

LMG (Laboraroty Molecular Genetics) 1 known 1

MCUG 1 known -

MicrobesNG 1 known -

Microbial stock center 1 known -

MLST database (Multi Locus Sequence Typing) 3 known -

MRC Climb (Cloud Infrastructure of Microbial Genomics) 1 known -

NCBI (Natiopnal Center for Biotechnology Information) 5 known 3

NCTC (National Collection of Types Cultures (UK laboratory)) 3 known 3

NIH BEI Resources (National Institutes of Health) 1 known 1

NIH Biobank (National Institutes of Health) 1 known -

NORM (Norwegian Surveillance Programme for AMR) 1 known -

Patric (bacterial bioinformatics resource center) 1 known 1

PDB (Protein Data Bank) 1 known 1

PlasmidFinder 1 known

Pseudomonas.com - - 2

PUBMLST (Public databases for molecular typing and microbial genome diversity)- - 1

Pulsenet 1 known -

REIPI (biobank of resistant isolates: Spanish Network Research in Infectious Diseases)3 known 3

RESFINDER 3 known 2

Resistance Gene database 1 known -

RIDOM (Ribosomal Differentiation of Medical Micro organisms) 1 known -

Salmonella genetic stock centre 1 known 1

Surveillance des infections en reanimation adulte (outcomerea rearaisin) 1 known 1


Others:

Culture collections 2 known -

RCT databases 1 known -

University biobanks 1 known -

PubChem - - 1

ChEMBL - - 1

Chemical abstracts - - 1

None 12 - 5


Clustered results – remaining questions

JPIAMR Survey on Research Infrastructures and AMR

Question 3: What existing RI’s would you like to use? --> Reasons for wish to use

RI Reason

Joint Programming Initiative on Antimicrobial Resistance (JPIAMR)

Don’t know what’s in it for me;

Infrastructure for Protein Production Platforms (PCUBE)

Difficulty in identifying experts in the field

Diverse compound collections including natural products

Important and urgent

EUROPEAN CONSORTIUM OF MICROBIAL RESOURCES CENTRES (EMBARC)

I would like to compare different Clinical strains of S.epidermidis from different countries with our French strains; Could be useful for future studies in order to get standard Strains or DNA controls as well as samples.

JPGAC Very important;

Unclear Possibilities/access unclear; Insufficient knowledge of international RIs available

Any any, for young researchers, which do not require national funding. Very important, quite urgent.; a RI that has biological and spectroscopical infrastructur under one roof.; Animal-model facility.; Curated databases AMR; national level RIs + cooperation with groups from other countries; whole genome sequencing infrastructures and bioinformatic tools for whole genome sequencing; Access to any plasmid bank; Protein production, structural biology, chemical biology and screening are all important for my research

Biobanking and Biomolecular Resources Research Infrastructure (BBMRI)

Could be useful for future studies in order to get standard Strains or DNA controls as well as samples.

Spanish Network Research Infectious Diseases (REIPI)

For collaboration on ESBL-project for next JPIAMR call;

Integrating Structural Biology (INSTRUCT)

Very important

Question 4: Which RIs haven’t or can’t be used? Why?

Type of RI Can’t use because

Not sure/don’t know

lack of performant AST equipment in our hospital; Insufficient knowledge of international RIs available; not clear to me, possibilities/access unclear; Rather have national initiatives on burden of illness and risk research

None Not yet appropriate to the project aims;

INSTRUCT Grant support needed , highly important

TGAC Lack of funding

U.S. CDC lack of access due to limited resources to support and provide


analytical services to university research on AMR


Question 5: RIs missing?

Type of RI Missing Importance

Enhanced culture collections containing resistant strains

Focussed specialist hubs able to provide a global facility e. g. Underpinning provision of wall intermediates and

Directory of active labs by funding criteria eg recipient of MRC AMR grant,fBBSRC AMR area grant etc

An public database for AMR-genetic determinants

More national and regional Infrastructure and facilities to support the further characterization and antimicrobial resistance properties of ARB isolates from research efforts on monitoring and surveillance from non-clinical sources, such as animal agriculture and environmental samples of health concern (e.g., wastewater impacting water supplies, recreational waters and irrigation waters)

Setting priorities, cost of AMR, evaluation interventions

high throughput testing of novel developed antibiotics against relevant MDR pathogens

The high throughput screening facility at McMaster University under the auspice of Dr. Gerald Wright

Database of known resistance genes. Cloned resistance genes with identified phenotypes

A global hit finding initiative

European reference centre

a centralized centre for storing and comparing full sequences

Phenotypic database of all resistant strains

1. compound screening platform 2. genome analysis platform

Some international organisation-network which will be able to influence national authorities

Easy access to well characterized (multi)drug resistant reference strains, for testing of new antibiotics. Also access to mutator strains for resistance development testing would be welcome.

Urgent

a RI that has biological and spectroscopical infrastructur under one roof

An AMR RI (institute)

research on defining veterinary clinical breakpoints for more drug/bug combinations and per animal species and per site of infection and on


characterisation of antibiotic resistance genes

Open access database of industry research. Community keeps being told that industry has done with it all and failed to discover new drugs so cannot be done. No evidence and probably some studies now being replicated with public money

annotated bacterial genome sequences. Sequencing is becoming so cheap that antibiotic resistant clones should be sequenced and the genome sequence should be available to the scientific community.

Compound libraries, high throughput whole bacterial cell screening facilities, experimental animal infection models coupled with advanced imaging

Urgent

a library of problem organisms. A European facility for medicinal chemistry, early drug development and animal facility.

ADME-tox specialized RI?

Curated databases

access to biobanking resources (clinical collections) focused on well characterized resistant clinical isolates

centralized bank of chemical and natural compounds and drug screening facilities

centralized bank of chemical and natural compounds and drug screening facilities

n RI where it would be possible to perform analysis at whole genome level of bacterial isolates/plasmids, by having the possibility to compare a given isolate/plasmid with an updated database containing all sequenced isolates/plasmids; rapidly and accurately investigate on the genetic differences between two or more genomes or plasmids by comparing the WGS data

Again, a google RI on sequencing and bioinformatics

Coordination of microbial biobanks on national and pan

European levels

A WGS database aimed specifically to AR A WGS database aimed specifically to AR

Open access small molecule HTS facilities Extremely important

Access to biomarker databases. Important for developing new combinatorial biomarkers and for use as control data


Infrastructures that specialize in assay development and screening for antimicrobials of synthetic and natural origin as well as support for academic drug discovery.

Infrastructures that specialize in assay development and screening for antimicrobials of synthetic and natural origin as well as support for academic drug discovery.


Question 9: What is necessary in order to be able to use data collections?

What is needed # resp

Suggestions

(Open) access 10 More publicly available information about biobanks and ease of access; depositing data in open access pubs; Criteria related to grants such as open access to the data generated; Establishment of new and improved accessible repositories and data and biobanks that can be accessed by AMR researchers; Information about the infrastructure and easy access.; open access repositories of data linked to access to collections; Access to patient-level data;

Availability and Location

8 More publicly available information about biobanks and ease of access; A single repository , hosted by the EBI; Centralisation; Visibility. One platform website.; Public information about availability and content; May be a list of collections with a concise description?; That their content is available in common registers so it is possible to perform search their content;

Infrastructure 11 Establishment of new and improved accessible repositories and data and biobanks that can be accessed by AMR researchers; Information about the infrastructure and easy access.; A single repository , hosted by the EBI; Centralisation; data warehouse... a complex task; Visibility. One platform website.; Long term data and biological sample archiving and storage; web site devoted to AMR related data; Probably a centralized database management resource with open-access to scientific community, able to collate data from all the facilities producing data on AMR (ambitious but potentially useful); better publicity of their existence: Often lost due to staff movement - needs permanent repositories of cultures etc; Specific databases for AMR; A centralized RI, possibly as a task of teh existing RIs e.g. DSMZ? Also clear rules on ownership, use and IP issues.;

Funding (criteria) 3 Criteria related to grants such as open access to the data generated; Support of funding for maintenance of metadata linking antibiotic resistance, genomics and markers and clinical data; Funding for an EU archive; MONEY. It is necessary to support the platforms necessary to keep and organize all the data and samples;

Other 16 Unify and modify legislations (patient data confidentiality and consent); Provision of reagents that are difficult or expensive to produce and for which replication of effort makes no sense; Recognition that these are accepted standards and of immediate relevance/importance; Better communication; database similar to www.straininfo.net; communication, advertising; More information; promoting the existence; Curated databases; May be a list of collections with a concise description?; Wider information.; more information or a website; Information and coordination.; Extension of Ethics Approvals; Connection among Institutions and Investigators; More information;

None/Don’t Know 5

http://www.straininfo.net/


Question 10: (Pre)-conditions for better (re)-use of data?

(Pre)condition # resp Suggestions

Open Access 6 publishing in open access journals (there is a role for JPIAMR to facilitate (or even require in funding decision) this; Public domain;

Location 2 All publications that use this data should be hosted/accessible from the bio-bank website; Visibility;

Information 1 cf definitions of data warehouse (definitions of variables, dictionaries etc...);

Role JPIAMR 3 publishing in open access journals (there is a role for JPIAMR to facilitate (or even require in funding decision) this; I encourage JPIAMR to furhter take a leading role in creating awareness about the availability of such database, as I was not aware in spite of approx 6 year work in the field of drug discovery; description of the different databases and biomaterials on the JPIAMR website;

Funding 1 Public funded with open access

Ownership and IP

3 Clear rules on ownership, use and IP issues.; Easy access and guarantee of IP; Involvement of the originator of the data in any use/re-use

Other 13 Provision by Ethics Approvals; Loosening of extreme data safety and patient data protection; Standards in data generation and nomenclature; to be able to sort the data; building on earlies data in a ever growing database; Open access publication, requirement for deposition of omics other relevant data in suitable repositories; agreement to provide strains etc to other researchers in the field; Rules for use; It is necessary to establish a simple and intuitive protocol to introduce the data in the database as well as the criteria and protocol to include strains in the biobank; contact interested researchers, universities, even clinica hospitals; registration, declaration of goals, declaration of interest; international collaboration on metadata availability and analysis; None for users who seek information on existing ARB but documentation for new ARBs to be submitted to collections, databases and bio-bases; Optimize sample conservations and information integration

None/ don’t know

10


Question 11: Suggestions from Respondents

Area # resp Suggestions

Funding 5 cooperation in funding;; positively promote interactions via funding calls.; Funding funding funding. Woefully inadequate for the size of the problem; Provide funding for next generation sequencing so that the AMR community can use such resources freely.; Match the provision with the need and priority;

Information 5 give for each European country the list of RI involved in AMR with 3-5 key words describing their contribution and identified contacts to start collaboration more easily; Ensure that AMR community is aware of which RI's are available and accessible for AMR research; positively promote interactions via funding calls.; Prepare some leaflets with very simple information regarding the relevance of infectious diseases and the problems we are facing to treat them to the academic authorities (universities), schools, research funding agencies, newspapers, hospitals,....; Brief description of the different research projects ongoing on antimicrobial resistance; Improve communication and knowledge related of available RIs. Encourage/promote their use in projects and grants. Other already suggested in the questionnaire

Research areas/proposals

4 Host bacteria interactions; broaden the scope of grant proposal to upstream basic research (undiscovered antibiotic resistance, new molecules...); Provide funding for next generation sequencing so that the AMR community can use such resources freely.; I don't think that access to infrastructure is a priority, although it would greatly facilitate The big need is chemical hits, for classic drug discovery, and wild-ass ideas from academia for new approaches (as well as better management of existing drugs); To facilitate access of resource-poor facilities to grant proposals for equipment and reagent acquisition

Over-arching Infrastructure

6 promote the establishment of appropriate infrastructure to tackle AMR; A coordinated European WGS data base focused on AMR; "- Foresee a reference informatic facility able to connect different resources to be used as a reference infrastructure for the scientific community working on AMR; Open access to this facility and to all RIs and database"; A web interface; overarching web site listing all currently funded JPAIMR, AMR labs, PIs and CoIs-and the abstracts/summaries of the grants that got funded given alongside; I am aware that over the European Antimicrobial Resistance Surveillance Network (EARS-Net) studies in Microbiology have generated collections of microbes within institutions which have been discarded because of the lack of any money/infrastructure to maintain once the investigator retires. These are a precious resource in relation to studying the development of AMR. A central UK repository (necessarily larger than the current NCTC but which could be an expansion of this) to which these collections could be offered would make a lot of sense. In addition, the best and cheapest long-term storage of bacteria is by freeze-drying. This is now pretty much a lost art, with the use frozen storage which is less reliable and costly, in


terms of money and energy usage, to maintain. Encouragement to re-introduce freeze drying as the gold standard for culture storage and the research and development of faster/simpler technologies for multiple culture freeze-drying would facilitate culture storage. The potential for a centralised freeze-drying facility should be considered. Central archiving of bacterial isolates generated by funded research should be an expectation rather than a possible after-thought, but to do this the infrastructure/funding has to be in place to facilitate.

Conferences, etc.

3 Outreach is/should be integrated in the RI activities. JPIAMR could possibly arrange workshops to promote the infrastructures with respect to the AMR research community.; To organize a conference on AMR issues; Have an international meeting of all JPIAMR funded participants. Call it: The 1st International JIAMR Symposia;

Other 4 Include national networks; involve more molecular scientists (biologists, chemists) to also develop novel antibiotics; Establishment of environmental surveillance and monitoring systems and protocols for ARBs at international, regional and national levels. Linking and harmonization of AMR surveillance and monitoring systems and protocols among the medical, veterinary, animal husbandry, aquaculture and environmental sectors to improve information and understanding of the ecology, natural history and emergence, spread and reservoirs of ARB and to improve identification and response efforts to new ARB threats that emerge and impact human and animal health; overarching web site listing all currently funded JPAIMR, AMR labs, PIs and CoIs-and the abstracts/summaries of the grants that got funded given alongside;


Annex 3 – Draft programme strategy meeting

Draft program for the AMR Strategy Meeting on Research Network for sharing and re-

using data, collections and bio-banks within the AMR domain

10.30 Opening, welcome, framing of the event by Laura Piddock, chair

10.45 Presentation of the main results of the survey held in the second quarter

of 2015,

by Dunja Dreesens, programme officer

11.00 Flash presentation by experts in the field

11.25 Explanation of the interactive part of the meeting by Gerard Muller,

facilitator

11.30 First interactive session WHAT. The objectives of which are:

- to have an intensive knowledge exchange between participants;

- to identify the key elements of our strategy.

12.50 Conclusions

13.00 Lunch

13.45 Second interactive session HOW, the objectives of which are:

- to have an intensive knowledge exchange between participants;

- how the strategy could be implemented

- to create a support base for the next steps

15.10 Plenary session, conclusions and an opportunity for participants to give

suggestions

to the secretariat on how to move forward.

Preview – next steps, closing

16.00 End of meeting


Annex 2: Presentation survey autumn 2015


Annex 3: Minutes Strategy Meeting October 28th

2015

Organisation ZonMw - JPIAMR (Joint Programming Initiative on

Antimicrobial Resistance)

Theme Strategy Meeting

Date October 28, 2015

Venue Schiphol WTC

Chair Mr H. Goossens

Minutes Mrs Y. van Lanen - Het Notuleercentrum

List of participants:

Name Organisation

Herman Goossens (chair) University Hospital Antwerp

Mathias Winterhalter IMI project TRANSLOCATION

Manfred Kohler IMI project TRANSLOCATION

Andrew Smith ELIXIR

Gunnar Skov Simonsen University of Tromsø

Gert-Jan Ommen Leiden University Medical Centre

Tanel Tenson University of Tartu

Marc Bonten University Medical Centre Utrecht

Phil Gribbon Fraunhofer IME / TRANSLOCATION

Pieter Moons University of Antwerp

Christine Prat EVAg – European Virus Archive

Jan van Heuverswyn MB JPIAMR – Dept. Economy, Science &

Innovation

Arjen van Rijn e-IRG, The National Institute for Nuclear

Physics and High Energy Physics

Margreet Bloemers ZonMw

Maria Starborg (observer) JPIAMR secretariat, Swedish Research

Council

Gerard Muller Facilitator

Thera Habben Jansen

Host, Programme officer AMR, The

Netherlands Organisation for Health

Research and Development (ZonMw)


Strategy Meeting on AMR Chairman Mr Goossens starts the meeting at 10:30 a.m. and welcomes the

participants. Today’s topic is challenging. Hopefully there will be very interesting

discussions and ideas.

The participants introduce themselves and mention their relevant expertise.

Ylse van Lanen will be taking the minutes today.

Jan van Heuverswyn is from Belgium and is working at the Department of Economy,

Science and Innovations. In Belgium, five, six years ago the creation of a biobank was

started. This project was not very successful and will stop at the end of this month.

Pieter Moons is also from Belgium. He is working at the University of Antwerp and is

involved in a number of European projects concerning biobanks and sustainability.

Tanel Tenson is a professor of technology of antimicrobial compounds at the University

of Tartu, Estonia. He is active in a national programme that attempts to integrate

research and data collection and samples on antibiotic resistance in medical,

veterinarian, food safety and environmental settings.

Marc Bonten is a physician and microbiologist in Utrecht. He is involved in several

European consortia and projects, for example ACE, MOSAR, the COMBACTE projects

and the MARS project (concerning the collection of data and samples from ICU

patients in a data warehouse system).

Maria Starborg is from Sweden, from the JPIAMR secretariat and the Swedish

Research Council.

Gunnar Skov Simonsen is from Norway and a clinical microbiologist, chief physician,

MD at the University of Tromsø, member of the SAB of the JPIAMR, a combination of a

database and a biobank. He has been involved in a lot of perspective population based

cohort studies, which can be used for research purposes.

Christine Prat is from France and working at the European Virus Archive EVAg. Her

expertise is in biobanking viruses.

Andrew Smith is head of external relations with ELIXIR, infrastructure for biological

information. He is not an expert on AMR; two of his colleagues would also have liked to

be here, but unfortunately they could not make it.

Manfred Kohler is from Germany, from the Fraunhofer Research Organisation, IMI. He

will tell more about his work in his presentation.

Phil Gribbon is a colleague of Manfred Kohler’s. His main role is the recruitment of data

users.

Mathias Winterhalter is also a colleague and leader of the managing entity of

TRANSLOCATION. He will tell more about this later.

Margreet Bloemers is from The Netherlands and working at ZonMw. This organisation

is engaged in data management and stimulates data infrastructures. She is very

interested in how the other participants are handling these topics.


Gerard Muller is from Denmark and an experienced specialist in designing and

facilitating meetings in which the knowledge of the participants can be used.

Thera Habben Jansen is from the Netherlands and working at ZonMw, the Dutch

funding agency for health research and medical science. ZonMw represents The

Netherlands in the Management Board (MB) of the JPIAMR, the organisation that is

hosting today’s meeting. The question is: how can efficiency on all the collected data,

strains, samples collected through European funding be increased? The JPIAMR is

very glad that the participants are here today, to advise the MB on this topic.

Gert Jan Ommen comes in later. He is from The Netherlands and working at the

Leiden University Medical Centre. He participates in the BBMRI-ERIC project, about

which he will give a presentation.

Mr Goossens remarks that the field at hand is indeed a difficult one. Some of the

participants are experts on the topic, others are not; people from various fields were

asked to attend this meeting in order to obtain advice from different angles. He hopes

that at the end of the day, an advice for the MB of JPIAMR will be generated.

Flash Presentations

(the sheets of all the presentations will be sent to the participants and are part of the

minutes/the report; relevant additions or questions asked, will be reported in the

minutes)

JPIAMR

Mrs Habben Jansen presents two surveys during this meeting. One of them giving an

impression of the research infrastructures, databases, biobanks and collections known

within the AMR research community. The other one informing on what has actually

been collected; how large are the databases? How many samples, strains and data are

being collected in European funded research? She also informs about the JPIAMR

initiative.

Mr Goossens remarks that these results were expected, and that they are confirmed by

these quick surveys.

Biobanking within the GRACE project

Mr Goossens gives a flash presentation on the GRACE project (Genomics to combat

Resistance against Antibiotics in Community-acquired LRTI in Europe). He finds it very

frustrating that the fantastic European collections cannot be accessed and that there

are also no procedures to make access possible. This is a huge waste of money. He

had many discussions with other scientists about finding ways to keep the information

sustainable, and to at least build biobanks that can be accessed by many users. Very


few organisations have managed to do that so far but it is really necessary to find a

way to do this on a large scale.

Basically, when a project ends, the collection is kept in an unknown place, gets lost, or

even worse: if someone retires the whole collection is destroyed.

GRACE tries to deal with these issues and has worked out a procedure. It seems to be

a fairly good procedure, but still there are some gaps, for instance in legislation.

Legislation appears to be different in European countries. In Belgian hospitals, patients

are supposed to agree to the collection and use of left-over body tissue, if they do not

actively refuse. No informed consent is needed in this opt-out strategy, which is very

different from procedures in most other countries.

Unfortunately funding of the GRACE biobank will stop in 2016, but the samples are

very valuable and should not be lost. Many of the participants are probably struggling

with the same problem: freezers filled with samples, maybe linked to patient data, how

can they be kept sustainable?

In the established procedure, the biobank and database belong to the GRACE-

consortium. Everybody can request the use of information, including the private sector.

In The Netherlands, for instance, sharing information with the private sector is not a

common case. A formal request from the industry actually never came, but a lot of

diagnostic companies are desperate to get good samples, to validate their diagnostic

tests.

In solving the problem of how to get and provide access to samples, setting up an

external ethical committee has never been considered. This is, however, necessary.

So, the following questions are addressed in this meeting:

How is biobanking regulated? By whom?

Who will have access to the samples?

Who owns the samples?

How long will/can they be stored?

With whom/what labs (universities, private sector etcetera) might the samples

be shared with in the future?

For which tests might they be used?

Questions/comments

Mr Bonten is not in favour of another medical ethical review; there has been an opt-out

procedure or an informed consent, so there is no need for it.

Mr Simonsen asks how much patient based information is allowed to be used along

with the samples. There must be some sort of mechanism to regulate how much and to

what extent the GRACE samples and related data are available. Mr Goossens answers

that parties need to specify what kind of data they need. Mr Bonten confirms that

legislation may differ per country. In one European country for instance, samples were

collected from ICU patients, using an anonymised patient identifier and the date the

patient was admitted to the ICU and the date the sample was taken. In another country,


it was not allowed to use the actual date of the sampling and due to that, samples

would be useless. As a consequence, all kinds of tricks are used to enable the use of

the information.

Mr Van Ommen agrees with Mr Bonten. In case of a biobank, one should anticipate in

the initial informed consent on the possible future use of the samples and information.

If later a new aspect or use of the samples and information would come up, one might

go back to the Ethics Committee. If samples are completely anonymised, it is

impossible to use them longitudinally. Biobanks should not be reviewed by more ethic

regimes than the one it was originally established under.

Mr Tenson asks how a consent or opt-out is handled in case a patient cannot respond,

for instance at the ICU. Mr Goossens suggests asking the patient’s relatives. Mr

Bonten points out that this procedure also differs in the various European countries.

Due to legislation issues, Mr Goossens is not sure if the GRACE samples, which come

from all over Europe, are actually all allowed to be used. The committee has probably

been a bit naïve about these issues.

TRANSLOCATION

In their presentation, Mr Winterhalter, Mr Kohler and Mr Gribbon inform the meeting on

TRANSLOCATION, topic 2 of the IMI (Innovative Medicine Initiative), New Drugs for

Bad Bugs (ND4BB), a private-public partnership.

The Information Centre that was established, is not a biobank.

There is one single legal agreement for everybody to deposit the data, which makes

things less complicated.

BBMRI-ERIC

Mr Van Ommen outlines the BBMRI-ERIC (Biobanking and BioMolecular Resources

Research Infrastructure - European Research Infrastructure Consortium). Biobanking is

of great importance for future health care, in which personalized medication is used

more and more. In December 2014, this research infrastructure consortium has been

set up in which seventeen countries and a World Health Organisation party participate.

There are thirteen full members and five observers. Its mission is to facilitate access to

high quality biomolecular resources, to have a central catalogue of European biobank

samples, to ensure scientific excellence and quality of samples and also the ethical and

legal compliance and long-term sustainability. Countries outside of Europe have the

opportunity to join in.

One of the three Common Services is ELSI (Ethical-Legal-Societal Issues). As Mr Van

Ommen earlier said, the jurisdiction of the ethics committees of the biobanks should be

respected. Biobanks have the final say on what can and cannot be done with their

samples. People can turn to ELSI for advice and guidance. General Data Protection

Regulation (GDPR) is also an important issue in this field.


In Europe are about 1692 million tissue samples. The biggest problem is not the

illegitimate use of these samples; actually the underuse and lack of access are the

main problems.

Slowly, BBMRI is heading its goal: getting a sustainable operation of tools to actually

help projects on the way. A private data cloud for biobanking is now being developed.

BBMRI-LPC (large population cohort) is a project making the first steps on actual

crossed country sample and data sharing. Mr Van Ommen is responsible for the

interaction with the industry, which is a - very difficult - field within BBMRI-LPC. A white

paper was written on this issue and published in the European Journal of Human

Genetics. One of the described models states that there are actually two parties, with

very different goals. BBMRI Expert Centres will try to create some sort of middle

ground, in a not-for-profit setting, where the industry and academies can share

samples and funding, and derive data (more data for the academic world and insights

that might lead to further product development for the industry).

In every deliverable to the European Union, BBMRI has to look for information from all

the different national nodes. What turns out to be most difficult, is to get a good

inventory of the public-private interactions in the different biobanks. Mr Van Ommen

likes the first presentation, because this inventory, while being part of the process, is in

fact already a product itself.

However, it is really difficult to get a view of who is doing what. Therefore, academics

are now interviewing all those biobanks by phone: what are you doing, with whom,

where and which future opportunities are there? The amount of information is

unbelievable, but in many countries, people do not perceive this knowledge as

something that might be of value to others. The interviewers really have to drill deep to

find the problems and solutions, and get lots of information about things that do and do

not work, and why. It is probably a good thing to go through this stage of making

inventories at a very decentralised level. Such inventories should be made available for

the whole community, to see if there are actually points of connection.

Finally, the physical exchange of samples between countries will not be necessary

anymore, just the exchange of data will remain. Data exchange is much cheaper, better

scalable and will meet with fewer legislative restrictions.

Mr Goossens remarks that this information is very interesting. There is a lot going on.

He finds it amazing that many projects and trials do not consider what should happen

with the data after the trial and how they can be made accessible. Very often there is

no sustainability plan.

Mr Van Ommen considers this the fundamental difference between a project and an

infrastructure. It is really difficult to explain this difference to those in Brussels who are

responsible. In fact there are two communities, one of which does not really exist; it

consists of reviewers that only come to Brussels occasionally and think in terms of

projects, not infrastructures. BBMRI is trying not to be a project, but a framework in

which projects can collect information, that is ultimately entered for maintenance and


safe storage. This is still difficult to explain to the biobanking world. In the biobanking

world, there are still communities that see BBMRI as a competitor. Funding generates

approximately 3 million euros a year. However, the costs of biobanking science amount

to about 500 million euros. Half of the BBMRI money invisibly comes from the

universities that help building this central infrastructure.

Mr Goossens remarks that the BBMRI concept might be very interesting for the MB.

This topic will be discussed after lunch.

Mrs Bloemers states that in The Netherlands the use of existing research infrastructure

is being stimulated, but that many researchers are not yet very familiar with the idea.

ZonMw puts a lot of effort in improving this. Mr Van Ommen mentions the Netherlands

Federation of University Medical Centres (NFU) which has a joint programme on how

to deal with research infrastructures. They actively interfere or guide – sometimes more

active than governments would like - the research infrastructure policy in The

Netherlands, which is a good signal.

BBMRI Netherlands is a consortium, consisting of the seven university medical centres

and other parties, like the RIVM and the Netherlands Cancer Institute. It was suggested

that it would probably be more productive to create some sort of project based

infrastructure development. BBMRI Netherlands responded by saying that big projects

are needed under the condition that everyone in The Netherlands who matters in that

particular field should be involved. This forces people to work together or at least have

contact. Here also, the process itself became a product.

Mr Van Ommen remarks that sometimes it is best to decide not to spend too much

money in keeping a database or biobank up to date. As an example he mentions the

inflammatory bowel disease material collection; it was decided to leave it as it is, as a

legacy database and to start again with new samples and information when a frequent

disease is at hand.

Mr Goossens suggests that criteria could be set to make biobanks and databases

eligible for sustainability.

Mr Goossens closes the first part of this meeting at 12:40 p.m.

Lunch

Mr Goossens reopens the meeting at 1:15 p.m. Two more flash presentations are

scheduled in the afternoon programme. After that, there will be group discussions.

ELIXIR

Mr Smith informs the meeting on the ELIXIR organisation. ELIXIR is building a

sustainable European infrastructure for biological information, supporting life science

research and its translation to medicine, agriculture, bio industries and society. ELIXIR

unites Europe’s leading life science organisations in managing and safeguarding the

massive amounts of data being generated every day by publicly funded research. It is a


pan-European research infrastructure for biological information. ELIXIR will provide the

facilities necessary for life science researchers - from bench biologists to

cheminformaticians – to retrieve the most from the rapidly growing store of information

about living systems, which is the foundation on which our understanding of life is built.

The rapid increase of database volumes is a big challenge; a model is needed that

allows to scale this. The whole publishing landscape is also an important factor in

keeping the literature database up to date.

Fourteen countries are full members of ELIXIR and contribute to the budget. There are

five observers, currently working towards becoming a full member. The actual

members are the ministries or the research councils of a country; ELIXIR is an

intergovernmental organisation. EMBL is the used legal model.

All countries have different nodes with often very strong local flavours. The ELIXIR –

EXCELERATE programme tries to connect these nodes and provide services, to make

sure that users from other countries can also access the archives and resources.

These nodes themselves are funded through national agencies. So, local investments

are being made and at the same time the member states contribute to the operation of

ELIXIR. That provides a technical budget, which enables the organisation to fund

activities in these nodes to link them together. Collectively, ELIXIR applies for

additional financing as well.

For example, the European Bioinformatics Institute (EBI) is a large European node in

ELIXIR that already runs a large number of archives that can be used to store data and

can be accessed by researchers.

As an example Mr Smith mentions that the ENA (European Nucleotide Archive) is a

broad platform for sharing integration of sequence data. The sustainability is high and

researchers confide in it for the deposition of their data, as well as companies that build

their own data pipelines on top of it. So, ELIXIR wants to build this sustainable public

infrastructure that is going to be around for a long time and allows academic users and

the industry to build services on top of it. This is also an effort on collaboration between

institutions, companies and countries etcetera. A solid foundation is necessary.

One of the challenges is data management in large research projects, which is

complicated. Part of it is about the research infrastructures themselves, showing what

services they offer, so that researchers become aware of them. Perhaps funders can

play a role here as well, encouraging researchers to think about these things in an

early stage.

Mr Smith proceeds on some other activities of ELIXIR by saying that most researchers

do know about the biggest archives, but there is also a long tail of smaller resources.

Therefore analysis tools are provided, which researchers might need to use for

processing data. There is a service registry that is being developed more and more and

reaches out to particular user groups. There is also a data nodes network, with experts

in the several countries that can support local research projects on their data

management needs. Moreover, there is a training portal that informs researchers about

the bioinformatics training courses that are available.


In ELIXIR Netherlands there is a “bring your own data” programme, which teaches

local communities about data standards and interoperability.

Mr Smith has some final thoughts on the issues at hand: clearly, the area of AMR is

very broad, it is huge. But if community archives are already in place, and if they are

relevant, people should also use them. That is just common sense. There is also a role

for funders and publishers to encourage people on open data principles in research

projects. The research infrastructures themselves have to ensure that researches know

about what services are being developed.

Mr Smith finally mentions that ELIXIR does not have a specific AMR database.

Mr Van Ommen asks if there is an overlap between the EGA genome and phenome

archive and ENA. Mr Smith answers that EGA would not be able to exist without ENA.

The added value comes on top of the data storage and that would be the EGA. This

information is updated every day.

EVAg

Mrs Prat presents on EVAg (the European Virus Archive goes Global), the “Amazon of

viruses”.

The main mission of EVAg is to deliver first quality virus-related products through a

professional organisation. The biobank is very active and has a large catalogue.

The consortium consists of sixteen European partners. All the main virology labs are

represented. There are nine non-European partners, which is a challenge.

There are eighteen associated partners. EVAg is trying to extend the consortium and

the number of end-users, which is one of the described challenges.

If partners sign the agreement they can get funding or access to facilities etcetera. It is

very important that partners trust the EVAg organisation, so therefore their rights will be

defended and they will retain ownership of their biological resources.

Access to data can sometimes be granted within two weeks, but might also take a

longer. This may be due to strict quality procedures and rules concerning the handling

of viruses. Therefore a centralised procedure for shipment of material is being

developed.

Other challenges are how to address legal issues and the discussion among partners

on intellectual property.

Mr Van Ommen states that the demand to publish is also a difficult issue.

Mr Goossens thanks all the speakers for their presentations. A lot was told about the

key issues and challenges that the participants are facing on their way forward.

In the next part of this meeting the participants will be asked to discuss the next steps

JPIAMR should take concerning sharing and re-using data/strains/samples in the AMR

field. Subtopics to take into account are:

- Mapping

- Quality issues

- Ethical issues


- Legal issues

Group discussions

Mr Muller asks the participants to imagine that they form a committee, established by

the MB six months ago. During the next forty minutes, the committee should conclude

on their key recommendations. These recommendations have to be presented in five

minute pitches, after the group discussions.

The participants are divided into two groups.

Pitches of recommendations

Mrs Bloemers remarks that the first part of this group discussion was about the exact

research question. Eventually the following recommendations were given and

questions were asked:

Do not start something entirely new. There are many existing, good infrastructures; use

them.

To decide on which one is most suitable for the AMR field, interviews of the large

infrastructures will be needed.

Is making a choice for one infrastructure actually wise? That would mean directing an

applicant towards that particular infrastructure. That could be against the openness of a

call. Mrs Bloemers however thinks that a very open call is still scientifically possible, if

the researcher is directed to an infrastructure.

Which issues do you want to retrieve from that infrastructure? A really good catalogue

will be needed to be able to find relevant databases for AMR, and support on legal

issues that occur when sharing data with other countries.

The reusability of data was discussed: how to judge the relevance and usefulness of

existing data, and what can be learned from that for new databases?

Mr Van Rijn remarks that another recommendation would be to come up with

determinations of the quality of data, strains or samples. In order to do so, one can

learn from how this was done in other fields.

Mr Smith asks if there was a discussion on maybe the use of more infrastructures,

instead of only one. Mr Winterhalter thinks that the question at hand is most important;

after that a determination of the most suitable database can take place.

Mr Muller did not hear any arguments for the recommendation not to start something

new. After a few remarks from the participants, he concludes that this is recommended

due to the many examples of failed attempts and an increased likelihood of

sustainability of the joined model.

Do not reinvent the wheel, Mrs Bloemers concludes.


Mr Bonten remarks that a few baselines occurred and a couple of questions were

raised:

Publicly funded data should be publicly available. There are no rules on that yet and it

will be very difficult to start enforcing physicians and researchers to share their data. For

coming grants, something should be developed to ensure this will happen and how. The

actual situation is actually a unique opportunity for JPIAMR to do this.

There are existing infrastructures; do not create something completely new, but build on

what is already there. Pick the best structure and try to avoid the mistakes that were

made in the past. Learn from what has already been done.

A decentralised approach is what most existing infrastructures use; a connection across

Europe. This seems most suitable and will also be less expensive than actually having

a physical place.

The patent period is a difficult issue. It is probably a good idea to give researchers a

certain period of time to finalise their work, but after that the data should be available to

others. Legal issues are very important and should of course be worked out.

When the time comes that all data are being shared, should a catalogue be produced

as well as a description of what the database is, the quality of the data etcetera? Or

would the data just be kept in some sort of resting place, where it is the responsibility of

the person who wants data to approach you?

Mr Van Ommen remarks, on the retrospective type of data, that many parties that have

generated data cannot be legally obliged to make their data available. However, these

parties are often still active and searching to fund the prospective part. So, the funding

parties can play an encouraging role in this. It is also important that a minimal data set

will be defined, so that researchers know what they minimally have to collect to make

databases more integratable and interoperable.

Plenary session

Mr Goossens concludes that both groups recommend the same thing: do not start a

whole new infrastructure. He asks if anyone has a last question or suggestion.

Mr Winterhalter remarks that some American colleagues are very jealous of the IMI

project. They are very interested in databases and the exchange of information and

data.

Mr Goossens agrees that it is not only a European issue; there certainly is global

interest when it comes to biobanks and databases. This is another opportunity for

JPIAMR.


Mr Winterhalter emphasizes the importance of a very clear question: what should be

the outcome in the end?

Preview, next steps, closing

Mrs Habben Jansen will make sure that the participants receive the sheets of all the

presentations.

Today’s input will be used to make an advice for the MB meeting in March 2016. This

will take some time, because probably some additional information is needed. The

concept advice will be sent to the participants in January, so that they can comment on

it.

Travel costs etcetera can be reimbursed until November 15.

Mr Goossens closes the meeting at 3:10 p.m.

He thanks all the participants for their contribution and wishes them a safe trip home.

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