Joint Programming Initiative on Antimicrobial Resistance

Research Infrastructure

Sharing bio-specimens and data from research and practice strongly contributes to the progress of knowledge on AMR. To date, a number of research infrastructure (RI) platforms are available, some of which provide information about biological and biomedical resources and service. The AMR research community, however, lacks an overview or catalogue of well documented (AMR specific) collections, databases and services. This gap is widely recognised by individual researchers as well as research institutes, funders and policymakers.  JPIAMR aims to develop approaches to overcome these key barriers in AMR research field: the limited sharing, linkage and sustainability of collections of samples, strains and data.

JPIAMR has set up its Working Group (WG) on research infrastructure (RI) that aims  at enhancing the findability and reusability of existing and future databases, collections, and infrastructure providing services and facilities through (1) guidance to RIs that are relevant for AMR research; (2) guidelines & tooling for FAIR research data management and stewardship (RDMS) in AMR research projects. This is in alignment with the framework of the European Strategy Forum on Research Infrastructures (ESFRI) and its Roadmap 2018.

Findable – reusable – sustainable resources

Already a large amount of collections and data are present: member states have provided financial and scientific investments, and thousands of citizens have voluntarily contributed data and bio-specimens to biobanks and databases. Nevertheless, the reusability of these resources is poor. To benefit from these resources, researchers must be able to find them and reuse them, and the resources must be sustainable in years to come. Apart from AMR specific catalogue of resources that is missing, there is no agreement in the AMR research community on whether and how such resources can be made (and kept) available for reuse in new research. The issues to be solved are numerous and complex. JPIAMR aims to improve findability, to create openness about reusability, and address issues concerning sustainability. It does so for existing resources within its network, and for new resources from future JPIAMR funded projects.

Open science and FAIR principles

JPIAMR’s efforts to make resources and services available, will take advantage from the growing awareness among research communities for the current transition of science to open science. An important part of open science is optimal (re)use of research data (and other resources), which starts from the FAIR Guiding Principles for scientific data management and stewardship. These are guidelines for improving the findability, accessibility, interoperability, and reuse of digital assets. For the AMR community, this would relate to resources such as biobanks harbouring collections of biological material such as samples from human, animal and environmental origin, and microbial strains and molecular components derived from them and their metadata.

JPIAMR’s actions and collaborations for Research Infrastructure

JPIAMR is taking various actions to contribute to improving findability, reusability end sustainability of resources and services:

  1. Search & find collections, databases and services for AMR research
  2. Guide & support to good practices for research data management
  3. Solving barriers for reusing and sharing
  4. Overview of JPI AMR activities related to research infrastructures

One of the outcomes will be practical information for researchers to find reusable resources, or make new ones reusable for future research. This information will become available on the JPIAMR Virtual Research Institute (VRI).

JPIAMR activities related to research infrastructures

  • April 2019: JPIAMR collaborates with the recently granted IMI-consortium VALUE-Dx. Launch of VALUE-dx, a public-private research consortium to transform medical practice to achieve more personalised, evidence-based antibiotic prescription and use in community care settings through the widespread use of clinical and cost-effective innovative diagnostic strategies. JPIAMR and VALUE-dx will collaborate in conducting a survey about AMR resources and services. The aim of the survey is to get an overview of existing resources and services that are relevant for AMR research. It will made available on the JPIAMR-VRI for the entire AMR research community. A next step will be to integrate the overview in an already existing and established catalogue.
  • March 2019: preparing a survey to be conducted about resources for AMR research (collections, databases, biobanks and RI-services) to get an overview of information that can be used as a catalogue of databases and biobanks available in AMR research that would be made available through the JPIAMR Virtual Research Institute (JPIAMR-VRI).
  • February 2018: adoption by the MB of the action plan for promoting the use of RI and applying research data management in JPIAMR research projects.
  • February 2017, MIUF published a report on biological and medical RI’s.
  • January 2016: The first Medical Infrastructures/Users Forum (MIUF) meeting organized by ECRIN. JPIAMR participated and ascertained that AMR becomes a recognizable part of actions undertaken by this platform.
  • October 2015: Strategy meeting on RI, data sharing and data re-use. Invited specialists in AMR research and specialists in RI discussed the barriers of sharing strains, samples and data. The outcome of the survey, the discussions of the strategy meeting, and recommendations for JPIAMR are published in this report.
  • Autumn 2015: A survey on strains and samples collected in research funded by the Framework Programmes was conducted. Collections of over 10000 samples or strains are recorded in European funded research. Information on those samples and strains are quite often shared within the consortium but not so often outside the consortium.
  • Spring 2015: A survey on AMR related research infrastructures was conducted. The aim of this survey was to find out the needs and wishes of the AMR research community for the workshop in autumn 2015. Main outcome was that knowledge and use of RI’s is scattered (published in the report of October 2015)