Survey AMR - joint effort JPIAMR & VALUE-Dx

Join the survey about collections of biological material, databases and services relevant for AMR research

ZonMw (the Netherlands Organisation for Health Research and Development) invites you, on behalf of JPIAMR and the recently started consortium VALUE-Dx, to take part in a survey on resources (collections of biological material and databases) that are relevant for antimicrobial resistance (AMR) research. In parallel, we set out to collect information about services that are provided by research infrastructures and some biobanks.

Please follow this link to the survey: https://nl.surveymonkey.com/r/8Z2B9L9

Figure 1: Overview of the resources and services relevant to AMR research, that are targeted by this survey.

Figure 1 description
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The survey addresses existing resources from all the ‘One Health’ domains: human, animal, environment. Figure 1 shows how resources and services are defined. For resources we distinguish (1) biobanks (see ‘1’) and ‘non-sample’-databases (see ‘2’) that are generated in AMR research. Looking more closely to the biobanks, we distinguish:

(1a) Collections of biological material containing e.g.:

  • Biospecimens (e.g., blood, stool, urine, ….)
  • Samples that are derived from the biospecimens: micro-organisms, or molecular derivatives (e.g., DNA, RNA, protein)

(1b) Databases that are associated with the collections to provide information about the specimens, samples and derivatives. For example, the host it was taken from, the antimicrobial resistance of the bacterial strains, genomics, host health status, diagnostics, treatment, quality, protocols and/or publications based upon them.

By services we mean those offered by research infrastructures for managing and using the collections and databases (see ‘3’). Some biobanks also provide services to third parties (see ‘1d’). Finally, the survey addresses the documentation(or metadata) for describing the resources (see ‘4’).

Background of the AMR survey

Introduction to the survey
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About

ZonMw (the Netherlands Organisation for Health Research and Development) invites you, on behalf of JPIAMR and the recently started consortium VALUE-Dx, to take part in a survey on resources (collections of biological material and databases) that are relevant for AMR research. In parallel, we set out to collect information about services that are provided by research infrastructures and some biobanks.    

This invitation is addressed to owners / custodians, and researchers or other contributors to resources and services, including AMR-related research laboratories, institutes, reference laboratories/centres, infrastructures and networks.

Why should you participate?  

By participating in this survey, you are contributing to closing the current gap of information, and establishing a strong basis for AMR research.
The AMR research community is eager to gain better and accurate knowledge about resources and services available in the field, where to find them, how they compare to one another, and to assess their fitness for reuse in new research. Moreover, researchers need information to contact the owner or custodian of such resources to make arrangements for sharing them.
As the survey is initiated by a large network of active AMR researchers, participation may also open up opportunities for future collaboration, publications, and research funding. Finally, you will get first-hand information from the report that will be constructed from this survey.

Aim and ambition of the survey    

The aim is to get an overview of existing resources and services that are relevant for AMR research, forming a central source of information about former as well as future research. Our ambition is to improve their findability and reusability, and thereby their sustainability. The AMR research community will benefit from this initiative, as it will expand options for innovative research. In turn, this may result in new strategies to tackle the global challenge of AMR.

The overview will become available for the entire AMR research community. To optimise the exposure of the overview and its sustainability, we plan to publish it on the webpage of JPIAMR and VALUE-Dx. Next, we will explore opportunities to integrate it into an already existing and established catalogue, such as the BBMRI-ERIC directory.

In our ambitions, we are aware of a number of prerequisites.  For instance, the overview itself must remain constantly accurate and timely updated. It must provide descriptive information (metadata) that is documented with common standards (a standardised language or terminology) to facilitate comparison of resources.

The initiators JPIAMR, VALUE-Dx and ZonMw
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JPIAMR is the Joint Programming Initiative on Antimicrobial Resistance. The objective of JPIAMR’s work package for Research Infrastructures is to attribute to the return on investment of AMR research funding by supporting enabling activities and infrastructures concerning sharing and re-using data, strains and samples important for AMR research. ‘Research infrastructures’(RI) in the context of JPIAMR are databases and collections of strains and samples, including services to use them.

VALUE-Dx is a recently started project (April 2019) and will run for four years. VALUE-Dx is a public private partnership, involving European universities, research institutes and private sector companies active in the development of diagnostic tests for infectious diseases. Its purpose is 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. VALUE-Dx is funded by Innovative Medicines Initiative (IMI) and co-funded by Wellcome Trust and private companies. The consortium is coordinated by the University of Antwerp, bioMérieux and Wellcome Trust.

VALUE-Dx aims at developing sustainable biobanking (with associated databases) and a business model to ensure continuation beyond its funding. The current survey and planned overview will contribute to making resources and services more sustainable.

ZonMw is the Netherlands Organisation for Health Research and Development, the public funder of health research in the Netherlands. ZonMw is a member of JPIAMR, and amongst others leader of the work package Research Infrastructures. ZonMw also participates in the consortium of VALUE-Dx. Creating an overview of collections of biological resources, databases and services for AMR research, is a joint initiative of JPIAMR and VALUE-Dx. ZonMw coordinates this project.

Approach: a two-step survey towards an overview and catalogue
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To gather the required information for the overview of resources and services relevant for AMR research, we will perform two surveys. In the first survey we will investigate, on a highly aggregated level, the type of resources and services that respondents hold. We will send out a second survey to collect more detailed information about individual resources and services, and address issues related to their findability, reuse and sustainability. Both surveys will be set out in 2019.

The results of the two surveys will be reported to the VALUE-Dx and JPIAMR management boards, and shared with the respondents.

The information about the resources and services will be made available for the entire research community. We will start out with an online overview of the information on the JPIAMR website. Next, we will explore opportunities to integrate the information about the resources into a catalogue that is well known in the life sciences (e.g. BBMRI-ERIC directory) to improve the exposure of the resources, and options for searching information about them.

Figure of the different steps: from survey to overview to catalogue

Prerequisites for improving findability, reusability, and sustainability
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Our ambition for the surveys, the resulting overview and possible integration in a catalogue is to improve the findability and reusability of the resources and services, and thereby their sustainability. In our actions, we are aware of the following prerequisites:

  • The overview itself must remain constantly accurate and timely updated
  • The overview must include metadata (i.e. ‘data about data or collections’), providing descriptive information about e.g. the characteristics of the resources, the sampling and storage conditions, quality, etc. Metadata enable researchers to find and compare resources, and to assess their fitness for reuse.    
  • The information provided through the metadata must be documented with common standards (a standardised language or terminology). The recently published bacterial dataset of Swiss Biobanking Platform uses such standards to describe the biobank-related categories of the survey (see 1a and 1b of figure 1).
  • The overview and the information about the resources and services should comply as much as possible with the open science related FAIR principles to ensure the findability of the resources, and contribute to their reusability.

 

The overview of AMR resources in relation to FAIR data, open data, metadata and data sharing
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Researchers can improve opportunities for sharing their resources by taking the FAIR principles into account when planning their data management. FAIR is the acronym for data (or collection) that are Findable, Accessible, Interoperable and Reusable. Data have a certain level of FAIRness, depending upon the number of principles that are applied.

Ideally, data have rich metadata (‘data about data’) that describe what they are, and how they have been processed. It enables researchers to assess whether the data are fit for reuse in their research project. For that reason, also collections of biological material should have metadata.

It is important to note that FAIR data are not necessarily open data. In other words, the ‘findability’ of data implies that people outside your research group get the opportunity to know that your dataset (or collection) exists. Through the principles ‘accessibility’ and ‘reusability’, you define the conditions for reusing them. To get access to the data (or collection) researchers need to contact the owner or custodian and agree on the conditions for sharing.

Making data (or data about a collection) FAIR therefore allows researchers to show the data and collections they hold. Whether they are publicly or privately funded, making data FAIR allows one to keep control on the conditions for sharing them.

 

Glossary
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For the overview we aim to choose topics and terminology that are commonly used in biobanking and AMR research. In this glossary you will find some definitions that we use for the survey and/or overview, and the sources from which they were derived.

Topics and terminology:

Defintions and their sources
 

PDF of the survey questions
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Please do not use this document to complete the survey, but only as a way to look back at the questions. Please use the survey link indicated above to complete the survey online.

PDF of the survey questions

Contact information
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If you have any questions, you can contact us at jpiamr@zonmw.nl

Margreet Bloemers

Lisa Scheefhals

ZonMw, Infectious Diseases and Antimicrobial Resistance

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