Final Report Summary - Q-COLLECT (Coordination and Collaboration between reference collections of plant pests and diseases for EU Plant Health Policy)
Executive Summary:
International trade and travel has increased tremendously in recent years with plants and plant products being moved into and from the European Union. As a consequence, the rate of introduction and establishment of new, economically or environmentally damaging plant organisms and invasive species has increased steadily. In addition, climate change may also increase the probability of establishment of organisms in more areas than their area of origin. Such organisms include plant pathogens, arthropods and invasive plants. Some may have already been identified as posing an unacceptable risk to agricultural and horticultural crops, forest and the wider environment and have consequently been included in the Annexes of the Directive 2000/29/EC as pests of the European Union (these lists of organisms are also called quarantine pest lists). As highlighted many times before, the capability of National Plant Protection Organizations (NPPOs) to quickly and reliably detect and identify these organisms is critical for effective phytosanitary measures to be taken and for ensuring safe transnational movement of plants and plant products. Laboratories are increasingly working under quality assurance systems (including accreditation) and need to have access to validated tests using reference material from reference collections.
A significant number of plant pathogens and pest collections are present within Europe but they are dispersed, widespread and of very variable quality. NPPO’s within the EU and EPPO region, mandated laboratories, universities and research institutes all have their own collections related to their specific work and scope. Many of these collections are connected to a single specialist. Within Europe there is a need to improve the infrastructure supporting phytosanitary important collections so as to more efficiently use the available infrastructure and improve collaboration in the field of phytosanitary infrastructure with regard to means, knowledge, expertise on taxonomy and development of detection methods.
In the frame of the Q-collect project, by means of a questionnaire, an inventory within Europe was made on the nature, size, availability, and quality of important phytosanitary collections. The rate of answers was satisfactory as 93 laboratories/institutes out of the 154 completed the questionnaire describing 152 collections, 83% of which hosting quarantine organisms and/or look alike. Experts considered that almost all important collections were described and that the results of the questionnaire were representative of the state of the art.
Based on the inventory and standard requirements defined for reference collections, gaps in those collections were listed with a series of recommendations to overcome them. Guidelines for application of quality standards, for access to specimens and for design and building a network of reference collections have been proposed, adapted and agreed at the last workshop. An info-portal containing relevant information on phytosanitary important collections has been set up and final activities and results of the project have been and will be further disseminated to stakeholders, including collections and all NPPO diagnostic laboratory end-users within the EU and EPPO region who are not participating directly in the project. Links have been made to relevant ongoing EU projects, including MIRRI, which has similar objectives covering the wider field of microbiology.
Two Workshops for collections and potential stakeholders have been organized. The first one on 27/28 nov 2014 in Kleinmachnow (Germany) aimed at presenting the preliminary plans toward a sustainable collaboration, coordination for the maintenance of transnational reference collections and databases. The second workshop (8/9 sep 2015, Rome (Italy) discussed guidelines for application of quality standards, for access to specimens and for design and building a network of reference collections. A white paper, covering all the important recommendations from the project, was drafted and approved during the meeting.
Deliverables are available from the Q-collect website: www.q-collect.eu
A paper containing the results of Q-collect will be published in EPPO Bulletin, August 2016.
Project Context and Objectives:
International trade and travel has increased tremendously in recent years with plants and plant products being moved into and from the European Union. As a consequence, the rate of introduction and establishment of new, economically or environmentally damaging plant organisms and invasive species has increased steadily. In addition, climate change may also increase the probability of establishment of organisms in more areas than their area of origin. Such organisms include plant pathogens, arthropods and invasive plants. Some may have already been identified as posing an unacceptable risk to agricultural and horticultural crops, forest and the wider environment and have consequently been included in the Annexes of the Directive 2000/29/EC as pests of the European Union (these lists of organisms are also called quarantine pest lists). As highlighted many times before, the capability of National Plant Protection Organizations (NPPOs) to quickly and reliably detect and identify these organisms is critical for effective phytosanitary measures to be taken and for ensuring safe transnational movement of plants and plant products. Laboratories are increasingly working under quality assurance systems (including accreditation) and need to have access to validated tests. It was noted that in order to ensure proper development, validation and effective and reliable use of tests, it is essential that the infrastructure in Plant Health is strengthened, in particular aiming that:
• Expertise in taxonomy and phytosanitary science is secured.
• Maintenance of reference collections is ensured and accessibility and links are developed further.
• Easilyy accessible databases containing reliable data are maintained and developed further.
• Phytosanitary research (including research on taxonomy) continues in particular for diagnostic test development.
A significant number of plant pathogens and pest collections are still present within Europe but they are dispersed, widespread and of very variable quality. NPPO’s within the EU and EPPO region, mandated laboratories, universities and research institutes all have their own collections related to their specific work and scope. Many of these collections are connected to a single specialist. Within Europe there is a need to improve the infrastructure supporting phytosanitary important collections so as to more efficiently use the available infrastructure and improve collaboration in the field of phytosanitary infrastructure with regard to means, knowledge, expertise on taxonomy and development of detection methods.
Main Objectives
Q-collect has identified the major challenges in the development of a network of relevant phytosanitary collections, collectively harbouring quarantine organisms and their closely related species as well as other organisms with similar diagnostic features (so-called look-a-likes). Within Q-collect we aim to develop guidelines and reference criteria for the quality, access and maintenance for important phytosanitary collections, harbouring viruses, bacteria, phytoplasmas, fungi, arthropods, nematodes and invasive plants. Q-collect will cover all regulated plant health pests to be used by any plant diagnostic centre, national reference organisation and authority freely using the internet, to underpin the implementation of Council Directive 2000/29/EC and follow-up legislative EU-regulations.
To address these major challenges, six principal project objectives have been formulated and are shown below:
1. make an inventory of existing phytosanitary important collections within Europe and their content
2. develop guidelines for quality standards
3. develop guidelines to improve the accessibility of these collections
4. design and build a network of reference collections
5. develop an info-portal on the web to provide information on the outcome of the project
6. disseminate the results to stakeholders
In this way we will:
- support a better network of national reference collections relevant to national and EU phytosanitary policy,
- provide guidelines for restoring, improving and updating the quality, accessibility of national reference collections (specimens, tissue and DNA) and consequently ensuring harmonization of collection maintenance across Europe,
- Support a better collaboration between EU and third country diagnostic laboratories and also the international community.
The six principal Q-collect project objectives will be achieved through a range of measurable objectives, each related to a specific Work Package and will encompass all quarantine-group taxa within the viruses, phytoplasmas, bacteria, fungi, nematodes, arthropods and invasive plants.
The objectives of the seven Work Packages are:
Work Package 1. Coordination
1.1. To coordinate project activities, including project meetings and reporting.
1.2. To develop and maintain the internal project webportal.
1.3. To manage all administrative, financial, legal and contractual aspects of the project.
Work Package 2. Inventory
2.1. To make an inventory of existing relevant phytosanitary collections.
2.2. To describe the main phytosanitary relevant collections and their characteristics.
2.3. To identify gaps within the content of phytosanitary important collections.
2.4. To define strategies to fill the gaps previously identified.
Work Package 3. Quality Standards
3.1. To review current quality control standards in the main EU collections of quarantine organisms.
3.2. To define and agree minimum quality standards that can be applied within the main EU collections of quarantine organisms involved in the project.
3.3. To produce harmonised guidelines towards achievement of recommended quality standards during preparation, conservation, shipment/access and use of reference materials of all quarantine organisms.
3.4. To facilitate consultation with other collections and end-users in EU Member States and EPPO countries to harmonise and increase their awareness of quality standards in provision and use of reference materials of quarantine organisms.
Work Package 4. Access
4.1. To summarize all information on the biological resources available (what is where and how from WP2) and on the stakeholders needs (who needs what, in which format and why) and how material can be deposited and accessed.
4.2. To organize the structured frame for deposition in collections (respecting CDB and Nagoya protocol) and distribution (respecting European and national laws) (using tools such as MTA) for those collections for which it is not available already.
Work Package 5. Info-portal
5.1. To make an inventory of all existing tools, websites, databases that might be complementary to the inventory on collections (WP2).
5.2. From other WPs, obtain the information on the existing systems, strengths and missing features that might need to be implemented within this project and associated databases. Summarize the wishes of the different WPs and make a proposal how future information should be made accessible for the end-users.
5.3. To create an integrated system (info-portal) hosting the information and end-results generated by all other WPs.
Work Package 6. Design and development of a sustainable European network of collections of plant health quarantine organisms
6.1. To provide defined and internationally compatible reference criteria for the establishment of a sustainable network of European reference collections of plant health quarantine organisms resp. taxonomically related organisms.
6.2. To provide defined and internationally compatible reference criteria for the virtual access to reference collections and connected databases of plant health quarantine organisms within a sustainable European and international infrastructure network.
6.3. To provide a process description (e.g. flow chart) for the application of the developed and defined reference criteria for a sustainable network of European reference collections of plant health quarantine organisms.
Work Package 7. Dissemination.
7.1. To develop a website for the project.
7.2. To disseminate efficiently, through the website, relevant information from the project to stakeholders, in particular the plans for sustainable collaboration, coordination for the maintenance of transnational reference collections and databases.
7.3. To make a general presentation of the project to be used in national or international communications about the project.
7.4. To develop EPPO standards on quality control on phytosanitary collections.
7.5. To organize two workshops for collections and stakeholders.
Project Results:
Work package 1 – Coordination and Management.
Partners involved:
WP Coordinator: DLO (Partner 1)
Objectives
1.1. To coordinate project activities, including project meetings and reporting.
1.2. To develop and maintain the internal project webportal.
1.3. To manage all administrative, financial, legal and contractual aspects of the project.
Tasks
Task 1.1 Organize project meetings
• Project meetings were held on 2 December 2013 in Leiden (kick off meeting), on 28 November 2014 in Kleinmachnow (Germany) and on 7 September 2015 in Rome (Italy) where all Partners had the opportunity to report and review progress and take forward tasks within each individual work package. Minutes of these meetings have been reported in D1.1 D1.3 and D1.4.
• An extra project meeting has been organised by EPPO (partner 13) on 24-25 March 2015 to discuss with (dpt)WP leaders and experts the outcome of the questionnaire and how to interprete the data.
Task 1.2 Develop webportal
• A webportal has been developed for projects partners hosting all relevant project information (Proposal, DoW, GAcontract, CA, program/minutes meetings, etc.)
https://teamsites.wur.nl/sites/Q-collect/SitePages/Home.aspx
All reports, deliverables were made available for all partners through this webportal.
Task 1.3 Write project reports
Two project reports have been made and submitted (1st period report and 2nd period report)
This was coordinated and submitted by the Coordinator. The Coordinator also acted as the main interface with the Commission.
• Incorporate in the project and activity reports mentioned above specifically on exchanges and dialogue with the Advisory Board, stakeholders and end-users.
• Partner 1 (month 24)
Task 1.4 Manage project administration
All financial; legal; contractual and administrative aspects of the project have been managed by partner 1 (DLO).
Deliverables
D1.1) Minutes of Kick off Meeting [month 2]
D1.2) Webportal for hosting all relevant project information (Proposal, DoW, GA contract, CA, program/minutes meetings, etc.) [month 2]
D1.3) Minutes of Second Meeting [month 12]
D1.4) Minutes of Third Meeting [month 24]
Work package 2 – Inventory of relevant phytosanitary collections.
This work package was mandated to make a state of the art of collections of quarantine organisms in Europe, with four objectives:
2.1. To make an inventory of existing important phytosanitary collections.
2.2. To describe the main phytosanitary important collections and their characteristics.
2.3. To identify gaps within the list of phytosanitary important collections.
2.4. To define strategies to fill the gaps previously identified.
Partners involved:
Six persons have been involved in the preparation of the different tasks and deliverables during the project: the WP leader (Jean-Claude Streito), the deputy WP leader (Françoise Peter) two EPPO staff members Jean Perchet and Damien Griessinger, and Emmanuelle Artige (INRA).
All of the following Q-collect partners were also involved and consulted:
DLO (partner 1), DEFRA (partner 2), ILVO (partner 3), UGent (partner 4), UNIBO (partner 5), KNAW (partner 6), EVD-ACW (partner 7), ANSES (partner 8), INRA (partner 9), NATURALIS (partner 10), DSMZ (partner 11), AGES (partner 12), EPPO (partner 13), FGU VNIIKR (partner 14), JKI (partner 15) and NVWA (partner 16).
2.1. Identify and list the main quarantine collections.
All taxonomic groups of quarantine organisms were included in the study: Viruses & Viroids, Phytoplasmas, Bacteria, Fungi, Arthropods, Nematodes and Invasive Plants. Lists of collections of quarantine organisms already available (EPPO, INRA, DLO) were compiled and an on-line interactive list was provided to all partners by 2014/02/11. All partners were invited to complete and correct the list, especially to update the addresses, from 2014/02/11 to 2014/05/06. The list was cleaned and formatted. It was validated and available for the survey (task 2.2) by 2014/05/12.
The list included 154 laboratories and institutions that house collections of quarantine organisms and/or look alike. All groups of organisms are represented (Viruses & Viroids, Phytoplasmas, Bacteria, Fungi, Arthropods, Nematodes and Invasive Plants).
2.2. Based on the list a second questionnaire was sent to relevant collections for details on scope, size, quality, availability and sustainability of material preserved.
A first version of the questionnaire was produced by WP2 leaders based on a brainstorming session organized in the framework of the kick off meeting (Leiden, 2013/12/02) and was further developed taking into account questions included in the MIRRI questionnaires. It was provided to all Q-collect WP leaders, especially WP3 and WP4, for comments and suggestions. Comments from WP leaders were reviewed by WP2 coordinator and the EPPO staff involved and a revised version was prepared. This revised version was submitted on-line to all Q-collect partners who were given the possibility to provide feedback from 2014/02/11 to 2014/02/28. Comments received were reviewed by WP2 coordinator and the EPPO staff involved and a second revised version of the Questionnaire was tested by 2014/04/30 by INRA. The final version of the questionnaire was made available on-line on 2014/05/15 for the survey to start.
The questionnaire included 36 questions for a total of about 220 fields. Most fields had to be completed for each collection declared. Topics addressed were: scope, size, quality, availability and sustainability of material preserved.
To identify the gaps in the different taxonomic groups, institutes/laboratories were requested to complete the questionnaire separately for the different groups of pests and declare as many collections as they deemed necessary. One of the strengths of the questionnaire was indeed the possibility for the respondent to create forms for as many collections as necessary (depending on the type of organism, including the possibility to create sub-collections) and to give details for each collection, although this was more time-consuming for the respondents who wished to give that level of detail. Approximately one hour was required to fill the on-line form per collection (according to the test carried out in Montpellier).
By 2014/05/15 an invitation to complete the Questionnaire on-line was sent to all curators of quarantine collections listed in task 2.1. Furthermore, information on the questionnaire was disseminated to all of the laboratories registered in the EPPO database on diagnostic expertise as well as to all EPPO Panels on diagnostic. An article was published in the EPPO Reporting Service no. 4 to publicise the survey (publication 2014/06/10).
The deadline to complete the questionnaire was 2014/07/31.
An extraction of the information gathered was done and a file containing a presentation of the raw results was prepared by EPPO. The document was circulated on 2014-09-30 to all members of the consortium for possible feedback.
Information was gathered from 110 collections. Results were presented and discussed with partners at the first Q-collect Workshop (Kleinmachnow, Germany, 2014-11-27/28). Bias, additional ideas for interpretation and future steps were discussed. Participants commented that some important collections seemed to be missing from the answers received. The questionnaire was consequently reopened and the deadline to complete it was the end of January 2015. Results were reanalysed and sent to Q-collect partners for comments by 2015-03-03.
The rate of answers was satisfactory as 93 laboratories/institutes out of the 154 completed the questionnaire describing 152 collections, 83% of which hosting quarantine organisms and/or look alike. It was valuable to reopen the questionnaire as 42 new important laboratories/institutes finalized it. Results were reanalysed and sent to Q-collect partners for comments by 2015-03-03.
Figure 1: Number and location of collections that took part in the survey (the size of the spots is linked with the number of collections in the locality).
An extra project meeting was organized in Paris on 2015-03-24/25 attended by Q-collect Work package leaders and representatives of European collections from each discipline. During this meeting final results of the survey were discussed and bias and gaps were identified and listed. Experts considered that almost all important collections were described and that the results of the questionnaire were representative of the state of the art.
2.3. Based on results of Task 2.1 and 2.2 and on requirements defined by WP3, 4 and 6 to identify and list the gaps (lack of specimens or specialists, quality, availability, sustainability).
During the project meeting mentioned above bias and gaps were identified and discussed.
A draft version of the questionnaire results and gaps identified was sent to WP leaders for comment. Comments were discussed between INRA and EPPO and a version of this Deliverable made available on web portal by 2015-09-02.
Current situation:
The main results of the Q-collect questionnaire and gaps identified are provided. For more details see the deliverable 2.3.
1. The survey organized during the Q-collect EU funded project confirmed that although there is a significant number of plant pathogens and pest collections still present within Europe (more than 150 reported), they are dispersed, widespread and of very variable quality.
Figure 2: Number of collections by laboratory / institute.
The majority of respondents host one collection. Only 25 institutes/laboratories host more than 2 collections. One disadvantage of scattered collections is that the information is dispersed so it is more difficult for the users to find biological material.
2. Most collections are working or research collections and only few of these collections are likely to be organized to provide services to outside users.
The consortium considered that this could be an indicator that these are active collections updated regularly and probably associated with specialists of the pest groups. However it was also considered that few of these collections are likely to be organized to provide services to outside users.
There are very few collections dedicated to the conservation and the provision of services for (quarantine) pests organisms (commercial / public deposit / national or international status). But differences are important by discipline: several important and international collections well organized exist for bacteriology, a few number for fungi, viruses and viroids, a few number of working collections are organized to provide services punctually in entomology, acarology and nematology, no collection of invasive plants is organized to provide services.
Figure 3: Graph illustrating the total cumulated numbers of collections for each purpose. Multiple answers were possible.
3. There is a limited number of information on collection’s holdings available online.
Although collections were not asked to provide a list of species held, it can be inferred from the answers that the lists that could have been provided would have been partial. General collections host a large number of species and possibly regulated species, however these are usually difficult to access. The average number of quarantine species represented in each collection is low (less than 10 for most discipline). The number of specimens is difficult to interpret but some species are probably represented by a very low number of specimens (e.g. 1 or 2).
The limited number of information available online is a gap to allow easy and straightforward online access to information on where biological material can be found.
Figure 4: Number of collections that provide an online consultation.
4. Many collections have no quality system in place, and accreditation of collections is scarce.
The percentage of collections sharing material with no quality assurance in place corresponds to more than half of the collections which answered the questionnaire. In such cases exchange of material is assumed to be based on trust, there is no formalized process ensuring the quality and authenticity of the specimens, which excludes in principle the use of such material in a formalized framework (such as use in the framework of official diagnostics performed under accreditation).
More details on quality assurance are provided by WP3.
Figure 5:Graph illustrating the quality assurance and sharing policies
5. Sharing of material between collections to ensure resilience is not common and can be considered as a high risk for loss of important biological material in case of incidents with buildings or equipment.
Almost 2/3 of collections (up to 70% for insects) do not share material for duplication. Although this can be linked with the type of specimens for the taxa (insects, acari, plants) where collections are mostly dead material that cannot be multiplied, it can be considered a gap for collections of live cultures, where incidents with buildings or equipment can lead to very fast destruction of samples. Q-collect partners think that these numbers are too optimistic, it is possible that some collections answered that they shared material but not necessarily for the purposes of duplication to ensure preservation of specimens following accidental loss of all or part of a collection held at one location.
Figure 6: Graph illustrating the policy of sharing material with other collections for duplication purposes by discipline.
Figure 7: Graph illustrating the policy of sharing material with other collections for duplication purposes overall.
6. Appropriate basic funding is not secured enough and there is a need for a common policy towards collection management throughout the region.
Figure 8: Graph illustrating the proportion of collections with a dedicated annual budget.
A structural weakness of a majority of collections can be identified here. 2/3rd of collections do not have an annual dedicated budget, possibly meaning that they function on fund allocated for other activities such as research or diagnostics. This could mean that the funds necessary for maintenance of the collection could be difficult to identify. It also questions the long term future of the collections.
2.4. With WP3, 4 and 6, propose a guideline of recommendations how to fill the gaps for decision-makers of the phytosanitary policies.
Results of the survey on collections and main gaps identified were presented to partners and stakeholders during the last project meeting (2015-09-07/08 in Rome). Based on deliverable D2.3 recommendations were discussed and approved by partners. A white paper covering all the important recommendations (deliverable D2.4) was drafted and approved during the meeting. Here are presented recommendations supported by WP2 inventory.
Goal for the future should be the following: for every organism group/discipline there are at least at 2 locations official reference collections situated and through online catalogue(s) these reference collections can be accessed by a specialist to search and order material.
All the initiatives of the past years (Q-bank, QBOL, Q-collect, etc) have given a boost to the phytosanitary collections. Much energy, knowledge and hard work has been given to the collections. The challenge is to keep the good work up and follow this road. In the coming years it is unlikely collections will be supported with big additional budgets or project funding. However, a database like Q-bank has proved that it is possible to connect specialists and their collections on an online platform. Other projects have proved that the network of phytosanitary specialists is strong and people are willing to collaborate. In the framework of Euphresco there are many international cooöperations especially between official NPPO related laboratories. The laboratories in the EPPO region do not need a reference collection in every country or at every laboratory, but they do need access to these collections. By connecting collections online and clustering collections the result can be an international coverage for reference materials. With quality systems in place the collections can offer reliable, well defined reference material. The new EU regulation with extra demands on reference material and the forming of EU-RL’s can help to speed up this movement. Official collections as part of or related to an EU-RL and partly financed by the EU provide possibilities. Through coöperations like EUPHRESCO an even distribution of the reference collections should be possible.
Recommendations
To reach the above mentioned, first steps should be taken in the near future. The need to improve the infrastructure supporting phytosanitary collections and use them more efficiently and improve collaboration will be the main ingredients.
A: Priority to making/maintaining inventories
It is essential to be able to know where biological material is available. Collections should make an inventory of their holdings and provide this information in a format that could allow sharing on a platform.
B: Establish a long term sustainable online platform
Encourage and support the creation of a long term single platform to access the information. Choose the online platform to be used and assure a long time hosting.
C: Improvement of Quality systems for collections
The implementation of quality systems in collections is essential to ensure that proper reference material is used in the development and performance of tests. The upgrade of working collections should be a short term objective.
D: Establish networks for collections
Networks of collections should be established in order to share the responsibility of maintaining reference material and also for duplication purposes whenever necessary. Using existing networks like EUPHRESCO will be the most efficient.
E: Establish a common policy for reference material
A common policy should be established for developing and maintaining reference material among member states as one of the basic requirements for a sustainable network of National Reference Laboratories and EU Reference Laboratories in the new EU control directive on official controls. Exchange of material and concentration of material in yet well-established collections will be a first step.
In case of outbreaks it is essential that not only information on the location of collections is accessible but also prompt and organised/regulated exchange of material is possible. Therefore a common policy for issuing of material and shipment in compliance with legislation should be developed.
The basis for the above steps originate from the different collection projects. Now there is a strong need for further implementation from within our field and our organisations.
Work package 3 – Quality Standards.
Partners involved:
WP leader John Elphinstone (FERA, partner 2) and Dpt WP leader Marianne van der Blom (NVWA, partner 16)
All of the following Q-collect partners were also involved and consulted:
DLO (partner 1), DEFRA (partner 2), ILVO (partner 3), UGent (partner 4), UNIBO (partner 5), KNAW (partner 6), EVD-ACW (partner 7), ANSES (partner 8), INRA (partner 9), NATURALIS (partner 10), DSMZ (partner 11), AGES (partner 12), EPPO (partner 13), FGU VNIIKR (partner 14), JKI (partner 15) and NVWA (partner 16).
1. Introduction
In 2001, the Organisation for Economic Cooperation and Development (OECD) Working Party on Biotechnology concluded that there was a need to provide greater quality assurance than was already exercised by culture collections and databases of biological resources (1). As a result, a series of best practices was published in 2007 (2) to provide guidance for biological resource centres (BRCs) seeking to improve the quality standards of their repositories of living and preserved organisms, their genomes and other information related to their heredity, function, taxonomic classification and diversity. These included specific best practice guidelines on biosecurity for BRCs, for the micro-organism domain and for animal and plant BRCs. Some of the aims of these guidelines were:
• To safeguard biodiversity through repositories for reliable preservation and curation of biological resources.
• To support R&D and diagnostic laboratories by making available biological reference materials of guaranteed identity and quality.
• To underpin accurate taxonomic classification and identification to provide consistent naming of organisms of statutory, agricultural, horticultural, industrial and environmental importance.
• To provide the same level of quality service irrespective of the source of biological materials or information requested.
These guidelines provide basic quality management guidance for culture collections by setting the standard for quality management and biosecurity, building capacity, preservation of biological resources and data management. Although the detailed guidelines were intended to improve quality assurance in current collections and databases, it was recognised that full compliance with the guidelines would be difficult for many collections and that they may remain somewhat aspirational. Indeed, to date, only a few of the larger reference collections containing quarantine organisms have been able to fully comply with the best practices proposed through the OECD guidelines.
The larger reference collections of micro-organisms (including viruses, bacteria and fungi) have probably made most progress in terms of organised quality assurance. The EU demonstration project known as CABRI (Common Access to Biological Resources and Information) was initiated in 1996 and its database (http://cabri.org) is now maintained by seven member BRCs, some of which hold plant quarantine organisms, including the Belgian Co-ordinated Collection of Micro-organisms (BCCM), the CABI collections of bacteria and filamentous fungi, Centraalbureau voor Schimmelcultures (CBS) collections of bacteria and filamentous fungi and Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) collections of bacteria, filamentous fungi and plant viruses. A CABRI accreditation scheme has been developed by reviewing and collating methodologies and quality standards appropriate for each biological resource category for accessioning material into member and other collections. These are then measured and critiqued by comparing methods and results obtained with common representatives from each of the collections and randomly checking customer satisfaction.
Whereas the OECD and CABRI guidelines are intended for use by well-resourced public service collections, the World Federation for Culture Collections (WFCC) has also issued general guidelines (http://www.wfcc.info/guidelines) which aim to provide a first step towards the implementation of the OECD Best Practice. These include advice on appropriate operational facilities, staffing levels to allow operation at a high standard and training for staff with research expertise related to the aims of the collection. The guidance also demands compliance with national legislation, rules and regulations and addresses the capability of collections to meet relevant national and international regulations concerning the control, transportation and health and safety aspects of resource handling and distribution.
For botanical collections of plants, The Herbarium Handbook (3) is a widely-used standard text covering best practice for many relevant activities. Further modern administrative procedures are available through the BRAHMS database management system (http://herbaria.plants.ox.ac.uk/bol) for botanical researchers managing collections in herbaria, botanic gardens and seed banks. Developed at Plant Sciences, University of Oxford, it provides wide-ranging and innovative functionality to gather, edit, analyse and publish botanical data, optimizing its use for the widest possible range of curation services and research outputs.
This work package was aimed at service reference collections receiving, maintaining and providing access to specimens and reference materials representative of listed quarantine pests (4,5,6), invasive plants (7) or of other organisms that can interfere with their correct identification, e.g. as a result of shared diagnostic features, close taxonomic relatedness, or occurrence in a similar biological niche such as a particular commodity or shared habitat. The objectives were to review current quality standards, assess gaps where standards were missing or required improvement and then to produce guidelines on the application of minimum quality standards appropriate for each discipline of quarantine organisms.
2. Methods
Task 3.1. Review of currently used quarantine standards.
Current quality standards were reviewed through collaboration with WP2 on the preparation of the inventory questionnaire sent to all 110 identified reference collections of quarantine and related organisms. Key questions were formulated to obtain as much information as possible regarding existing quality standards used by each collection. Extra care was taken to ensure that the questions were relevant for collections of different organisms (viruses, phytoplasmas, bacteria, fungi, nematodes, insects and plants). Contributions were also made to the database of known reference collections of quarantine organisms (for intended receipt of the questionnaire) by updating information on the EPPO website. Responses to the questionnaire were received at the end of Month 12 and were used to prepare a draft report on the status of quality control within EU reference collections of quarantine organisms, which was presented to the workshop for collections and stakeholders in Kleinmachnow, Germany (28-29th November 2014) and circulated to all participants and project partners for further feedback and additions.
Task 3.2. Definition of minimum quality standards.
A preliminary list of minimum quality standards, appropriate for collections within each discipline of quarantine organisms (viruses, phytoplasmas, bacteria, fungi/oomycetes, nematodes, insects/mites and invasive plants), was compiled and tabulated by the Leaders of WP 3 and experts from each discipline. These took into account the gaps in currently-applied standards, as identified through the questionnaire undertaken in WP2. The tables were then posted on the project web portal for further discussion and amendment by all Q-Collect project participants and quality managers associated with the various collections represented within the project.
Task 3.3. Production of draft guidelines to achieve minimum quality standards.
Guidelines on suggested application of the agreed quality standards by service reference collections of quarantine organisms were then drafted by the Leaders of WP 3. These took into account:
a. Existing quality standards used by the various collections and gaps identified in Task 3.1.
b. Previously published guidelines for biological resource centres from OECD, CABRI and WFCC.
c. International (ISO) standards for establishment of quality management systems and certification of specific procedures appropriate for use in service reference collections.
d. European and Mediterranean Plant Protection Organisation (EPPO) standards on quality management and accreditation of diagnostic activities in diagnostic laboratories (8,9).
The draft guidelines were discussed amongst quality managers and a panel of other identified experts from the reference collections represented in the Q-collect project and were posted on the project web portal for further comment and modification by other project participants.
Task 3.4. Harmonisation of guidelines to achieve minimum quality standards
The draft guidelines were amended according to the feedback from project participants and other experts and were presented at the second project workshop held in CRA, Rome (8-9th September, 2015). A final harmonised version was produced, incorporating comments from Heads of plant health laboratories in the EPPO region and representatives from additional collections of quarantine organisms.
3. Results and Discussion
Task 3.1. Review of currently used quarantine standards.
Results from the questionnaire highlighted a wide variation in current quality standards across 152 EU reference and research collections, around 84% of which contained quarantine or relevant related organisms. Less than half of the collections maintained a catalogue of their accessions, although around two-thirds could provide at least a partial list of the specific quarantine and related organisms held. The breadth of information stored for each accession also varied across collections. Of 106 respondents, 50% reported that their host institutes/laboratories had a formal quality system covering maintenance of the collection. Of these 70% (33 collections) were officially accredited or certified, representing 9 collections of bacteria, 5 of fungi, 6 of insects, 3 of invasive plants, 4 of nematodes, 4 of phytoplasmas and 5 of viruses/viroids. A total of 30 collections conformed to ISO 17025 but only 8 to ISO 9001. To date there appears to be only one virus collection accredited to ISO 17025 together with ISO Guide 34:2009 for the production of reference materials.
Of 53 responding collections with no official accreditation, over 60% used validated methods or published keys for initial identification of specimens. Less than 50% applied document controls or monitored performance of laboratory equipment used in identification or preparation of reference materials. Less than 40% monitored training of personnel, customer complaints or preventative actions and less than 30% used calibrated equipment, monitored corrective actions or performed management reviews. Around 10% or less maintained any quality or technical records or performed internal audits. A high proportion of collections (75%) used a recognised method (published or generally agreed procedures) for identification and authentication of quarantine organisms. Over 70% of responding collections had documented procedures and records for primary identification of specimens. For those specifically using classical morphological identification, DNA/RNA sequencing, phenotyping methods or pathogenicity determinations, the proportion reporting documented procedures and data fell to 59%, 52%, 38% and 33% respectively. The collections also varied in their keeping of procedures and records relating to handling, storage and external supply of specimens. Characterisation of specimens was reported to be performed by an expert in 82% of the cases, although the definition of expert varied, mostly referring either to specialists with a higher degree, with some years of experience or specifically dedicated to working on the collection. Around a third of collections did not carry out checks on the stability or authenticity of specimens during storage or loan periods, although they considered such checks relevant. A full report on the current status of quality standards was produced as deliverable DL 3.1.
Task 3.2. Definition of minimum quality standards.
Whilst the choice of quality management system is similar for reference collections of all types of plant quarantine pests, specific quality requirements vary with the type of organism or reference material in question and according to whether reference materials are maintained and provided as live organisms or as fixed specimens or other material. Minimum quality standards were identified where specific competencies and/or standard operating procedures would benefit the routine activities of the reference collections. The following activities were considered:
• Information required on accession
• Data storage and maintenance
• Authentication
• Identification methods
• Storage and conservation
• Production of reference materials
Following feedback from project partners and other experts attending the Workshop in Kleinmachnow, minimum standards appropriate for each discipline of quarantine organisms were compiled according to the various activities and are shown in Table 1 (Deliverable DL3.2).
Task 3.3. Production of draft guidelines to achieve minimum quality standards.
Draft guidelines on the application of minimum quality standards were agreed through consultation amongst experts associated with reference collections of plant quarantine pests, including viruses, phytoplasmas, bacteria, fungi and oomycetes, nematodes, insects and invasive plants (Deliverable DL3.3).
Task 3.4. Harmonisation of guidelines to achieve minimum quality standards
Following presentation at the second project workshop in Rome and further consultation with project participants and other experts and quality managers from relevant collections, only minor changes to the draft guidelines were necessary. A final harmonised version of the guidelines on minimum quality standards (deliverable DL3.4) incorporating the table of the minimum quality standards agreed for each discipline, is attached as Appendix 1. This version was then forwarded, for potential publication as a future EPPO standard, to be considered by experts in each relevant discipline at the various meetings of EPPO diagnostic panels.
4. References
1. OECD (2001). Biological Resource Centres: Underpinning the future of life sciences and biotechnology. OECD Publications, Paris, France. pp 66.
2. OECD (2007). Best Practice Guidelines for Biological Resource Centres (June 2007),http://www.oecd.org/document/36/0,3343,en_2649_34537_38777060_1_1_1_1,00.html
3. Forman L, Bridson D, (eds.) (1989). The herbarium handbook. Royal Botanic Gardens,Kew, London.
4. http://ec.europa.eu/food/plant/plant_health_biosecurity/legislation/index_en.htm
5. http://www.eppo.int/QUARANTINE/listA1.htm; http://www.eppo.int/QUARANTINE/listA2.htm;
6. http://www.eppo.int/QUARANTINE/Alert_List/alert_list.htm
7. http://www.eppo.int/INVASIVE_PLANTS/ias_lists.htm
8. EPPO/OEPP (2007). PM 7/84 (1): Basic requirements for quality management in plant pest diagnosis laboratories. Bulletin OEPP/EPPO Bulletin 37, 580–588.
9. EPPO/OEPP (2010). PM 7/98 (1): Specific requirements for laboratories preparing accreditation for a plant pest diagnostic activity. Bulletin OEPP/EPPO Bulletin 40, 5–22.
Table 1: Summary of minimum quality standards expected of reference collections of quarantine plant pests and invasive plants.
Work package 4 – Access.
Partners involved:
WP Coordinator: INRA (Partner 9)
DLO (partner 1), DEFRA (partner 2), ILVO (partner 3), UGent (partner 4), UNIBO (partner 5), KNAW (partner 6), EVD-ACW (partner 7), ANSES (partner 8), INRA (partner 9), NATURALIS (partner 10), DSMZ (partner 11), AGES (partner 12), EPPO (partner 13), FGU VNIIKR (partner 14), JKI (partner 15) and NVWA (partner 16).
The objectives of this work package were:
4.1: To summarize knowledge of the biological resources available (what is where and how from WP2) and of the stakeholders needs (who need what, in which format and why) and how material can be deposited.
4.2: Organize the structured frame for deposit in collection (respecting CDB and Nagoya protocol) and distribution (respecting European and national laws) (using tools such as MTA) for those collections for which it is not available already.
To answer these objectives 4 tasks had been designed:
Tasks
4.1: To design a questionnaire for collections
4.2: To design a second questionnaire to be transferred directly to the collections stakeholders
4.3: To gather results from both questionnaires and assess who are the stakeholders and what they need and how
4.4: To link offer and demand
Task 4.1:
To design a questionnaire for collections to be linked to WP2 questionnaire (Task 2.2) in order to assess:
-who are their stakeholders and what they ask for (what are their needs) to collections
-how access to the biological resources is organised inside the collections
The questionnaire will be sent within Europe and EPPO countries to NPPOs and institutions, universities and other parties which use phytosanitary important organisms from collections.
The main target of this task was to summarize knowledge of the biological resources available (what is where and how from WP2) and of the stakeholders’ needs (who need what, in which format and why ?) and how material can be deposited.
The objective of this task was to retrieve directly from collection information about their stakeholders and what they ask to collections, and to have insights in how the access to the resources is organised.
In order to simplify the access to collections, we decided to implement our specific questions regarding targets of the WP4 to the WP2 questionnaires.
WP4 worked with WP2 and add 2 questions to their questionnaire addressed to collections. These two questions were dedicated to a better understanding of the collection stakeholder needs and definitions. These two questions were:
• Question n°23 – who are the customers of your collection?
• Question n°24 – what are they most interested in?
Moreover, two questions set up by the WP2 were also highly interesting for the purpose of the WP4. These two questions were:
• Question n°7 – Does your institute / laboratory have an ordering process?
• Question n°8 – Does your institute / laboratory have a Material Transfer Agreement (MTA)?
The questionnaire was sent within Europe and EPPO countries to NPPOs and institutions, universities and other parties which use phytosanitary important organisms from collections. Data were analyzed by WP2 and a report was transmitted to Q-collect partners.
Deliverable 4.1:
The questions set up for collections were included in Questionnaire from Work Package 2 (Task 2.2).
Task 4.2:
To design a second questionnaire to be transferred directly to the collections stakeholders (via collections) to assess who are they and what are their needs.
The main target of this task is to assess the needs directly from the collections stakeholders. A Q-Collect questionnaire for users of quarantine organisms was designed. It had been sending to Q-collect partners interested in the WP4 for further comments and inputs. After review, the final version of the questionnaire was set up by EPPO and displayed on-line on the Q-collect website. The link to the questionnaire was directly sent to NPPO via EPPO, quarantine users of the CIRM-CFBP (Angers, FR) and to all Q-collect partners to be transmitted to their partners using Quarantine pests and their stakeholders.
Following, there are two screenshots displaying the aspect of the online questionnaire which was available on the Q-collect website during the month of September 2014:
Figure 9: Screenshot of the Q-collect website showing detail of the online questionnaire.
Figure 10: Screenshot of the Q-collect website showing detail of the online questionnaire.
The questionnaire was closed at the end of September 2014.
Deliverable D4.2:
Questionnaire for stakeholders: Questionnaire for stakeholders (who are they and what they need and how?)
Task 4.3:
To gather results from both questionnaires and assess who are the stakeholders and what they need and how?.
The analysis of answers from the two questionnaires permitted us to assess in one hand what is the offer from collections and from the other hand what are the needs of the stakeholders. The data of both questionnaires had been be analysed by WP4 participants and analysed further at the expert meeting in Paris in March 2015.
Deliverable D4.3:
Analysis of answers from both questionnaires (questions to collections and questionnaire to stakeholders)
The objective of WP4 “Access” is to assess the users needs. This will permit to better understand which services the collections should offer in order to better fit the user’s needs in the objective to facilitate research on quarantine organisms.
In this purpose, WP4 “access” implemented questions in the questionnaire dedicated to collections, and set up a questionnaire directed to quarantine organisms users. These questionnaires were disseminated during summer 2014.
This report contains the results from the users questionnaires, associated with the results from relevant questions of the collections questionnaire.
The analyses and comments gathered during the experts meeting who took place in March 2015 were added. Finally this report contains a summary of the different assessed needs.
This questionnaire helped to better understand the users needs. Moreover we were able to conclude that these answers correspond to the reality of users needs. The analysis permitted also to point out that collections should extend their holdings toward being exhaustive in quarantine resources and should improve visibility.
The results gathered from this questionnaire permitted to determine that there are no specific needs from a specific type of user (private company or NPPO for instance) neither specific need expressed by users of a specific kind of organism (i.e. bacteria or insects users).
However, there is major difference if they need dead or alive material.
General needs expressed by all users:
- Collections holding the whole diversity of quarantine organisms.
Remark: Unavailability of material considered as the first problem for users.
- Collections clearly visible: web-site including clear contact and on-line catalog.
- Easy ordering process.
- and in a limited extend a reasonable costs.
Needs expressed specifically by users of living material:
- Help for dealing with regulations
Emerging need:
- Nucleic acids.
Task 4.4:
To link offer and demand: To gather the solutions adopted by the different collection already having implemented these tools, to follow the ECCO recommendations. Determine the relevant information to be provided to the stakeholders, through the website and tools designed by WP5 and WP7. This will help to design the collection network (WP6).
Deliverable 4.4:
Guidelines for collection deposit and distribution
In accordance with the project coordinator, this D4.4 deliverable “Guidelines for collections deposit and distribution: Guidelines for collections to organize deposit and distribution of biological resources and information” was merged with the D6.2 “Survey and guidance document reference criteria for network collections: Inventory of reference criteria for access to reference collections & connected databases within a sustainable European network”. This was done due to their closeness.
The document outlines a strategy for an improved access to service reference collections and their connected databases within the Q-collect network. In a first step the needs of both the user and the provider community and the problems that arise to fulfill them were identified. For this purpose the information on the current level of access to biological material (i.e. resources), which was determined by analyzing the surveys conducted by the work packages focusing on inventory (WP2) and access (WP4), was used. Based on these data, strategies to improve the present situation are proposed.
Deliverable 4.5:
Recommendations for info-portal and website and tools
The aim of this final deliverable was to outline what must be displayed in a website in order to help efficiently the stakeholders to have access to the biological resources they need.
We propose that the info portal may be organized with a core part common to all collections, and specific pages associated to individual collections, or pointing to collection’s web-site.
This list of recommendations will help to strengthened the link between collections and stakeholders via an efficient website.
Work package 5 – Info-portal.
WP Coordinator: KNAW-CBS (Partner 6)
Task 5.1. Make an inventory of all existing tools for (a) identification, (b) classification, (c) websites and databases containing useful meta data of interest to Q-collections and their end-users
In total 99 existing websites have been listed in the Q-bank database in a specific table called Q-collect. The importance of each of the 99 is divided in 4 categories (A, B, C and D) where A is the most important and D the least. Each website is checked on the existence of a direct search tool, identification tool and classification tool.
• Level of Importance for all 99:
o A: 23
o B: 43
o C: 25
o D: 8
• Tools available:
o Search tool: 88
o Identification: 30
o Classification: 18
The complete list of the websites of quarantine interest is also available as a forty-six page document available at http://www.q-bank.eu/Files/QCollect%20report%20WP5.1_2.pdf.
Task 5.2. In collaboration with the other work packages, obtain a wish list of what the ideal integrated database and infrastructure should look like.
After discussion with all partners at Kleinmachnow in November 2014 and in Paris in March 2015 with a core group, what would really be needed in terms of database, software and website infrastructure to collect all the basic requirements for a sustainable and future proof Q-system, we produced a first draft document of 25 pages, in which the following topics were discussed with a certain level of technical details:
1. Desired functions
2. Management system for curators
2.1. Management of collection’s data using desktop applications
2.2. Management of collection’s data using web based applications
2.3. Create bespoke management software using in-house resources
2.4. Use of existing open-source or free software
2.5. Use existing commercial software
2.6. Choice of databases
2.7. Backup of databases
2.8. Installation of software, versioning Information and Technology (IT) resources needs
2.9. Hosted solutions
3. Publication of data for third parties and Interoperability
3.1. StrainInfo
3.2. World Data Centre for Microorganisms
3.3. Taxonomic databases
3.4. Global Biodiversity Information Facility
3.5. Molecular and associated data resources
4. Preliminary proposal for the future Q-collect infrastructure
As discussed in this document, collections are numerous and as diverse as the organisms they are hosting. The procedures, the databases and the software they use are very heterogeneous. Some databases are easily useable by third parties while others have extremely limited interest beyond typical cataloguing purposes. Many collections are only useful for their holdings but the associated data are so poor in number and in quality that the viability of the collection is at risk, even if the biological materials themselves are of interest. End-users and clients of collections want more than just a biological store. They want to be able to retrieve associated data, use and analyse them together with other data. Except for a few cases, Collections are unable to provide such advanced services.
In addition, even if the number of biological material available from culture collections is relatively large reaching more or less 2 to 3 million records and hundreds of million for plants and insects worldwide, this number remains an anecdotal portion of the real diversity. Out of the total number of biological material used in scientific papers every year, only 0.01 percent of them are deposited in official culture collections (Stackebrandt E (2010). Diversification and focusing: strategies of microbial culture collections. Trends Microbiol 18:283–287). Although this figure is not known for quarantine plant pathogens and their look-alikes, in general it means that collections are far from being used to their full-extent and that many studies are using material that will most likely not be reusable in the future. This is a serious problem. Mobilization of the gathered diversity and associated data is a key factor for the future usefulness and success of collections.
The future Q-collect infrastructure should contain the following building blocks that could be implemented gradually in time:
1. A modern, dynamic and efficient collection data management, analysis and publication system
2. Increased acquisition rate of biological material and associated data not stored in Collections
3. Each participating Collection should manage their internal system to be compatible with a common global system
4. Data should be shared and accessible via a central portal allowing researchers and other databases or web services to interact
5. Advanced statistical data analysis system available that would take advantage of database containing collections data and would link them to third parties data
6. Advanced ontological and semantic web technologies implemented in order to allow complex investigations on combined datasets.
One option proposed by WP5 members of the Q-collect to address the issues already discussed above, is to create a Q-Book system to be strongly associated, intermixed with Q-bank and EPPO’s databases. This option pre supposes that a long term solution is found for hosting the Q-bank information. The Q-Book system would consists in a series of software tools and databases allowing any researcher to gather, store and share data associated with their biological material (not limited to biological material from official collections) which is one of the gaps identified during the surveys performed in the framework of WP2 and WP4 . The Q-Book system would also include features allowing researchers to perform conventional statistical analyses of data stored in such system alone or in relation to other data coming from other databases or web services. The Q-Book Semantic system would allow to investigate relations between interconnected databases and to retrieve data and properties that could be associated with or linked to biological material.
The future and proposed infrastructure will have the form of a central database containing a list of all strains, specimens or biological material of quarantine interest and link them to other major collections.
Task 5.3. Make a final architecture of an ideal integrated database and infrastructure.
A plan has been developed for an infrastructure called Q-Book. The latter has temporarily been integrated in the Q-bank website for demonstration purposes and because, with the EPPO website, it is certainly the most relevant Quarantine resources available for the moment.
Q-Book Systems Pilot Project
The Q-Book section of the Q-bank website is the result of an initiative of work package 5 of the Q-collect project. The basic idea behind the Q-Book systems is to allow any researcher or collection working in quarantine related field to store, manage, analyze and publish data associated to their biological material on a freely available platform deeply associated, intermixed with Q-bank and EPPO system. The system would be able to cope with the needs of very small to very large Collections. The new pipeline will include:
1. A mobile application (IOS, Android and Windows Mobile) to collect sample information (pictures, GIS coordinates, time and miscellaneous metadata) directly in the field.
2. A lightweight desktop application that will synchronize with the mobile app and where a complete and extensible set of data will be recordable such as administration, bibliographical, geographical, ecological, chemical, physiological, medical, molecular, links to other specialized repositories (e.g. GenBank, GBIF, etc.) and many more. This application will not only allow the storage of data but also to perform advanced queries, polyphasic identifications and classifications based on any combination of characteristics.
3. Data will be stored in a local light weight database.
4. Data will be shareable using the central Q-Book facility that will be accessible, searchable by anyone or by a selected list of co-workers.
5. An online or web-based tool will also be created allowing the addition, edition and management of strains, specimens or any biological material data that could be used as an alternative to or complementing the lightweight desktop application mentioned above.
6. The Q-Book website will include user-friendly basic and advanced searching facilities, distribution maps, online polyphasic identifications and web services to download data.
7. A publication tool will also be available to produce e-books or to export data in basic data exchange formats.
Figure 11: Q-Book systems & associated systems
Since the Q-Book system would be able to cope with all types of data and organisms, it would be used by a very large panel of researchers and people worldwide. It would be used in many scenarios such as biodiversity management and conservation programs anywhere in the world, quarantine and invasive organisms fight, epidemiology or medical diagnostic. It will be especially beneficial to researchers or collections with no or low financial and technical resources.
There are no such projects proposing to record biodiversity at the unit level (strains, specimens or other biological material). Initiatives such as EOL, Catalogue of Life, Species 2000, IUCN, GenBank, StrainInfo, GCM, BOLD or GBIF are concentrating on species data and are, for some of them, referring to existing and officially recognized museums or culture collections. To our knowledge, there is no complete pipeline that proposes what we are going to initiate here. This ambitious project will be unique and used worldwide. African and lesser-developed countries as well as collections with no or little resources will certainly be the first to benefit from the proposed system since it will be freely and easily accessible. Most of the African Biodiversity remains unknown and very few African researchers have the ability to buy advanced tools to propose their results to third parties. The Q-Book system will allow them to be visible to the scientific and quarantine problematic community and will inevitably initiate collaborations between research groups that, otherwise, would never know about each other. Since the central database would include a very large range of organisms (from dead material to viruses to higher and large organisms), the diversity and the number of potentially useful data to characterize the biological materials will be huge.
Figure 12: Q-Book systems for data capture and edition
Where possible data deposited in Q-Book will be automatically enriched and linked to existing databases such as Genbank, PubMed or SwissProt (via provided accession numbers) but also, via geographic positioning (latitude, longitude, altitude, etc) to other datasets like climate, soils, agricultural practices, elevation, vegetation or many other environmental parameters such as demographic, socio-economic or cultural aspects.
Data stored in the Q-Book system will be archived in a coded and a highly structured way and everywhere possible, text data will be avoided to allow descriptive statistics (average, variance, frequencies, etc.) to be easily computed. Each data point will be considered by the system as a programing object and usable by object oriented programming languages. Such a system will allow the statistical tools to analyze large datasets and perform correlation analyses (for example but many more will be possible as well, like factorial analyses). The semantic system included in Q-Book will allow users to navigate through heterogeneous but highly connected datasets and to find biological material that have potential properties in view of specific Q related research. Statistical and semantic tools will be operable via simple user interfaces from either simple desktop applications or web based systems. This would allow non-advanced users to perform basic calculations, statistics or navigate through complex datasets in a simple way.
The proposed facility will create a virtual research environment where users will be able to find, connect, correct, combine, visualize, analyze and interpret new combinations of heterogeneous data that are relevant to address their Q-research areas. A framework for resource integration will be developed, combining the taxonomic backbone for species identification, geo-referenced environmental data, existing systems for observational data, and information on species traits and attributes. These resources will become accessible to users within seconds, by (i) providing searchable metadata that describe the data and its source, (ii) assigning unique identifiers as linkers between data according to accepted standards, (iii) creating interfaces and query systems, and (iv) installing routines for quality control and interpolation of data in space and time. The architecture is modular, flexible and scalable, and will be the first infrastructure in the world specifically designed for the integration of such Q-resources. Innovative new services will be made available, based on an analysis of the common needs of users in the prioritized areas: services to analyze genetic diversity of mixtures: ‘environmental DNA’, services for new observational methods using smart sensor technologies, services for constructing species interaction networks, services to link meta-omics data to ecosystem processes in (micro-) communities, for which physical model ecosystem facilities will be created. This being a service-based e-infrastructure means that users can access resources and computational facilities from any place, but also meet in person with technicians when needed to discuss progress and results: facilitating research collaboration is an integral part of the proposed system. Larger or more advanced collections already having strong CMS will also be able to participate to the project by sharing their data via web services. With their permission, their data will be retrieved through web services and will feed the central Q-Book database allowing to perform queries as well as data analyses on the broadest possible basis (see Figure 4).
Figure 13: Q-Book systems functional scheme
The Q-Book system will also allow small collections or the ones without an existing data management system to have a complete system allowing to integrate and publish their data using a mobile app, a desktop application or using the web based editor directly accessing their records stored in Q-Book. The development of the Q-Book systems will certainly not be achieved by the collections themselves since this would require advanced programming and databasing skills that are not or almost never available in current culture collections. Subcontractors with the relevant experience will have to be hired to build the wanted systems in close collaboration with collections experts and Q-bank as well as EPPO, but also with the end-users (existing and foreseeable new or potential ones).
The system will be completely free (free mobile and desktop applications) and the Q-Book system will be hosted and maintained by Q-bank and/or EPPO if the needed resources are made available by one or several financing bodies. The problem of sustainability is one of the major issues that need to be tackled in future projects.
During this project a pilot and preliminary version of the possible future Q-Book database was created and includes a large number of the suggestions and proposals made in all the WP of the Q-collect project. A sub-website of the Q-bank website was created and includes:
1. A welcome page containing the above text (see http://www.q-bank.eu/Defaultinfo.aspx?Page=Q-Book)
2. A search engine allowing to find Q-material of interest. For the moment, only bacterial strains from the CFBP collection (Anger, France) are included (see http://www.q-bank.eu/BioloMICS.aspx?Table=Q-Book)
3. A single deposit form to upload biological material data in the Q-Book system (see http://www.q-bank.eu/BioloMICSUpdate.aspx?Table=Q-Book%20deposit%20form). A registration system has also been implemented to avoid unwanted deposits. Only registered users can upload data.
4. A multiple/batch deposit sheet to upload biological material data in the Q-Book system (http://www.q-bank.eu/Files/Deposit.xlsx). The latter was used to import data from the CFBP collection.
5. A search engine for repositories of interest (deliverable 5.1. see http://www.q-bank.eu/biolomics.aspx?Table=Q-Repositories)
6. A list of repertories of interest as pdf document (http://www.q-bank.eu/Files/QCollect%20report%20WP5.1_2.pdf)
The very preliminary Q-Book system developed here could be used as starting point for a solid and future-proof Q-System (possibly included in Q-bank) including a complete version of all the feature describe above.
Task 5.4. (a) Collect and organize all the data, information and guidelines obtained from all WPs. (b) Make items collected in point (a) easily available for a restricted number of testers to ensure that it will be useful and user-friendly for the final end-users. (c) Make the infrastructure/information publically available through a website in collaboration with WP7.
Data and deliverables collected during the project have all been stored in and are publically available from the Q-collect website maintained by EPPO at www.q-collect.eu. As mentioned in report 5.3 a sub-website of the Q-bank website was also created and includes a number of features that were decided in deliverables 5.2 and 5.3. This includes, a welcome page containing the above text (see http://www.q-bank.eu/Defaultinfo.aspx?Page=Q-Book); a search engine allowing to find Q-material of interest. For the moment, only bacterial strains from the CFBP collection (Anger, France) are included (see http://www.q-bank.eu/BioloMICS.aspx?Table=Q-Book); a single deposit form to upload biological material data in the Q-Book system (see http://www.q-bank.eu/BioloMICSUpdate.aspx?Table=Q-Book%20deposit%20form); a registration system has also been implemented to avoid unwanted deposits; a multiple/batch deposit sheet to upload biological material data in the Q-Book system (http://www.q-bank.eu/Files/Deposit.xlsx); a search engine for repositories of interest (deliverable 5.1. see http://www.q-bank.eu/biolomics.aspx?Table=Q-Repositories); a list of repertories of interest as pdf document (http://www.q-bank.eu/Files/QCollect%20report%20WP5.1_2.pdf).
Work package 6 – Sustainable European Network of Reference Collections.
WP Coordinator: AGES (Partner 12)/ UGent (partner 4)
The objectives of work package 6 comprised first of all the provision of discussed, agreed and internationally compatible reference criteria for both the establishment and the maintenance of a sustainable network of European reference collections of plant health quarantine organisms resp. taxonomically related organisms. Furthermore reference criteria for the access to these reference collections and their connected databases should be established. Finally a process description for the application of the developed and defined reference criteria should be developed.
For the establishment of the reference criteria Q-Collect-project results from WP2 (“Inventory of important phytosanitary collections”), WP3 (“Quality standards”) and WP4 (“Access”) as well as data, standards and experiences from existing national and preliminary trans-national inventories from participant countries and recognized organisations, such as EPPO and information from ongoing complementary European research initiatives such as MIRRI were considered.
Eight general criteria and five specific criteria groups for seven taxonomic groups of phytosanitary organisms and invasive plants in Europe were determined to specify the Terms of References (ToRs) for the participation of service reference collections and working collections in the Q-collect network with regard to both the network establishment and the network maintenance. The general criteria comprise the legal requirements, the scope of relevant organisms harmful to plants (regulated, emerging and invasive plants) and the basic overall requirements concerning the quality and provision of reference material as well as metadata generation and delivery, inclusive the different rights and responsibilities connected to the two collection types considered (Q-collect-DL6.1 Annex 1). Overall about 65 criteria were identified for the five different specific criteria groups 1) inventory/catalogue establishment and maintenance, 2) identification methods, 3) authenticity of the material, 4) storage and conservation and 5) preparation and access for the seven taxonomic groups a) viruses/viroids, b) phytoplasmas, c) bacteria, d) fungi/oomycetes, e) insects/mites, f) nematodes and g) invasive plants which are listed in the five inventory tables (Q-collect-DL6.1 Annexes 2.1 2.2. 2.3 2.4 and 2.5).
Figure 14: WP6.1: Number of reference criteria in the specified reference criteria groups.
The major part of the developed and agreed collection reference criteria was applicable and could be accomplished according the current state of the art, especially for the four taxonomic groups viruses/viroids, bacteria, fungi/oomycetes and nematodes with 90.5% average applicability in both collection types. For the other taxonomic groups the applicability was lower ranging between 80.4% (arthropods, phytoplasmas) and 57.7% (invasive plants) of the reference criteria.
Figure 15: WP6.2.
Figure 16: WP6.3.
Figure 17:WP6.4.
Figures WP6.2 – WP6.4: Portion of required and optional reference criteria in the different types of reference collections for VIRUSES/VIROIDS (Fig. 15), INSECTS/MITES (Fig. 16) and INVASIVE PLANTS (Fig. 17)
Figure 18: WP6.5.Example of reference criteria annex table.
With regard to improved access to the different types of reference collections and their connected databases the user/provider community needs and the obstacles were identified by analyzing the results of the questionnaires in WP4 (“Access”). As primary intentions to obtain access to biological reference material and also to “lookalikes”, the use of the reference material for diagnostics (positive controls, development of methods), for research and for teaching purposes were reported by the addressed stakeholders. At the same time the retrieval of biological reference material was considered as severely hampered by the lack of accessible catalogues and of accessible information about the handling of resources by users, incl. MTA’s. It was concluded that there is an urgent necessity for an integrated information system accessible through a user-friendly web-portal, to improve the visibility and localization of resources as well as the order process and traceability of exchange. As a consequence a FAIR (Findable, Accessible, Interoperable, & Reusable) information system and web-portal is proposed. Several added values of the Q-collect network were identified, such as:
• the establishment of a well-designed Q-collect network portal to provide an inventory of existing phytosanitary important collections within Europe and their content
• a one point access to a broad range of biological resources and expertise,
• improved interoperability between collections as overarching network
• reduced fragmentation in resource availability
• adequate quality assured information on resources and related issues (growth conditions, regulations regarding transport, biosecurity, ...).
Guidelines for collections on how to achieve these criteria have been developed (DL6.2 and DL4.4.)
A feasible and practicable flow chart was developed to visualize the process steps for the application of the developed and defined reference criteria in a sustainable network of European reference collections of plant health quarantine organisms (Figure 19: WP6.6).
Figure 19: WP6.6.Flow-Chart for the application of the reference collection criteria
Work package 7 – Dissemination
WP Coordinator: EPPO (Partner 13)
Objectives
7.1. To develop and update a website
7.2. Disseminate efficiently relevant information of the project to stakeholders in particular the plans for a sustainable collaboration, coordination for the maintenance of transnational reference collections and databases through the website
7.3. General presentation of the project to be used in national or international communications about the project
7.4. To develop EPPO standards on quality control on phytosanitary collections
7.5. To organize two workshops for collections and relevant stakeholders.
Partners involved:
WP Coordinator: EPPO (Partner 13)
DLO (partner 1), DEFRA (partner 2), ILVO (partner 3), UGent (partner 4), UNIBO (partner 5), KNAW (partner 6), EVD-ACW (partner 7), ANSES (partner 8), INRA (partner 9), NATURALIS (partner 10), DSMZ (partner 11), AGES (partner 12), EPPO (partner 13), FGU VNIIKR (partner 14), JKI (partner 15) and NVWA (partner 16).
7.1. Website
A dedicated Website was established by the EPPO Secretariat at the start of the project. The beta version was prepared in January 2014 and was launched on the 27th of February 2014. The Website can be accessed at http://www.q-collect.eu/. The website included general information on the project as well as links to the questionnaires organized in the framework of the project. It was updated whenever needed (e.g. the section latest news was updated when the questionnaires were launched and to announce and report on project meetings and dissemination Workshops ).
The Website included 6 sections.
The layout is illustrated below
Figure 20: Website of Q-collect main page.
7.2. Online project leaflet
A leaflet was prepared by the EPPO Secretariat and presented at the Kick-off meeting of the project on the 2nd of December 2013. It was posted on the website on the 27th of February 2014 when the project Website was launched.
The leaflet is available on http://www.q-collect.eu/publications in two formats and is presented below:
Figure 21: Flyer of Q-collect.
7.2. Disseminate efficiently relevant information of the project to stakeholders in particular the plans for a sustainable collaboration, coordination for the maintenance of transnational reference collections and databases through the website.
In the course of the project information resulting from the two project meetings and two workshops were disseminated to stakeholders through the website. Meeting reports were posted, for the two workshops links to presentations made provided, allowing visitors to access detailed information presented during meetings.
Figure 22: Website of Q-collect events page.
7.3. General presentation of the project to be used in national or international communications about the project.
The project and its outcomes have been presented in different EPPO meetings: Panels on Diagnostics in the course of 2014 and 2015, Working Party on Phytosanitary Regulations in 2014 and 2015; Workshop for Heads of Plant Pest Diagnostic Laboratories (the Workshop included a special section on Q-collect). In addition a presentation of the white paper developed in the framework of the project was presented to the Heads of National Plant Protection Organizations (2015-09-15/16, Riga).
The outcomes of the Q-collect projects will be presented during the EPPO Conference on diagnostics for plant pests (2015-12-01/02, Angers, France).
7.4. To develop EPPO standards on quality control on phytosanitary collections
The deliverable prepared by WP3 for quality standards has been included in the agenda of all EPPO Panels on Diagnostics (horizontal Panel as well as Panels for the different disciplines). They will be reviewed in the course of 2016 with the objective to adopt EPPO Standards. A presentation was made at the last EPPO Panel on Diagnostics in Bacteriology (2015-10-20/22). Detailed review of the document by this Panel is expected to take place in June 2016. According to the EPPO Standard Setting procedure the development of a Standard needs approximately two years for from the presentation of a first draft. It can be expected that a version could be sent for Country Consultation of EPPO member Countries in 2017.
7.5 Feedback on criteria proposed for the establishment of a sustainable network
In addition to the review of the draft on quality control of collections, the criteria proposed for the establishment of a sustainable network will be reviewed in the EPPO Panels on diagnostics. The guidelines developed within Q-collect project will sent for information to the organizers of test performance studies (as these are laboratories sharing biological material from their collections in this framework). This will allow feedback to be gathered about the criteria proposed for the network.
7.6. Workshops for collections and relevant stakeholders.
Two workshops were organized during the Q-collect project.
The objective of the first Workshop (Kleinmachnow, DE) was to present the progress made after 12 months, and gather stakeholder expectations. A summary report of this first Workshop is available on the Q-Collect project website http://www.q-collect.eu/events/.
See 7.1 for details.
For these workshops all collections identified during the inventory organized in the framework of WP2 were invited to attend as well as all Heads of EPPO Plant Pest Diagnostic Laboratories.
The first Workshop took place at the Julius Kühn Institute in Kleinmachnow (DE) on 2014-11-27/28 and 45 participants from 16 countries attended.
The second Workshop was attended by 45 participants from 19 countries and including a representative of the International Plant Protection Convention Secretariat who stressed the importance of collection for official plant pest diagnostic.
Details on these Workshops are available on the Q-collect website.
Potential Impact:
In the Q-collect project an inventory was made on collections of phytosanitary importance within the EU and the EPPO region. Through answers on a questionnaire we got insight in the quality and the material available in those collections. Within the Q-collect consortium we identified gaps in those collections and a number of recommendations to fill these gaps were made. Priority needs and obstacles of the user/provider community with regard to the access to biological reference material and to the connected services were identified.
In proposing the creation of a sustainable network of reference collections and producing guidelines for quality criteria standards and access, Q-collect created a significant impact for collections in the near future as part of EU Reference Laboratories for plant health diagnostics (in line with the amendment of Regulations EC 882/2004). Furthermore, the inclusion of EPPO as partner within the consortium greatly strengthened the impact of this project. EPPO, as regional organization with 51 member countries, has a strong role in Plant Health and distributed by its network the outcome of the Q-collect project results most efficiently to all stakeholders interested in Plant Health.
A strong link has also been established with the MIRRI project. MIRRI (Microbial Resource Research Infrastructure) started in 2012 and is established on the European Strategy Forum for Research Infrastructures (ESFRI) road map with the goal to improve access to the microbial resources and services that are needed to accelerate research and discovery processes. The ESFRI Roadmap (2008) emphasises the evident need for improved availability of high quality materials and reagents for the study of species other than humans i.e. the animals, plants, bacteria - microorganisms. The objectives of MIRRI were completely in line with the objectives of Q-collect for microorganisms. Several partners of the Q-collect consortium were also participating in MIRRI and ensured most optimal cross exchange between both projects. Although MIRRI is only focusing on microbial collections and Q-collect is also including nematodes, arthropods and invasive plants, this collaboration helped Q-collect in obtaining its deliverables. A questionnaire which is developed within the first half year of the MIRRI project was used and adjusted to Q-collect needs and send to relevant collections and stakeholders .
The Q-collect project made an important first step to the harmonisation, interconnection and quality improvement of collections in the field of Plant Health, which is needed for a good infrastructure essential for the detection, interception and recognition of both established and new or emerging plant pathogens and pests. Plans for transnational access to the data of the established benchmark collections for quarantine pathogens and pests have been made by using existing state-of-the-art solutions for developing searchable networks of collected specimens in biodiversity informatics. With this implementation of a transnational accessible joint search info-portal for the establishment of databases and collection management systems, Q-collect provided the first step in improved services to the consortium partners and for the whole Plant Health scientific community.
The expected impact of Q-collect on the European Research Area of Plant Health will be improvement in the following areas:
- Models for sustainable collaboration, coordination and maintenance of trans-national reference collections
A key output from this project is the proposed establishment of initial networks with defined criteria of key international reference collections of quarantine plant pests and pathogens. In an initial phase, collections represented by the project partners will be involved, but this concept can be extended to all relevant collections through information posted on the project website, two international workshops involving the main stakeholders and also through on-going links through EPPO and the MIRRI project. The embryo networks and associated project outputs serve as models to catalyse on-going and more extensive collaborations amongst the other European reference collections. These collaborations will help to increase the diversity of reference materials and ensure that they are preserved under common standards, are easily located and made available to end-users across the whole community for the near future. The model system of transnational networks will also help to identify and safeguard specific reference materials which are in danger of being lost due to current lack of infrastructure, resources or taxonomic experience amongst the many informal (and often temporary) research (or working) collections that exist across the EU.
- Info-portal to improve sourcing of quality reference material as diagnostic tools.
The Q-collect project generated a pilot info-portal that will effectively catalogue in a simplified way all currently available reference materials of relevance to the plant health community, the locations where they are held under common quality standards and harmonised guidelines via which they can be obtained and used by end-users across the EU and wider EPPO region.
At the end of the Q-collect project only information was available for a few collections, but this needs to be extended to all collections included in the network. Once this information is available it will facilitate the procurement of standardised reference materials from a choice of reliable sources and guarantee their suitability for use in diagnosis, method validation, research and proficiency testing. Analyses of current gaps in the availability of particular quarantine reference organisms or important taxonomically or diagnostically similar organisms will similarly be made widely available, thus creating opportunities to extend the catalogue the holdings of the network either through deposition of key organisms via the reference collection networks or by incorporation of additional collections into the relevant networks.
- Harmonised guidelines to ensure reliability and sustainability of reference materials.
Within the Q-collect project, guidelines to standardise requirements of quality, maintenance, access, procurement and use of reference standards were produced. These quality criteria will be discussed in the different EPPO panels and once agreed they can be used as EPPO standards.
The further harmonisation and dissemination of those guidelines will also have impact far beyond the life of this project. The developed guidelines will help to increase the capacity of independent national reference collections thus enabling them to operate to the agreed international reference standards and either join the international collection networks or offer alternative independent sources of reference materials. In either way, the quality and diversity of these materials will be increased, sustaining and safeguarding their availability in the longer term.
- Training of staff involved in preservation, supply and correct use of reference materials.
Within the Q-collect project this part of collections was not discussed. However, it is expected that once the envisaged future network of important phytosanitary collections is established, training of staff members will be a particularly important task for such a network. Training should enable education of all persons involved in the preservation, supply and use of reference materials in the field of Plant Health. The long-term impact will be supporting networks of model reference collections of quarantine organisms with capacity to provide advice and training in:
- preservation methods,
- taxonomical verification of reference specimens or samples,
- minimum quality standards,
- diagnostic methods for detection and identification,
- correct use of reference materials, and
- regulations surrounding their safe movement and application.
In the questionnaire of the Q-collect project collections were asked to identify scientists with taxonomic expertise relating to key groups of quarantine pest and pathogens who will be highlighted as key contact persons for younger scientists wishing to work with those organisms. At the same time the project also identified those areas where expertise is currently lacking, and where future research and training needs to be focussed. This exercise in fully in line with the strategy that is also developed in the MIRRI research infrastructure.
- Relevance to creation of EU Reference Laboratories for plant health diagnostics, in line with Regulation (EC) 882/2004.
All of the above mentioned expected impacts is highly relevant towards the identification, strengthening, co-ordination and networking of pockets of national expertise on quarantine organisms and the possible creation of EU reference laboratories for plant health diagnostics in line with those that have been created for Regulation (EC) 882/2004. In this way, official controls performed to ensure the verification of compliance with feed and food law, animal health and animal welfare rules would also be applied to the verification of compliance with Plant Health law stipulated under Commission Directive 2000/29/EC.
Spreading excellence, exploiting results, disseminating knowledge
Q-collect disseminated the results during and at the end of the project in several ways to the stakeholders. Partner 13 (EPPO) is leader of WP7 Dissemination. They have disseminate the project and its results to the wider plant health stakeholder community in the following way:
- A dedicated website has been developed to show the objectives of the project,
- An electronic leaflet explaining the project has been made available via the website,
- Stakeholders have been contacted during the project with a questionnaire to guarantee that their wishes, in relation to relevant phytosanitary collections, are ensured,
- Two workshops have been organized: one after one year and the second at the end of the project to disseminate the results and discuss other collections, institutes, NPPOs within the EU and EPPO region, inspection services and other stakeholders the outcome of the different work packages.
Relevant targeted stakeholder groups (NPPOs within the EU and EPPO region, industrial sector, policy, end-users and other stakeholders were contacted by a questionnaire to ensure that their requirements are incorporated into the project. They have also been invited to attend the two workshops, which were organized within the project (year 1 and year 2).
Dissemination to laboratories of National Plant Protection Organisation was ensured through EPPO via different channels (direct contacts with Heads of NPPOs, dissemination thought EPPO Panels on Diagnostics, and workshops for heads of plant pest diagnostic laboratories).
Project results such as inventory results, quality standards, access criteria, reference criteria and other deliverables from the seven different work packages have been made available to participating organisations and in part to other interested groups by publication in guidance documents
Information about the content and location of the reference collections, service reference collections and working collections and the trans-national accessible info-portal will be made publicly available through the project website.
The external project website presents descriptions of Q-collect objectives, of the project consortium, reports of meetings, the project outputs and links to other appropriate websites of each participating organisation/country and other relevant organisations. Recipients of information will be EU Plant Health diagnostic laboratories, Regional Plant Protection Organisations (RPPOs), and key non-EU National Plant Protection Organisations (NPPOs). RPPOs and some key non-EU NPPOs who are active in relevant phytosanitary-related research, or key exporting countries to the EU, will be contacted early in the project. They have been informed of the project’s aims and objectives and were invited to discuss issues and explore possible interactions with the Q-collect network, including joint activities beyond the end of the project.
Publishing information materials (plus printable leaflet versions in English only) about Q-collect have been produced for the consortium members to be distributed at meetings and conferences.
Progress reports were produced for the EC. The outputs of the project have been presented to the participants of the Final Project Dissemination Workshop, such as research funders, research providers, Plant Health policy makers, ‘industry’ representatives and interested parties from across Europe, and from outside Europe (e.g. RPPO’s and, as appropriate, key non-EU NPPO’s).
The Q-collect project results can be exploited by the NPPOs and associated diagnostic laboratories. The guidelines on Quality Assurance for reference collections will be further developed with EPPO Panels for each group of organisms in order to prepare an EPPO Standard.
Additionally, the joint search portal of the connected databases of benchmark and reference collections will be used both by the consortium members and other NPPOs within Europe.
White Paper
During the project a white paper on phytosanitary important collections has been written and discussed at the second workshop in Rome (September 2015).
Phytosanitary diagnosis and collections
Introduction
International trade and movement of plants and plant products into and from Europe has increased tremendously in recent years leading to higher numbers of consignment imported. The type of commodities imported and the origins have also diversified. As an illustration; imports of woody plants from Asian origins have become more frequent than in the past where most woody plants were traded between European countries. As a result, the rate of introduction and establishment of new organisms in Europe has increased steadily as well as the phytosanitary risk of introducing such new organisms.
Organisms relevant in plant health include plant pathogens, arthropods and invasive plants. Some may have already been identified as posing an unacceptable risk to agricultural and horticultural crops, forests and the wider environment and currently approximately 250 organisms are included in the Annexes of the Directive 2000/29/EC as pests of the European Union (also called quarantine pest lists). However, it should be noted that some of the pests recently introduced in Europe had not been identified as posing an unacceptable risk before they established in Europe. Consequently the phytosanitary vigilance to detect unknown pests needs to become more and more efficient.
As plants may be latently infected, inspection of consignments and of places of production of plants and plant products often involves laboratory analysis of samples collected during these inspections. In outbreak situations the accurate identification of the causal agent relies on laboratory testing as well. In all these situations the capability of National Plant Protection Organizations (NPPOs) and the affiliated laboratories to quickly and reliably detect and identify organisms is critical for effective phytosanitary measures to be taken. Plant pest diagnostic is also essential to support the phytosanitary certification of consignments of plants and plant products exported from Europe.
In order to better ensure the reliability of diagnostics, laboratories are increasingly working under quality assurance systems (including accreditation, ISO 17025) and this is becoming a requirement of National Plant Protection Organizations for laboratories performing official tests.
Under such circumstances, laboratories need to have access to well characterised biological reference material for morphological identifications and the use for development and validation of tests. Moreover, in tests biological reference material is needed as a base for positive and negative controls.
Validation of tests is carried out to provide data on the performance of a test and in particular regarding its analytical sensitivity and specificity. Reproducibility of a test is also essential and is often determined in test performance studies. In order to be able to establish these performance characteristics, well-defined biological reference material is needed for the organism to be identified with the test but also for those organisms with which the target organism may be confused with (look-alikes). Availability of biological material coming from reliable, curated collections is thus essential for test development and validation. In order for laboratories to confirm its competence to correctly perform tests, participation in proficiency testing schemes is recommended. Although offers to participate in proficiency testing are currently still limited in the plant health sector, they are increasing. Laboratories organizing proficiency testing need to have access to well-defined biological material of the target organism but also material of look-alikes.
Finally biological material is also essential to ensure the quality of analyses at different levels: for each diagnosis as well as for global quality control of the laboratory. Although molecular tests are based on nucleic acid sequences, biological material is essential for the development, validation and quality assurance of these tests. Reliability of the sequences on which the tests are based depends on the correct identification of the original biological material.
The biological material also needs to be kept in collections as a current source of reference DNA. New molecular technologies like Next Generation Sequencing (whole genome sequencing) will increase new taxonomic insights in essence on the short term for bacteria, viruses (viroids) and fungi. Therefore it is essential to be able to re-examine the original biological material. Biological material is also needed for quality control of nucleic acid isolation. Biological material is kept in collections and these should provide appropriate guarantee regarding this material in term of quality.
New legislations
The Nagoya Protocol
The Nagoya Protocol on ‘Access to Genetic Resources and the Fair and Equitable Sharing for Their Utilization’ was adopted in 2014 and will have impact on all researchers working with biological resources1. It is a legal binding instrument for the implementation of the Convention on Biological Diversity (CBD). The CBD has three main goals i) the conservation of biological diversity; ii) the sustainable use of its components and iii) the fair and equitable sharing of benefits arising from its utilization. Basically the CBD recognises the sovereign rights of countries over their own biological resources and the so-called genetic resources contained therein. Access to genetic resources in a country that is party to the CBD (i.e. a country that has signed and ratified the CBD) requires prior informed content (PIC) from the competent authority in that country and a setting of mutually agreed terms (MAT) between provider and user. Parties are free to decide whether access to genetic resources is subject to such requirements or not. But the Party must assure that, within their territory, genetic resource, originating from other Parties (countries) are handled according the CBD and that benefits arising from the use of the genetic resources or traditional knowledge associated with these resources are shared fairly and equitable.
The Nagoya Protocol aims to provide guidance for the parties to implement the CBD’s fair and equitable sharing of benefits arising from the utilization of the resources by adopting their national access and benefit sharing (ABS) legislation. The biological material (including DNA extracts) held in collections is covered by the Nagoya Protocol. This Protocol is now going to be implemented in the EU 2 and guidelines are being prepared and are currently under consideration by different groups. The objective at European level (http://eur-lex.europa.eu/legal-content/FR/TXT/?uri=uriserv:OJ.L_.2015.275.01.0004.01.FRA ) is an implementation of the Nagoya Protocol on the 12th of October 2015. It should be noted that this legislation seems to create conflict with obligations under the IPPC, for example it is not clear if specimens isolated from imported consignments can be stored and used for diagnostic and research purposes. This needs to be clarified.
New EU control directive
For EU member states, a major change in the organization of plant pest diagnostic laboratories performing official diagnostic will happen with the revision of the EU Regulation No. 882/2004 on official controls. The new Regulation proposal of the European Commission will extend the scope of the above Regulation to plant health. One of the changes foreseen will be the establishment in the plant health sector of a network of official laboratories, National Reference Laboratories (NRL) and EU Reference Laboratories (EU-RL). For these laboratories performing tests the requirements will include accreditation and the use of standardised methods. The EU-RL will (among other tasks) play a dominant role in elaboration and harmonization of tests, analyses and diagnosis and providing reference methods, providing reference material, organisation of test performance studies and proficiency testing. The EU-RL therefore needs (the access to) a reference collection. Therefore the need of well-established reference collection will increase even more in the coming years.
Current situation
Results of Q-collect project
The survey organized during the Q-collect EU funded project confirmed that although there is a significant number of plant pathogens and pest collections still present within Europe, they are dispersed, widespread and of very variable quality. The main findings of the project are as follows:
- Most collections are working or research collections and only few of these collections are likely to be organized to provide services to outside users.
- There is a limited number of information on collection’s holdings available online.
- Many collections have no quality system in place, and accreditation of collections is scarce.
- Sharing of material between collections to ensure resilience is not common and can be considered as a high risk for loss of important biological material in case of incidents with buildings or equipment.
- Appropriate basic funding is not secured enough and there is a need for a common policy towards collection management throughout the region.
Achievements of the project
• Guidelines have been drafted on Quality assurance for reference collections and will be further developed with Panels for each group of organisms in order to prepare an EPPO Standard.
• The Project proposed criteria for the establishment of a sustainable network. This network will bring together previously dispersed information on biological material and stimulate collaboration. The criteria will be reviewed in the EPPO framework.
• The Project recommended that an online platform should be established and maintained to stimulate and facilitate networking and data sharing. This platform will improve accessibility and visibility of biological material (and related information) available in collections. A pilot platform will be established to include a deposit form for information on biological material, a search engine and links to additional relevant information available online.
Other initiatives
Online access to collections can facilitate the availability of collection. Since 2010 a database called Q-bank has been elaborated. This database links information, sequences and collections of the most important organisms (Q-organisms, look-alikes and other important organisms). The database can be used for diagnosis, but gives also the possibilities of finding organisms in collections. This initiative originally started as a Dutch project. The EU funded project QBOL has been using Q-bank to serve as a repository of DNA sequences. Nowadays this database is maintained by a group of international scientific curators responsible for their discipline. In the past 4 years the Dutch government has supported this group and the database was further elaborated. During the Q-collect project more work on this database has been done especially on quality criteria.
Future
Goal for the future: for every organism group/discipline there are at least at 2 locations official reference collections and through online catalogue(s) these reference collections can be accessed by interested users to search and order material.
All the initiatives of the past years (Q-bank, QBOL, Q-collect, etc.) have given a boost to the phytosanitary collections. Much energy, knowledge and hard work has been given to the collections. The challenge is to keep up the good work and follow this road. In the coming years it is unlikely collections will be supported with big additional budgets or project funding. However, a database like Q-bank has proved that it is possible to connect specialists and their collections on an online platform. Other projects have proved that the network of phytosanitary specialists is strong and people are willing to collaborate. In the framework of Euphresco there are many international co-operations especially between official NPPO related laboratories. The laboratories in the EPPO region do not need a reference collection in every country or at every laboratory, but they do need access to these collections. By connecting collections online and clustering collections an international coverage for reference materials can be achieved. With quality systems in place the collections can offer reliable, well defined reference material. The new EU regulation with extra demands on reference material and the forming of EU-RL’s can help to speed up this movement. Official collections as part of or related to an EU-RL and partly financed by the EU provide possibilities. Through co-operations like EUPHRESCO an even distribution of the reference collections should be possible.
Recommendations
To reach the above mentioned, first steps should be taken in the near future. The need to improve the infrastructure supporting phytosanitary collections and use them more efficiently and improve collaboration will be the main ingredients.
A: Priority to making/maintaining inventories
It is essential to be able to know which and where biological material is available. Collections should make an inventory of their holdings and provide this information in a format that could allow sharing on a platform.
B: Establish a long term sustainable online platform
Encourage and support the creation of a long term single platform to access the information. Choose the online platform to be used and assure a long time hosting.
C: Improvement of Quality systems for collections
The implementation of quality systems in collections is essential to ensure that proper reference material is used in the development and performance of tests. The upgrade of working collections should be a short term objective.
D: Establish networks for collections
Networks of collections should be established in order to share the responsibility of maintaining reference material and also for duplication purposes whenever necessary. When quarantine organisms are involved the network should have a link with Euphresco.
E: Establish a common policy for reference material
A common policy should be established for developing and maintaining reference material among member states as one of the basic requirements for a sustainable network of National Reference Laboratories and EU Reference Laboratories in the new EU control directive on official controls. Exchange of material and concentration of material in yet well-established collections will be a first step.
In case of outbreaks it is essential that not only information on the location of collections is accessible but also prompt and organised/regulated exchange of material is possible. Therefore a common policy for issuing of material and shipment in compliance with legislation should be developed.
F: Nagoya Protocol
Consequences for plant health related collections should be clarified and in case of conflict with plant health legislation, derogations should be sought.
The basis for the above steps originate from the different collection projects. Now there is a strong need for further implementation from within our field and our organisations.
List of Websites:
www.q-collect.eu
International trade and travel has increased tremendously in recent years with plants and plant products being moved into and from the European Union. As a consequence, the rate of introduction and establishment of new, economically or environmentally damaging plant organisms and invasive species has increased steadily. In addition, climate change may also increase the probability of establishment of organisms in more areas than their area of origin. Such organisms include plant pathogens, arthropods and invasive plants. Some may have already been identified as posing an unacceptable risk to agricultural and horticultural crops, forest and the wider environment and have consequently been included in the Annexes of the Directive 2000/29/EC as pests of the European Union (these lists of organisms are also called quarantine pest lists). As highlighted many times before, the capability of National Plant Protection Organizations (NPPOs) to quickly and reliably detect and identify these organisms is critical for effective phytosanitary measures to be taken and for ensuring safe transnational movement of plants and plant products. Laboratories are increasingly working under quality assurance systems (including accreditation) and need to have access to validated tests using reference material from reference collections.
A significant number of plant pathogens and pest collections are present within Europe but they are dispersed, widespread and of very variable quality. NPPO’s within the EU and EPPO region, mandated laboratories, universities and research institutes all have their own collections related to their specific work and scope. Many of these collections are connected to a single specialist. Within Europe there is a need to improve the infrastructure supporting phytosanitary important collections so as to more efficiently use the available infrastructure and improve collaboration in the field of phytosanitary infrastructure with regard to means, knowledge, expertise on taxonomy and development of detection methods.
In the frame of the Q-collect project, by means of a questionnaire, an inventory within Europe was made on the nature, size, availability, and quality of important phytosanitary collections. The rate of answers was satisfactory as 93 laboratories/institutes out of the 154 completed the questionnaire describing 152 collections, 83% of which hosting quarantine organisms and/or look alike. Experts considered that almost all important collections were described and that the results of the questionnaire were representative of the state of the art.
Based on the inventory and standard requirements defined for reference collections, gaps in those collections were listed with a series of recommendations to overcome them. Guidelines for application of quality standards, for access to specimens and for design and building a network of reference collections have been proposed, adapted and agreed at the last workshop. An info-portal containing relevant information on phytosanitary important collections has been set up and final activities and results of the project have been and will be further disseminated to stakeholders, including collections and all NPPO diagnostic laboratory end-users within the EU and EPPO region who are not participating directly in the project. Links have been made to relevant ongoing EU projects, including MIRRI, which has similar objectives covering the wider field of microbiology.
Two Workshops for collections and potential stakeholders have been organized. The first one on 27/28 nov 2014 in Kleinmachnow (Germany) aimed at presenting the preliminary plans toward a sustainable collaboration, coordination for the maintenance of transnational reference collections and databases. The second workshop (8/9 sep 2015, Rome (Italy) discussed guidelines for application of quality standards, for access to specimens and for design and building a network of reference collections. A white paper, covering all the important recommendations from the project, was drafted and approved during the meeting.
Deliverables are available from the Q-collect website: www.q-collect.eu
A paper containing the results of Q-collect will be published in EPPO Bulletin, August 2016.
Project Context and Objectives:
International trade and travel has increased tremendously in recent years with plants and plant products being moved into and from the European Union. As a consequence, the rate of introduction and establishment of new, economically or environmentally damaging plant organisms and invasive species has increased steadily. In addition, climate change may also increase the probability of establishment of organisms in more areas than their area of origin. Such organisms include plant pathogens, arthropods and invasive plants. Some may have already been identified as posing an unacceptable risk to agricultural and horticultural crops, forest and the wider environment and have consequently been included in the Annexes of the Directive 2000/29/EC as pests of the European Union (these lists of organisms are also called quarantine pest lists). As highlighted many times before, the capability of National Plant Protection Organizations (NPPOs) to quickly and reliably detect and identify these organisms is critical for effective phytosanitary measures to be taken and for ensuring safe transnational movement of plants and plant products. Laboratories are increasingly working under quality assurance systems (including accreditation) and need to have access to validated tests. It was noted that in order to ensure proper development, validation and effective and reliable use of tests, it is essential that the infrastructure in Plant Health is strengthened, in particular aiming that:
• Expertise in taxonomy and phytosanitary science is secured.
• Maintenance of reference collections is ensured and accessibility and links are developed further.
• Easilyy accessible databases containing reliable data are maintained and developed further.
• Phytosanitary research (including research on taxonomy) continues in particular for diagnostic test development.
A significant number of plant pathogens and pest collections are still present within Europe but they are dispersed, widespread and of very variable quality. NPPO’s within the EU and EPPO region, mandated laboratories, universities and research institutes all have their own collections related to their specific work and scope. Many of these collections are connected to a single specialist. Within Europe there is a need to improve the infrastructure supporting phytosanitary important collections so as to more efficiently use the available infrastructure and improve collaboration in the field of phytosanitary infrastructure with regard to means, knowledge, expertise on taxonomy and development of detection methods.
Main Objectives
Q-collect has identified the major challenges in the development of a network of relevant phytosanitary collections, collectively harbouring quarantine organisms and their closely related species as well as other organisms with similar diagnostic features (so-called look-a-likes). Within Q-collect we aim to develop guidelines and reference criteria for the quality, access and maintenance for important phytosanitary collections, harbouring viruses, bacteria, phytoplasmas, fungi, arthropods, nematodes and invasive plants. Q-collect will cover all regulated plant health pests to be used by any plant diagnostic centre, national reference organisation and authority freely using the internet, to underpin the implementation of Council Directive 2000/29/EC and follow-up legislative EU-regulations.
To address these major challenges, six principal project objectives have been formulated and are shown below:
1. make an inventory of existing phytosanitary important collections within Europe and their content
2. develop guidelines for quality standards
3. develop guidelines to improve the accessibility of these collections
4. design and build a network of reference collections
5. develop an info-portal on the web to provide information on the outcome of the project
6. disseminate the results to stakeholders
In this way we will:
- support a better network of national reference collections relevant to national and EU phytosanitary policy,
- provide guidelines for restoring, improving and updating the quality, accessibility of national reference collections (specimens, tissue and DNA) and consequently ensuring harmonization of collection maintenance across Europe,
- Support a better collaboration between EU and third country diagnostic laboratories and also the international community.
The six principal Q-collect project objectives will be achieved through a range of measurable objectives, each related to a specific Work Package and will encompass all quarantine-group taxa within the viruses, phytoplasmas, bacteria, fungi, nematodes, arthropods and invasive plants.
The objectives of the seven Work Packages are:
Work Package 1. Coordination
1.1. To coordinate project activities, including project meetings and reporting.
1.2. To develop and maintain the internal project webportal.
1.3. To manage all administrative, financial, legal and contractual aspects of the project.
Work Package 2. Inventory
2.1. To make an inventory of existing relevant phytosanitary collections.
2.2. To describe the main phytosanitary relevant collections and their characteristics.
2.3. To identify gaps within the content of phytosanitary important collections.
2.4. To define strategies to fill the gaps previously identified.
Work Package 3. Quality Standards
3.1. To review current quality control standards in the main EU collections of quarantine organisms.
3.2. To define and agree minimum quality standards that can be applied within the main EU collections of quarantine organisms involved in the project.
3.3. To produce harmonised guidelines towards achievement of recommended quality standards during preparation, conservation, shipment/access and use of reference materials of all quarantine organisms.
3.4. To facilitate consultation with other collections and end-users in EU Member States and EPPO countries to harmonise and increase their awareness of quality standards in provision and use of reference materials of quarantine organisms.
Work Package 4. Access
4.1. To summarize all information on the biological resources available (what is where and how from WP2) and on the stakeholders needs (who needs what, in which format and why) and how material can be deposited and accessed.
4.2. To organize the structured frame for deposition in collections (respecting CDB and Nagoya protocol) and distribution (respecting European and national laws) (using tools such as MTA) for those collections for which it is not available already.
Work Package 5. Info-portal
5.1. To make an inventory of all existing tools, websites, databases that might be complementary to the inventory on collections (WP2).
5.2. From other WPs, obtain the information on the existing systems, strengths and missing features that might need to be implemented within this project and associated databases. Summarize the wishes of the different WPs and make a proposal how future information should be made accessible for the end-users.
5.3. To create an integrated system (info-portal) hosting the information and end-results generated by all other WPs.
Work Package 6. Design and development of a sustainable European network of collections of plant health quarantine organisms
6.1. To provide defined and internationally compatible reference criteria for the establishment of a sustainable network of European reference collections of plant health quarantine organisms resp. taxonomically related organisms.
6.2. To provide defined and internationally compatible reference criteria for the virtual access to reference collections and connected databases of plant health quarantine organisms within a sustainable European and international infrastructure network.
6.3. To provide a process description (e.g. flow chart) for the application of the developed and defined reference criteria for a sustainable network of European reference collections of plant health quarantine organisms.
Work Package 7. Dissemination.
7.1. To develop a website for the project.
7.2. To disseminate efficiently, through the website, relevant information from the project to stakeholders, in particular the plans for sustainable collaboration, coordination for the maintenance of transnational reference collections and databases.
7.3. To make a general presentation of the project to be used in national or international communications about the project.
7.4. To develop EPPO standards on quality control on phytosanitary collections.
7.5. To organize two workshops for collections and stakeholders.
Project Results:
Work package 1 – Coordination and Management.
Partners involved:
WP Coordinator: DLO (Partner 1)
Objectives
1.1. To coordinate project activities, including project meetings and reporting.
1.2. To develop and maintain the internal project webportal.
1.3. To manage all administrative, financial, legal and contractual aspects of the project.
Tasks
Task 1.1 Organize project meetings
• Project meetings were held on 2 December 2013 in Leiden (kick off meeting), on 28 November 2014 in Kleinmachnow (Germany) and on 7 September 2015 in Rome (Italy) where all Partners had the opportunity to report and review progress and take forward tasks within each individual work package. Minutes of these meetings have been reported in D1.1 D1.3 and D1.4.
• An extra project meeting has been organised by EPPO (partner 13) on 24-25 March 2015 to discuss with (dpt)WP leaders and experts the outcome of the questionnaire and how to interprete the data.
Task 1.2 Develop webportal
• A webportal has been developed for projects partners hosting all relevant project information (Proposal, DoW, GAcontract, CA, program/minutes meetings, etc.)
https://teamsites.wur.nl/sites/Q-collect/SitePages/Home.aspx
All reports, deliverables were made available for all partners through this webportal.
Task 1.3 Write project reports
Two project reports have been made and submitted (1st period report and 2nd period report)
This was coordinated and submitted by the Coordinator. The Coordinator also acted as the main interface with the Commission.
• Incorporate in the project and activity reports mentioned above specifically on exchanges and dialogue with the Advisory Board, stakeholders and end-users.
• Partner 1 (month 24)
Task 1.4 Manage project administration
All financial; legal; contractual and administrative aspects of the project have been managed by partner 1 (DLO).
Deliverables
D1.1) Minutes of Kick off Meeting [month 2]
D1.2) Webportal for hosting all relevant project information (Proposal, DoW, GA contract, CA, program/minutes meetings, etc.) [month 2]
D1.3) Minutes of Second Meeting [month 12]
D1.4) Minutes of Third Meeting [month 24]
Work package 2 – Inventory of relevant phytosanitary collections.
This work package was mandated to make a state of the art of collections of quarantine organisms in Europe, with four objectives:
2.1. To make an inventory of existing important phytosanitary collections.
2.2. To describe the main phytosanitary important collections and their characteristics.
2.3. To identify gaps within the list of phytosanitary important collections.
2.4. To define strategies to fill the gaps previously identified.
Partners involved:
Six persons have been involved in the preparation of the different tasks and deliverables during the project: the WP leader (Jean-Claude Streito), the deputy WP leader (Françoise Peter) two EPPO staff members Jean Perchet and Damien Griessinger, and Emmanuelle Artige (INRA).
All of the following Q-collect partners were also involved and consulted:
DLO (partner 1), DEFRA (partner 2), ILVO (partner 3), UGent (partner 4), UNIBO (partner 5), KNAW (partner 6), EVD-ACW (partner 7), ANSES (partner 8), INRA (partner 9), NATURALIS (partner 10), DSMZ (partner 11), AGES (partner 12), EPPO (partner 13), FGU VNIIKR (partner 14), JKI (partner 15) and NVWA (partner 16).
2.1. Identify and list the main quarantine collections.
All taxonomic groups of quarantine organisms were included in the study: Viruses & Viroids, Phytoplasmas, Bacteria, Fungi, Arthropods, Nematodes and Invasive Plants. Lists of collections of quarantine organisms already available (EPPO, INRA, DLO) were compiled and an on-line interactive list was provided to all partners by 2014/02/11. All partners were invited to complete and correct the list, especially to update the addresses, from 2014/02/11 to 2014/05/06. The list was cleaned and formatted. It was validated and available for the survey (task 2.2) by 2014/05/12.
The list included 154 laboratories and institutions that house collections of quarantine organisms and/or look alike. All groups of organisms are represented (Viruses & Viroids, Phytoplasmas, Bacteria, Fungi, Arthropods, Nematodes and Invasive Plants).
2.2. Based on the list a second questionnaire was sent to relevant collections for details on scope, size, quality, availability and sustainability of material preserved.
A first version of the questionnaire was produced by WP2 leaders based on a brainstorming session organized in the framework of the kick off meeting (Leiden, 2013/12/02) and was further developed taking into account questions included in the MIRRI questionnaires. It was provided to all Q-collect WP leaders, especially WP3 and WP4, for comments and suggestions. Comments from WP leaders were reviewed by WP2 coordinator and the EPPO staff involved and a revised version was prepared. This revised version was submitted on-line to all Q-collect partners who were given the possibility to provide feedback from 2014/02/11 to 2014/02/28. Comments received were reviewed by WP2 coordinator and the EPPO staff involved and a second revised version of the Questionnaire was tested by 2014/04/30 by INRA. The final version of the questionnaire was made available on-line on 2014/05/15 for the survey to start.
The questionnaire included 36 questions for a total of about 220 fields. Most fields had to be completed for each collection declared. Topics addressed were: scope, size, quality, availability and sustainability of material preserved.
To identify the gaps in the different taxonomic groups, institutes/laboratories were requested to complete the questionnaire separately for the different groups of pests and declare as many collections as they deemed necessary. One of the strengths of the questionnaire was indeed the possibility for the respondent to create forms for as many collections as necessary (depending on the type of organism, including the possibility to create sub-collections) and to give details for each collection, although this was more time-consuming for the respondents who wished to give that level of detail. Approximately one hour was required to fill the on-line form per collection (according to the test carried out in Montpellier).
By 2014/05/15 an invitation to complete the Questionnaire on-line was sent to all curators of quarantine collections listed in task 2.1. Furthermore, information on the questionnaire was disseminated to all of the laboratories registered in the EPPO database on diagnostic expertise as well as to all EPPO Panels on diagnostic. An article was published in the EPPO Reporting Service no. 4 to publicise the survey (publication 2014/06/10).
The deadline to complete the questionnaire was 2014/07/31.
An extraction of the information gathered was done and a file containing a presentation of the raw results was prepared by EPPO. The document was circulated on 2014-09-30 to all members of the consortium for possible feedback.
Information was gathered from 110 collections. Results were presented and discussed with partners at the first Q-collect Workshop (Kleinmachnow, Germany, 2014-11-27/28). Bias, additional ideas for interpretation and future steps were discussed. Participants commented that some important collections seemed to be missing from the answers received. The questionnaire was consequently reopened and the deadline to complete it was the end of January 2015. Results were reanalysed and sent to Q-collect partners for comments by 2015-03-03.
The rate of answers was satisfactory as 93 laboratories/institutes out of the 154 completed the questionnaire describing 152 collections, 83% of which hosting quarantine organisms and/or look alike. It was valuable to reopen the questionnaire as 42 new important laboratories/institutes finalized it. Results were reanalysed and sent to Q-collect partners for comments by 2015-03-03.
Figure 1: Number and location of collections that took part in the survey (the size of the spots is linked with the number of collections in the locality).
An extra project meeting was organized in Paris on 2015-03-24/25 attended by Q-collect Work package leaders and representatives of European collections from each discipline. During this meeting final results of the survey were discussed and bias and gaps were identified and listed. Experts considered that almost all important collections were described and that the results of the questionnaire were representative of the state of the art.
2.3. Based on results of Task 2.1 and 2.2 and on requirements defined by WP3, 4 and 6 to identify and list the gaps (lack of specimens or specialists, quality, availability, sustainability).
During the project meeting mentioned above bias and gaps were identified and discussed.
A draft version of the questionnaire results and gaps identified was sent to WP leaders for comment. Comments were discussed between INRA and EPPO and a version of this Deliverable made available on web portal by 2015-09-02.
Current situation:
The main results of the Q-collect questionnaire and gaps identified are provided. For more details see the deliverable 2.3.
1. The survey organized during the Q-collect EU funded project confirmed that although there is a significant number of plant pathogens and pest collections still present within Europe (more than 150 reported), they are dispersed, widespread and of very variable quality.
Figure 2: Number of collections by laboratory / institute.
The majority of respondents host one collection. Only 25 institutes/laboratories host more than 2 collections. One disadvantage of scattered collections is that the information is dispersed so it is more difficult for the users to find biological material.
2. Most collections are working or research collections and only few of these collections are likely to be organized to provide services to outside users.
The consortium considered that this could be an indicator that these are active collections updated regularly and probably associated with specialists of the pest groups. However it was also considered that few of these collections are likely to be organized to provide services to outside users.
There are very few collections dedicated to the conservation and the provision of services for (quarantine) pests organisms (commercial / public deposit / national or international status). But differences are important by discipline: several important and international collections well organized exist for bacteriology, a few number for fungi, viruses and viroids, a few number of working collections are organized to provide services punctually in entomology, acarology and nematology, no collection of invasive plants is organized to provide services.
Figure 3: Graph illustrating the total cumulated numbers of collections for each purpose. Multiple answers were possible.
3. There is a limited number of information on collection’s holdings available online.
Although collections were not asked to provide a list of species held, it can be inferred from the answers that the lists that could have been provided would have been partial. General collections host a large number of species and possibly regulated species, however these are usually difficult to access. The average number of quarantine species represented in each collection is low (less than 10 for most discipline). The number of specimens is difficult to interpret but some species are probably represented by a very low number of specimens (e.g. 1 or 2).
The limited number of information available online is a gap to allow easy and straightforward online access to information on where biological material can be found.
Figure 4: Number of collections that provide an online consultation.
4. Many collections have no quality system in place, and accreditation of collections is scarce.
The percentage of collections sharing material with no quality assurance in place corresponds to more than half of the collections which answered the questionnaire. In such cases exchange of material is assumed to be based on trust, there is no formalized process ensuring the quality and authenticity of the specimens, which excludes in principle the use of such material in a formalized framework (such as use in the framework of official diagnostics performed under accreditation).
More details on quality assurance are provided by WP3.
Figure 5:Graph illustrating the quality assurance and sharing policies
5. Sharing of material between collections to ensure resilience is not common and can be considered as a high risk for loss of important biological material in case of incidents with buildings or equipment.
Almost 2/3 of collections (up to 70% for insects) do not share material for duplication. Although this can be linked with the type of specimens for the taxa (insects, acari, plants) where collections are mostly dead material that cannot be multiplied, it can be considered a gap for collections of live cultures, where incidents with buildings or equipment can lead to very fast destruction of samples. Q-collect partners think that these numbers are too optimistic, it is possible that some collections answered that they shared material but not necessarily for the purposes of duplication to ensure preservation of specimens following accidental loss of all or part of a collection held at one location.
Figure 6: Graph illustrating the policy of sharing material with other collections for duplication purposes by discipline.
Figure 7: Graph illustrating the policy of sharing material with other collections for duplication purposes overall.
6. Appropriate basic funding is not secured enough and there is a need for a common policy towards collection management throughout the region.
Figure 8: Graph illustrating the proportion of collections with a dedicated annual budget.
A structural weakness of a majority of collections can be identified here. 2/3rd of collections do not have an annual dedicated budget, possibly meaning that they function on fund allocated for other activities such as research or diagnostics. This could mean that the funds necessary for maintenance of the collection could be difficult to identify. It also questions the long term future of the collections.
2.4. With WP3, 4 and 6, propose a guideline of recommendations how to fill the gaps for decision-makers of the phytosanitary policies.
Results of the survey on collections and main gaps identified were presented to partners and stakeholders during the last project meeting (2015-09-07/08 in Rome). Based on deliverable D2.3 recommendations were discussed and approved by partners. A white paper covering all the important recommendations (deliverable D2.4) was drafted and approved during the meeting. Here are presented recommendations supported by WP2 inventory.
Goal for the future should be the following: for every organism group/discipline there are at least at 2 locations official reference collections situated and through online catalogue(s) these reference collections can be accessed by a specialist to search and order material.
All the initiatives of the past years (Q-bank, QBOL, Q-collect, etc) have given a boost to the phytosanitary collections. Much energy, knowledge and hard work has been given to the collections. The challenge is to keep the good work up and follow this road. In the coming years it is unlikely collections will be supported with big additional budgets or project funding. However, a database like Q-bank has proved that it is possible to connect specialists and their collections on an online platform. Other projects have proved that the network of phytosanitary specialists is strong and people are willing to collaborate. In the framework of Euphresco there are many international cooöperations especially between official NPPO related laboratories. The laboratories in the EPPO region do not need a reference collection in every country or at every laboratory, but they do need access to these collections. By connecting collections online and clustering collections the result can be an international coverage for reference materials. With quality systems in place the collections can offer reliable, well defined reference material. The new EU regulation with extra demands on reference material and the forming of EU-RL’s can help to speed up this movement. Official collections as part of or related to an EU-RL and partly financed by the EU provide possibilities. Through coöperations like EUPHRESCO an even distribution of the reference collections should be possible.
Recommendations
To reach the above mentioned, first steps should be taken in the near future. The need to improve the infrastructure supporting phytosanitary collections and use them more efficiently and improve collaboration will be the main ingredients.
A: Priority to making/maintaining inventories
It is essential to be able to know where biological material is available. Collections should make an inventory of their holdings and provide this information in a format that could allow sharing on a platform.
B: Establish a long term sustainable online platform
Encourage and support the creation of a long term single platform to access the information. Choose the online platform to be used and assure a long time hosting.
C: Improvement of Quality systems for collections
The implementation of quality systems in collections is essential to ensure that proper reference material is used in the development and performance of tests. The upgrade of working collections should be a short term objective.
D: Establish networks for collections
Networks of collections should be established in order to share the responsibility of maintaining reference material and also for duplication purposes whenever necessary. Using existing networks like EUPHRESCO will be the most efficient.
E: Establish a common policy for reference material
A common policy should be established for developing and maintaining reference material among member states as one of the basic requirements for a sustainable network of National Reference Laboratories and EU Reference Laboratories in the new EU control directive on official controls. Exchange of material and concentration of material in yet well-established collections will be a first step.
In case of outbreaks it is essential that not only information on the location of collections is accessible but also prompt and organised/regulated exchange of material is possible. Therefore a common policy for issuing of material and shipment in compliance with legislation should be developed.
The basis for the above steps originate from the different collection projects. Now there is a strong need for further implementation from within our field and our organisations.
Work package 3 – Quality Standards.
Partners involved:
WP leader John Elphinstone (FERA, partner 2) and Dpt WP leader Marianne van der Blom (NVWA, partner 16)
All of the following Q-collect partners were also involved and consulted:
DLO (partner 1), DEFRA (partner 2), ILVO (partner 3), UGent (partner 4), UNIBO (partner 5), KNAW (partner 6), EVD-ACW (partner 7), ANSES (partner 8), INRA (partner 9), NATURALIS (partner 10), DSMZ (partner 11), AGES (partner 12), EPPO (partner 13), FGU VNIIKR (partner 14), JKI (partner 15) and NVWA (partner 16).
1. Introduction
In 2001, the Organisation for Economic Cooperation and Development (OECD) Working Party on Biotechnology concluded that there was a need to provide greater quality assurance than was already exercised by culture collections and databases of biological resources (1). As a result, a series of best practices was published in 2007 (2) to provide guidance for biological resource centres (BRCs) seeking to improve the quality standards of their repositories of living and preserved organisms, their genomes and other information related to their heredity, function, taxonomic classification and diversity. These included specific best practice guidelines on biosecurity for BRCs, for the micro-organism domain and for animal and plant BRCs. Some of the aims of these guidelines were:
• To safeguard biodiversity through repositories for reliable preservation and curation of biological resources.
• To support R&D and diagnostic laboratories by making available biological reference materials of guaranteed identity and quality.
• To underpin accurate taxonomic classification and identification to provide consistent naming of organisms of statutory, agricultural, horticultural, industrial and environmental importance.
• To provide the same level of quality service irrespective of the source of biological materials or information requested.
These guidelines provide basic quality management guidance for culture collections by setting the standard for quality management and biosecurity, building capacity, preservation of biological resources and data management. Although the detailed guidelines were intended to improve quality assurance in current collections and databases, it was recognised that full compliance with the guidelines would be difficult for many collections and that they may remain somewhat aspirational. Indeed, to date, only a few of the larger reference collections containing quarantine organisms have been able to fully comply with the best practices proposed through the OECD guidelines.
The larger reference collections of micro-organisms (including viruses, bacteria and fungi) have probably made most progress in terms of organised quality assurance. The EU demonstration project known as CABRI (Common Access to Biological Resources and Information) was initiated in 1996 and its database (http://cabri.org) is now maintained by seven member BRCs, some of which hold plant quarantine organisms, including the Belgian Co-ordinated Collection of Micro-organisms (BCCM), the CABI collections of bacteria and filamentous fungi, Centraalbureau voor Schimmelcultures (CBS) collections of bacteria and filamentous fungi and Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) collections of bacteria, filamentous fungi and plant viruses. A CABRI accreditation scheme has been developed by reviewing and collating methodologies and quality standards appropriate for each biological resource category for accessioning material into member and other collections. These are then measured and critiqued by comparing methods and results obtained with common representatives from each of the collections and randomly checking customer satisfaction.
Whereas the OECD and CABRI guidelines are intended for use by well-resourced public service collections, the World Federation for Culture Collections (WFCC) has also issued general guidelines (http://www.wfcc.info/guidelines) which aim to provide a first step towards the implementation of the OECD Best Practice. These include advice on appropriate operational facilities, staffing levels to allow operation at a high standard and training for staff with research expertise related to the aims of the collection. The guidance also demands compliance with national legislation, rules and regulations and addresses the capability of collections to meet relevant national and international regulations concerning the control, transportation and health and safety aspects of resource handling and distribution.
For botanical collections of plants, The Herbarium Handbook (3) is a widely-used standard text covering best practice for many relevant activities. Further modern administrative procedures are available through the BRAHMS database management system (http://herbaria.plants.ox.ac.uk/bol) for botanical researchers managing collections in herbaria, botanic gardens and seed banks. Developed at Plant Sciences, University of Oxford, it provides wide-ranging and innovative functionality to gather, edit, analyse and publish botanical data, optimizing its use for the widest possible range of curation services and research outputs.
This work package was aimed at service reference collections receiving, maintaining and providing access to specimens and reference materials representative of listed quarantine pests (4,5,6), invasive plants (7) or of other organisms that can interfere with their correct identification, e.g. as a result of shared diagnostic features, close taxonomic relatedness, or occurrence in a similar biological niche such as a particular commodity or shared habitat. The objectives were to review current quality standards, assess gaps where standards were missing or required improvement and then to produce guidelines on the application of minimum quality standards appropriate for each discipline of quarantine organisms.
2. Methods
Task 3.1. Review of currently used quarantine standards.
Current quality standards were reviewed through collaboration with WP2 on the preparation of the inventory questionnaire sent to all 110 identified reference collections of quarantine and related organisms. Key questions were formulated to obtain as much information as possible regarding existing quality standards used by each collection. Extra care was taken to ensure that the questions were relevant for collections of different organisms (viruses, phytoplasmas, bacteria, fungi, nematodes, insects and plants). Contributions were also made to the database of known reference collections of quarantine organisms (for intended receipt of the questionnaire) by updating information on the EPPO website. Responses to the questionnaire were received at the end of Month 12 and were used to prepare a draft report on the status of quality control within EU reference collections of quarantine organisms, which was presented to the workshop for collections and stakeholders in Kleinmachnow, Germany (28-29th November 2014) and circulated to all participants and project partners for further feedback and additions.
Task 3.2. Definition of minimum quality standards.
A preliminary list of minimum quality standards, appropriate for collections within each discipline of quarantine organisms (viruses, phytoplasmas, bacteria, fungi/oomycetes, nematodes, insects/mites and invasive plants), was compiled and tabulated by the Leaders of WP 3 and experts from each discipline. These took into account the gaps in currently-applied standards, as identified through the questionnaire undertaken in WP2. The tables were then posted on the project web portal for further discussion and amendment by all Q-Collect project participants and quality managers associated with the various collections represented within the project.
Task 3.3. Production of draft guidelines to achieve minimum quality standards.
Guidelines on suggested application of the agreed quality standards by service reference collections of quarantine organisms were then drafted by the Leaders of WP 3. These took into account:
a. Existing quality standards used by the various collections and gaps identified in Task 3.1.
b. Previously published guidelines for biological resource centres from OECD, CABRI and WFCC.
c. International (ISO) standards for establishment of quality management systems and certification of specific procedures appropriate for use in service reference collections.
d. European and Mediterranean Plant Protection Organisation (EPPO) standards on quality management and accreditation of diagnostic activities in diagnostic laboratories (8,9).
The draft guidelines were discussed amongst quality managers and a panel of other identified experts from the reference collections represented in the Q-collect project and were posted on the project web portal for further comment and modification by other project participants.
Task 3.4. Harmonisation of guidelines to achieve minimum quality standards
The draft guidelines were amended according to the feedback from project participants and other experts and were presented at the second project workshop held in CRA, Rome (8-9th September, 2015). A final harmonised version was produced, incorporating comments from Heads of plant health laboratories in the EPPO region and representatives from additional collections of quarantine organisms.
3. Results and Discussion
Task 3.1. Review of currently used quarantine standards.
Results from the questionnaire highlighted a wide variation in current quality standards across 152 EU reference and research collections, around 84% of which contained quarantine or relevant related organisms. Less than half of the collections maintained a catalogue of their accessions, although around two-thirds could provide at least a partial list of the specific quarantine and related organisms held. The breadth of information stored for each accession also varied across collections. Of 106 respondents, 50% reported that their host institutes/laboratories had a formal quality system covering maintenance of the collection. Of these 70% (33 collections) were officially accredited or certified, representing 9 collections of bacteria, 5 of fungi, 6 of insects, 3 of invasive plants, 4 of nematodes, 4 of phytoplasmas and 5 of viruses/viroids. A total of 30 collections conformed to ISO 17025 but only 8 to ISO 9001. To date there appears to be only one virus collection accredited to ISO 17025 together with ISO Guide 34:2009 for the production of reference materials.
Of 53 responding collections with no official accreditation, over 60% used validated methods or published keys for initial identification of specimens. Less than 50% applied document controls or monitored performance of laboratory equipment used in identification or preparation of reference materials. Less than 40% monitored training of personnel, customer complaints or preventative actions and less than 30% used calibrated equipment, monitored corrective actions or performed management reviews. Around 10% or less maintained any quality or technical records or performed internal audits. A high proportion of collections (75%) used a recognised method (published or generally agreed procedures) for identification and authentication of quarantine organisms. Over 70% of responding collections had documented procedures and records for primary identification of specimens. For those specifically using classical morphological identification, DNA/RNA sequencing, phenotyping methods or pathogenicity determinations, the proportion reporting documented procedures and data fell to 59%, 52%, 38% and 33% respectively. The collections also varied in their keeping of procedures and records relating to handling, storage and external supply of specimens. Characterisation of specimens was reported to be performed by an expert in 82% of the cases, although the definition of expert varied, mostly referring either to specialists with a higher degree, with some years of experience or specifically dedicated to working on the collection. Around a third of collections did not carry out checks on the stability or authenticity of specimens during storage or loan periods, although they considered such checks relevant. A full report on the current status of quality standards was produced as deliverable DL 3.1.
Task 3.2. Definition of minimum quality standards.
Whilst the choice of quality management system is similar for reference collections of all types of plant quarantine pests, specific quality requirements vary with the type of organism or reference material in question and according to whether reference materials are maintained and provided as live organisms or as fixed specimens or other material. Minimum quality standards were identified where specific competencies and/or standard operating procedures would benefit the routine activities of the reference collections. The following activities were considered:
• Information required on accession
• Data storage and maintenance
• Authentication
• Identification methods
• Storage and conservation
• Production of reference materials
Following feedback from project partners and other experts attending the Workshop in Kleinmachnow, minimum standards appropriate for each discipline of quarantine organisms were compiled according to the various activities and are shown in Table 1 (Deliverable DL3.2).
Task 3.3. Production of draft guidelines to achieve minimum quality standards.
Draft guidelines on the application of minimum quality standards were agreed through consultation amongst experts associated with reference collections of plant quarantine pests, including viruses, phytoplasmas, bacteria, fungi and oomycetes, nematodes, insects and invasive plants (Deliverable DL3.3).
Task 3.4. Harmonisation of guidelines to achieve minimum quality standards
Following presentation at the second project workshop in Rome and further consultation with project participants and other experts and quality managers from relevant collections, only minor changes to the draft guidelines were necessary. A final harmonised version of the guidelines on minimum quality standards (deliverable DL3.4) incorporating the table of the minimum quality standards agreed for each discipline, is attached as Appendix 1. This version was then forwarded, for potential publication as a future EPPO standard, to be considered by experts in each relevant discipline at the various meetings of EPPO diagnostic panels.
4. References
1. OECD (2001). Biological Resource Centres: Underpinning the future of life sciences and biotechnology. OECD Publications, Paris, France. pp 66.
2. OECD (2007). Best Practice Guidelines for Biological Resource Centres (June 2007),http://www.oecd.org/document/36/0,3343,en_2649_34537_38777060_1_1_1_1,00.html
3. Forman L, Bridson D, (eds.) (1989). The herbarium handbook. Royal Botanic Gardens,Kew, London.
4. http://ec.europa.eu/food/plant/plant_health_biosecurity/legislation/index_en.htm
5. http://www.eppo.int/QUARANTINE/listA1.htm; http://www.eppo.int/QUARANTINE/listA2.htm;
6. http://www.eppo.int/QUARANTINE/Alert_List/alert_list.htm
7. http://www.eppo.int/INVASIVE_PLANTS/ias_lists.htm
8. EPPO/OEPP (2007). PM 7/84 (1): Basic requirements for quality management in plant pest diagnosis laboratories. Bulletin OEPP/EPPO Bulletin 37, 580–588.
9. EPPO/OEPP (2010). PM 7/98 (1): Specific requirements for laboratories preparing accreditation for a plant pest diagnostic activity. Bulletin OEPP/EPPO Bulletin 40, 5–22.
Table 1: Summary of minimum quality standards expected of reference collections of quarantine plant pests and invasive plants.
Work package 4 – Access.
Partners involved:
WP Coordinator: INRA (Partner 9)
DLO (partner 1), DEFRA (partner 2), ILVO (partner 3), UGent (partner 4), UNIBO (partner 5), KNAW (partner 6), EVD-ACW (partner 7), ANSES (partner 8), INRA (partner 9), NATURALIS (partner 10), DSMZ (partner 11), AGES (partner 12), EPPO (partner 13), FGU VNIIKR (partner 14), JKI (partner 15) and NVWA (partner 16).
The objectives of this work package were:
4.1: To summarize knowledge of the biological resources available (what is where and how from WP2) and of the stakeholders needs (who need what, in which format and why) and how material can be deposited.
4.2: Organize the structured frame for deposit in collection (respecting CDB and Nagoya protocol) and distribution (respecting European and national laws) (using tools such as MTA) for those collections for which it is not available already.
To answer these objectives 4 tasks had been designed:
Tasks
4.1: To design a questionnaire for collections
4.2: To design a second questionnaire to be transferred directly to the collections stakeholders
4.3: To gather results from both questionnaires and assess who are the stakeholders and what they need and how
4.4: To link offer and demand
Task 4.1:
To design a questionnaire for collections to be linked to WP2 questionnaire (Task 2.2) in order to assess:
-who are their stakeholders and what they ask for (what are their needs) to collections
-how access to the biological resources is organised inside the collections
The questionnaire will be sent within Europe and EPPO countries to NPPOs and institutions, universities and other parties which use phytosanitary important organisms from collections.
The main target of this task was to summarize knowledge of the biological resources available (what is where and how from WP2) and of the stakeholders’ needs (who need what, in which format and why ?) and how material can be deposited.
The objective of this task was to retrieve directly from collection information about their stakeholders and what they ask to collections, and to have insights in how the access to the resources is organised.
In order to simplify the access to collections, we decided to implement our specific questions regarding targets of the WP4 to the WP2 questionnaires.
WP4 worked with WP2 and add 2 questions to their questionnaire addressed to collections. These two questions were dedicated to a better understanding of the collection stakeholder needs and definitions. These two questions were:
• Question n°23 – who are the customers of your collection?
• Question n°24 – what are they most interested in?
Moreover, two questions set up by the WP2 were also highly interesting for the purpose of the WP4. These two questions were:
• Question n°7 – Does your institute / laboratory have an ordering process?
• Question n°8 – Does your institute / laboratory have a Material Transfer Agreement (MTA)?
The questionnaire was sent within Europe and EPPO countries to NPPOs and institutions, universities and other parties which use phytosanitary important organisms from collections. Data were analyzed by WP2 and a report was transmitted to Q-collect partners.
Deliverable 4.1:
The questions set up for collections were included in Questionnaire from Work Package 2 (Task 2.2).
Task 4.2:
To design a second questionnaire to be transferred directly to the collections stakeholders (via collections) to assess who are they and what are their needs.
The main target of this task is to assess the needs directly from the collections stakeholders. A Q-Collect questionnaire for users of quarantine organisms was designed. It had been sending to Q-collect partners interested in the WP4 for further comments and inputs. After review, the final version of the questionnaire was set up by EPPO and displayed on-line on the Q-collect website. The link to the questionnaire was directly sent to NPPO via EPPO, quarantine users of the CIRM-CFBP (Angers, FR) and to all Q-collect partners to be transmitted to their partners using Quarantine pests and their stakeholders.
Following, there are two screenshots displaying the aspect of the online questionnaire which was available on the Q-collect website during the month of September 2014:
Figure 9: Screenshot of the Q-collect website showing detail of the online questionnaire.
Figure 10: Screenshot of the Q-collect website showing detail of the online questionnaire.
The questionnaire was closed at the end of September 2014.
Deliverable D4.2:
Questionnaire for stakeholders: Questionnaire for stakeholders (who are they and what they need and how?)
Task 4.3:
To gather results from both questionnaires and assess who are the stakeholders and what they need and how?.
The analysis of answers from the two questionnaires permitted us to assess in one hand what is the offer from collections and from the other hand what are the needs of the stakeholders. The data of both questionnaires had been be analysed by WP4 participants and analysed further at the expert meeting in Paris in March 2015.
Deliverable D4.3:
Analysis of answers from both questionnaires (questions to collections and questionnaire to stakeholders)
The objective of WP4 “Access” is to assess the users needs. This will permit to better understand which services the collections should offer in order to better fit the user’s needs in the objective to facilitate research on quarantine organisms.
In this purpose, WP4 “access” implemented questions in the questionnaire dedicated to collections, and set up a questionnaire directed to quarantine organisms users. These questionnaires were disseminated during summer 2014.
This report contains the results from the users questionnaires, associated with the results from relevant questions of the collections questionnaire.
The analyses and comments gathered during the experts meeting who took place in March 2015 were added. Finally this report contains a summary of the different assessed needs.
This questionnaire helped to better understand the users needs. Moreover we were able to conclude that these answers correspond to the reality of users needs. The analysis permitted also to point out that collections should extend their holdings toward being exhaustive in quarantine resources and should improve visibility.
The results gathered from this questionnaire permitted to determine that there are no specific needs from a specific type of user (private company or NPPO for instance) neither specific need expressed by users of a specific kind of organism (i.e. bacteria or insects users).
However, there is major difference if they need dead or alive material.
General needs expressed by all users:
- Collections holding the whole diversity of quarantine organisms.
Remark: Unavailability of material considered as the first problem for users.
- Collections clearly visible: web-site including clear contact and on-line catalog.
- Easy ordering process.
- and in a limited extend a reasonable costs.
Needs expressed specifically by users of living material:
- Help for dealing with regulations
Emerging need:
- Nucleic acids.
Task 4.4:
To link offer and demand: To gather the solutions adopted by the different collection already having implemented these tools, to follow the ECCO recommendations. Determine the relevant information to be provided to the stakeholders, through the website and tools designed by WP5 and WP7. This will help to design the collection network (WP6).
Deliverable 4.4:
Guidelines for collection deposit and distribution
In accordance with the project coordinator, this D4.4 deliverable “Guidelines for collections deposit and distribution: Guidelines for collections to organize deposit and distribution of biological resources and information” was merged with the D6.2 “Survey and guidance document reference criteria for network collections: Inventory of reference criteria for access to reference collections & connected databases within a sustainable European network”. This was done due to their closeness.
The document outlines a strategy for an improved access to service reference collections and their connected databases within the Q-collect network. In a first step the needs of both the user and the provider community and the problems that arise to fulfill them were identified. For this purpose the information on the current level of access to biological material (i.e. resources), which was determined by analyzing the surveys conducted by the work packages focusing on inventory (WP2) and access (WP4), was used. Based on these data, strategies to improve the present situation are proposed.
Deliverable 4.5:
Recommendations for info-portal and website and tools
The aim of this final deliverable was to outline what must be displayed in a website in order to help efficiently the stakeholders to have access to the biological resources they need.
We propose that the info portal may be organized with a core part common to all collections, and specific pages associated to individual collections, or pointing to collection’s web-site.
This list of recommendations will help to strengthened the link between collections and stakeholders via an efficient website.
Work package 5 – Info-portal.
WP Coordinator: KNAW-CBS (Partner 6)
Task 5.1. Make an inventory of all existing tools for (a) identification, (b) classification, (c) websites and databases containing useful meta data of interest to Q-collections and their end-users
In total 99 existing websites have been listed in the Q-bank database in a specific table called Q-collect. The importance of each of the 99 is divided in 4 categories (A, B, C and D) where A is the most important and D the least. Each website is checked on the existence of a direct search tool, identification tool and classification tool.
• Level of Importance for all 99:
o A: 23
o B: 43
o C: 25
o D: 8
• Tools available:
o Search tool: 88
o Identification: 30
o Classification: 18
The complete list of the websites of quarantine interest is also available as a forty-six page document available at http://www.q-bank.eu/Files/QCollect%20report%20WP5.1_2.pdf.
Task 5.2. In collaboration with the other work packages, obtain a wish list of what the ideal integrated database and infrastructure should look like.
After discussion with all partners at Kleinmachnow in November 2014 and in Paris in March 2015 with a core group, what would really be needed in terms of database, software and website infrastructure to collect all the basic requirements for a sustainable and future proof Q-system, we produced a first draft document of 25 pages, in which the following topics were discussed with a certain level of technical details:
1. Desired functions
2. Management system for curators
2.1. Management of collection’s data using desktop applications
2.2. Management of collection’s data using web based applications
2.3. Create bespoke management software using in-house resources
2.4. Use of existing open-source or free software
2.5. Use existing commercial software
2.6. Choice of databases
2.7. Backup of databases
2.8. Installation of software, versioning Information and Technology (IT) resources needs
2.9. Hosted solutions
3. Publication of data for third parties and Interoperability
3.1. StrainInfo
3.2. World Data Centre for Microorganisms
3.3. Taxonomic databases
3.4. Global Biodiversity Information Facility
3.5. Molecular and associated data resources
4. Preliminary proposal for the future Q-collect infrastructure
As discussed in this document, collections are numerous and as diverse as the organisms they are hosting. The procedures, the databases and the software they use are very heterogeneous. Some databases are easily useable by third parties while others have extremely limited interest beyond typical cataloguing purposes. Many collections are only useful for their holdings but the associated data are so poor in number and in quality that the viability of the collection is at risk, even if the biological materials themselves are of interest. End-users and clients of collections want more than just a biological store. They want to be able to retrieve associated data, use and analyse them together with other data. Except for a few cases, Collections are unable to provide such advanced services.
In addition, even if the number of biological material available from culture collections is relatively large reaching more or less 2 to 3 million records and hundreds of million for plants and insects worldwide, this number remains an anecdotal portion of the real diversity. Out of the total number of biological material used in scientific papers every year, only 0.01 percent of them are deposited in official culture collections (Stackebrandt E (2010). Diversification and focusing: strategies of microbial culture collections. Trends Microbiol 18:283–287). Although this figure is not known for quarantine plant pathogens and their look-alikes, in general it means that collections are far from being used to their full-extent and that many studies are using material that will most likely not be reusable in the future. This is a serious problem. Mobilization of the gathered diversity and associated data is a key factor for the future usefulness and success of collections.
The future Q-collect infrastructure should contain the following building blocks that could be implemented gradually in time:
1. A modern, dynamic and efficient collection data management, analysis and publication system
2. Increased acquisition rate of biological material and associated data not stored in Collections
3. Each participating Collection should manage their internal system to be compatible with a common global system
4. Data should be shared and accessible via a central portal allowing researchers and other databases or web services to interact
5. Advanced statistical data analysis system available that would take advantage of database containing collections data and would link them to third parties data
6. Advanced ontological and semantic web technologies implemented in order to allow complex investigations on combined datasets.
One option proposed by WP5 members of the Q-collect to address the issues already discussed above, is to create a Q-Book system to be strongly associated, intermixed with Q-bank and EPPO’s databases. This option pre supposes that a long term solution is found for hosting the Q-bank information. The Q-Book system would consists in a series of software tools and databases allowing any researcher to gather, store and share data associated with their biological material (not limited to biological material from official collections) which is one of the gaps identified during the surveys performed in the framework of WP2 and WP4 . The Q-Book system would also include features allowing researchers to perform conventional statistical analyses of data stored in such system alone or in relation to other data coming from other databases or web services. The Q-Book Semantic system would allow to investigate relations between interconnected databases and to retrieve data and properties that could be associated with or linked to biological material.
The future and proposed infrastructure will have the form of a central database containing a list of all strains, specimens or biological material of quarantine interest and link them to other major collections.
Task 5.3. Make a final architecture of an ideal integrated database and infrastructure.
A plan has been developed for an infrastructure called Q-Book. The latter has temporarily been integrated in the Q-bank website for demonstration purposes and because, with the EPPO website, it is certainly the most relevant Quarantine resources available for the moment.
Q-Book Systems Pilot Project
The Q-Book section of the Q-bank website is the result of an initiative of work package 5 of the Q-collect project. The basic idea behind the Q-Book systems is to allow any researcher or collection working in quarantine related field to store, manage, analyze and publish data associated to their biological material on a freely available platform deeply associated, intermixed with Q-bank and EPPO system. The system would be able to cope with the needs of very small to very large Collections. The new pipeline will include:
1. A mobile application (IOS, Android and Windows Mobile) to collect sample information (pictures, GIS coordinates, time and miscellaneous metadata) directly in the field.
2. A lightweight desktop application that will synchronize with the mobile app and where a complete and extensible set of data will be recordable such as administration, bibliographical, geographical, ecological, chemical, physiological, medical, molecular, links to other specialized repositories (e.g. GenBank, GBIF, etc.) and many more. This application will not only allow the storage of data but also to perform advanced queries, polyphasic identifications and classifications based on any combination of characteristics.
3. Data will be stored in a local light weight database.
4. Data will be shareable using the central Q-Book facility that will be accessible, searchable by anyone or by a selected list of co-workers.
5. An online or web-based tool will also be created allowing the addition, edition and management of strains, specimens or any biological material data that could be used as an alternative to or complementing the lightweight desktop application mentioned above.
6. The Q-Book website will include user-friendly basic and advanced searching facilities, distribution maps, online polyphasic identifications and web services to download data.
7. A publication tool will also be available to produce e-books or to export data in basic data exchange formats.
Figure 11: Q-Book systems & associated systems
Since the Q-Book system would be able to cope with all types of data and organisms, it would be used by a very large panel of researchers and people worldwide. It would be used in many scenarios such as biodiversity management and conservation programs anywhere in the world, quarantine and invasive organisms fight, epidemiology or medical diagnostic. It will be especially beneficial to researchers or collections with no or low financial and technical resources.
There are no such projects proposing to record biodiversity at the unit level (strains, specimens or other biological material). Initiatives such as EOL, Catalogue of Life, Species 2000, IUCN, GenBank, StrainInfo, GCM, BOLD or GBIF are concentrating on species data and are, for some of them, referring to existing and officially recognized museums or culture collections. To our knowledge, there is no complete pipeline that proposes what we are going to initiate here. This ambitious project will be unique and used worldwide. African and lesser-developed countries as well as collections with no or little resources will certainly be the first to benefit from the proposed system since it will be freely and easily accessible. Most of the African Biodiversity remains unknown and very few African researchers have the ability to buy advanced tools to propose their results to third parties. The Q-Book system will allow them to be visible to the scientific and quarantine problematic community and will inevitably initiate collaborations between research groups that, otherwise, would never know about each other. Since the central database would include a very large range of organisms (from dead material to viruses to higher and large organisms), the diversity and the number of potentially useful data to characterize the biological materials will be huge.
Figure 12: Q-Book systems for data capture and edition
Where possible data deposited in Q-Book will be automatically enriched and linked to existing databases such as Genbank, PubMed or SwissProt (via provided accession numbers) but also, via geographic positioning (latitude, longitude, altitude, etc) to other datasets like climate, soils, agricultural practices, elevation, vegetation or many other environmental parameters such as demographic, socio-economic or cultural aspects.
Data stored in the Q-Book system will be archived in a coded and a highly structured way and everywhere possible, text data will be avoided to allow descriptive statistics (average, variance, frequencies, etc.) to be easily computed. Each data point will be considered by the system as a programing object and usable by object oriented programming languages. Such a system will allow the statistical tools to analyze large datasets and perform correlation analyses (for example but many more will be possible as well, like factorial analyses). The semantic system included in Q-Book will allow users to navigate through heterogeneous but highly connected datasets and to find biological material that have potential properties in view of specific Q related research. Statistical and semantic tools will be operable via simple user interfaces from either simple desktop applications or web based systems. This would allow non-advanced users to perform basic calculations, statistics or navigate through complex datasets in a simple way.
The proposed facility will create a virtual research environment where users will be able to find, connect, correct, combine, visualize, analyze and interpret new combinations of heterogeneous data that are relevant to address their Q-research areas. A framework for resource integration will be developed, combining the taxonomic backbone for species identification, geo-referenced environmental data, existing systems for observational data, and information on species traits and attributes. These resources will become accessible to users within seconds, by (i) providing searchable metadata that describe the data and its source, (ii) assigning unique identifiers as linkers between data according to accepted standards, (iii) creating interfaces and query systems, and (iv) installing routines for quality control and interpolation of data in space and time. The architecture is modular, flexible and scalable, and will be the first infrastructure in the world specifically designed for the integration of such Q-resources. Innovative new services will be made available, based on an analysis of the common needs of users in the prioritized areas: services to analyze genetic diversity of mixtures: ‘environmental DNA’, services for new observational methods using smart sensor technologies, services for constructing species interaction networks, services to link meta-omics data to ecosystem processes in (micro-) communities, for which physical model ecosystem facilities will be created. This being a service-based e-infrastructure means that users can access resources and computational facilities from any place, but also meet in person with technicians when needed to discuss progress and results: facilitating research collaboration is an integral part of the proposed system. Larger or more advanced collections already having strong CMS will also be able to participate to the project by sharing their data via web services. With their permission, their data will be retrieved through web services and will feed the central Q-Book database allowing to perform queries as well as data analyses on the broadest possible basis (see Figure 4).
Figure 13: Q-Book systems functional scheme
The Q-Book system will also allow small collections or the ones without an existing data management system to have a complete system allowing to integrate and publish their data using a mobile app, a desktop application or using the web based editor directly accessing their records stored in Q-Book. The development of the Q-Book systems will certainly not be achieved by the collections themselves since this would require advanced programming and databasing skills that are not or almost never available in current culture collections. Subcontractors with the relevant experience will have to be hired to build the wanted systems in close collaboration with collections experts and Q-bank as well as EPPO, but also with the end-users (existing and foreseeable new or potential ones).
The system will be completely free (free mobile and desktop applications) and the Q-Book system will be hosted and maintained by Q-bank and/or EPPO if the needed resources are made available by one or several financing bodies. The problem of sustainability is one of the major issues that need to be tackled in future projects.
During this project a pilot and preliminary version of the possible future Q-Book database was created and includes a large number of the suggestions and proposals made in all the WP of the Q-collect project. A sub-website of the Q-bank website was created and includes:
1. A welcome page containing the above text (see http://www.q-bank.eu/Defaultinfo.aspx?Page=Q-Book)
2. A search engine allowing to find Q-material of interest. For the moment, only bacterial strains from the CFBP collection (Anger, France) are included (see http://www.q-bank.eu/BioloMICS.aspx?Table=Q-Book)
3. A single deposit form to upload biological material data in the Q-Book system (see http://www.q-bank.eu/BioloMICSUpdate.aspx?Table=Q-Book%20deposit%20form). A registration system has also been implemented to avoid unwanted deposits. Only registered users can upload data.
4. A multiple/batch deposit sheet to upload biological material data in the Q-Book system (http://www.q-bank.eu/Files/Deposit.xlsx). The latter was used to import data from the CFBP collection.
5. A search engine for repositories of interest (deliverable 5.1. see http://www.q-bank.eu/biolomics.aspx?Table=Q-Repositories)
6. A list of repertories of interest as pdf document (http://www.q-bank.eu/Files/QCollect%20report%20WP5.1_2.pdf)
The very preliminary Q-Book system developed here could be used as starting point for a solid and future-proof Q-System (possibly included in Q-bank) including a complete version of all the feature describe above.
Task 5.4. (a) Collect and organize all the data, information and guidelines obtained from all WPs. (b) Make items collected in point (a) easily available for a restricted number of testers to ensure that it will be useful and user-friendly for the final end-users. (c) Make the infrastructure/information publically available through a website in collaboration with WP7.
Data and deliverables collected during the project have all been stored in and are publically available from the Q-collect website maintained by EPPO at www.q-collect.eu. As mentioned in report 5.3 a sub-website of the Q-bank website was also created and includes a number of features that were decided in deliverables 5.2 and 5.3. This includes, a welcome page containing the above text (see http://www.q-bank.eu/Defaultinfo.aspx?Page=Q-Book); a search engine allowing to find Q-material of interest. For the moment, only bacterial strains from the CFBP collection (Anger, France) are included (see http://www.q-bank.eu/BioloMICS.aspx?Table=Q-Book); a single deposit form to upload biological material data in the Q-Book system (see http://www.q-bank.eu/BioloMICSUpdate.aspx?Table=Q-Book%20deposit%20form); a registration system has also been implemented to avoid unwanted deposits; a multiple/batch deposit sheet to upload biological material data in the Q-Book system (http://www.q-bank.eu/Files/Deposit.xlsx); a search engine for repositories of interest (deliverable 5.1. see http://www.q-bank.eu/biolomics.aspx?Table=Q-Repositories); a list of repertories of interest as pdf document (http://www.q-bank.eu/Files/QCollect%20report%20WP5.1_2.pdf).
Work package 6 – Sustainable European Network of Reference Collections.
WP Coordinator: AGES (Partner 12)/ UGent (partner 4)
The objectives of work package 6 comprised first of all the provision of discussed, agreed and internationally compatible reference criteria for both the establishment and the maintenance of a sustainable network of European reference collections of plant health quarantine organisms resp. taxonomically related organisms. Furthermore reference criteria for the access to these reference collections and their connected databases should be established. Finally a process description for the application of the developed and defined reference criteria should be developed.
For the establishment of the reference criteria Q-Collect-project results from WP2 (“Inventory of important phytosanitary collections”), WP3 (“Quality standards”) and WP4 (“Access”) as well as data, standards and experiences from existing national and preliminary trans-national inventories from participant countries and recognized organisations, such as EPPO and information from ongoing complementary European research initiatives such as MIRRI were considered.
Eight general criteria and five specific criteria groups for seven taxonomic groups of phytosanitary organisms and invasive plants in Europe were determined to specify the Terms of References (ToRs) for the participation of service reference collections and working collections in the Q-collect network with regard to both the network establishment and the network maintenance. The general criteria comprise the legal requirements, the scope of relevant organisms harmful to plants (regulated, emerging and invasive plants) and the basic overall requirements concerning the quality and provision of reference material as well as metadata generation and delivery, inclusive the different rights and responsibilities connected to the two collection types considered (Q-collect-DL6.1 Annex 1). Overall about 65 criteria were identified for the five different specific criteria groups 1) inventory/catalogue establishment and maintenance, 2) identification methods, 3) authenticity of the material, 4) storage and conservation and 5) preparation and access for the seven taxonomic groups a) viruses/viroids, b) phytoplasmas, c) bacteria, d) fungi/oomycetes, e) insects/mites, f) nematodes and g) invasive plants which are listed in the five inventory tables (Q-collect-DL6.1 Annexes 2.1 2.2. 2.3 2.4 and 2.5).
Figure 14: WP6.1: Number of reference criteria in the specified reference criteria groups.
The major part of the developed and agreed collection reference criteria was applicable and could be accomplished according the current state of the art, especially for the four taxonomic groups viruses/viroids, bacteria, fungi/oomycetes and nematodes with 90.5% average applicability in both collection types. For the other taxonomic groups the applicability was lower ranging between 80.4% (arthropods, phytoplasmas) and 57.7% (invasive plants) of the reference criteria.
Figure 15: WP6.2.
Figure 16: WP6.3.
Figure 17:WP6.4.
Figures WP6.2 – WP6.4: Portion of required and optional reference criteria in the different types of reference collections for VIRUSES/VIROIDS (Fig. 15), INSECTS/MITES (Fig. 16) and INVASIVE PLANTS (Fig. 17)
Figure 18: WP6.5.Example of reference criteria annex table.
With regard to improved access to the different types of reference collections and their connected databases the user/provider community needs and the obstacles were identified by analyzing the results of the questionnaires in WP4 (“Access”). As primary intentions to obtain access to biological reference material and also to “lookalikes”, the use of the reference material for diagnostics (positive controls, development of methods), for research and for teaching purposes were reported by the addressed stakeholders. At the same time the retrieval of biological reference material was considered as severely hampered by the lack of accessible catalogues and of accessible information about the handling of resources by users, incl. MTA’s. It was concluded that there is an urgent necessity for an integrated information system accessible through a user-friendly web-portal, to improve the visibility and localization of resources as well as the order process and traceability of exchange. As a consequence a FAIR (Findable, Accessible, Interoperable, & Reusable) information system and web-portal is proposed. Several added values of the Q-collect network were identified, such as:
• the establishment of a well-designed Q-collect network portal to provide an inventory of existing phytosanitary important collections within Europe and their content
• a one point access to a broad range of biological resources and expertise,
• improved interoperability between collections as overarching network
• reduced fragmentation in resource availability
• adequate quality assured information on resources and related issues (growth conditions, regulations regarding transport, biosecurity, ...).
Guidelines for collections on how to achieve these criteria have been developed (DL6.2 and DL4.4.)
A feasible and practicable flow chart was developed to visualize the process steps for the application of the developed and defined reference criteria in a sustainable network of European reference collections of plant health quarantine organisms (Figure 19: WP6.6).
Figure 19: WP6.6.Flow-Chart for the application of the reference collection criteria
Work package 7 – Dissemination
WP Coordinator: EPPO (Partner 13)
Objectives
7.1. To develop and update a website
7.2. Disseminate efficiently relevant information of the project to stakeholders in particular the plans for a sustainable collaboration, coordination for the maintenance of transnational reference collections and databases through the website
7.3. General presentation of the project to be used in national or international communications about the project
7.4. To develop EPPO standards on quality control on phytosanitary collections
7.5. To organize two workshops for collections and relevant stakeholders.
Partners involved:
WP Coordinator: EPPO (Partner 13)
DLO (partner 1), DEFRA (partner 2), ILVO (partner 3), UGent (partner 4), UNIBO (partner 5), KNAW (partner 6), EVD-ACW (partner 7), ANSES (partner 8), INRA (partner 9), NATURALIS (partner 10), DSMZ (partner 11), AGES (partner 12), EPPO (partner 13), FGU VNIIKR (partner 14), JKI (partner 15) and NVWA (partner 16).
7.1. Website
A dedicated Website was established by the EPPO Secretariat at the start of the project. The beta version was prepared in January 2014 and was launched on the 27th of February 2014. The Website can be accessed at http://www.q-collect.eu/. The website included general information on the project as well as links to the questionnaires organized in the framework of the project. It was updated whenever needed (e.g. the section latest news was updated when the questionnaires were launched and to announce and report on project meetings and dissemination Workshops ).
The Website included 6 sections.
The layout is illustrated below
Figure 20: Website of Q-collect main page.
7.2. Online project leaflet
A leaflet was prepared by the EPPO Secretariat and presented at the Kick-off meeting of the project on the 2nd of December 2013. It was posted on the website on the 27th of February 2014 when the project Website was launched.
The leaflet is available on http://www.q-collect.eu/publications in two formats and is presented below:
Figure 21: Flyer of Q-collect.
7.2. Disseminate efficiently relevant information of the project to stakeholders in particular the plans for a sustainable collaboration, coordination for the maintenance of transnational reference collections and databases through the website.
In the course of the project information resulting from the two project meetings and two workshops were disseminated to stakeholders through the website. Meeting reports were posted, for the two workshops links to presentations made provided, allowing visitors to access detailed information presented during meetings.
Figure 22: Website of Q-collect events page.
7.3. General presentation of the project to be used in national or international communications about the project.
The project and its outcomes have been presented in different EPPO meetings: Panels on Diagnostics in the course of 2014 and 2015, Working Party on Phytosanitary Regulations in 2014 and 2015; Workshop for Heads of Plant Pest Diagnostic Laboratories (the Workshop included a special section on Q-collect). In addition a presentation of the white paper developed in the framework of the project was presented to the Heads of National Plant Protection Organizations (2015-09-15/16, Riga).
The outcomes of the Q-collect projects will be presented during the EPPO Conference on diagnostics for plant pests (2015-12-01/02, Angers, France).
7.4. To develop EPPO standards on quality control on phytosanitary collections
The deliverable prepared by WP3 for quality standards has been included in the agenda of all EPPO Panels on Diagnostics (horizontal Panel as well as Panels for the different disciplines). They will be reviewed in the course of 2016 with the objective to adopt EPPO Standards. A presentation was made at the last EPPO Panel on Diagnostics in Bacteriology (2015-10-20/22). Detailed review of the document by this Panel is expected to take place in June 2016. According to the EPPO Standard Setting procedure the development of a Standard needs approximately two years for from the presentation of a first draft. It can be expected that a version could be sent for Country Consultation of EPPO member Countries in 2017.
7.5 Feedback on criteria proposed for the establishment of a sustainable network
In addition to the review of the draft on quality control of collections, the criteria proposed for the establishment of a sustainable network will be reviewed in the EPPO Panels on diagnostics. The guidelines developed within Q-collect project will sent for information to the organizers of test performance studies (as these are laboratories sharing biological material from their collections in this framework). This will allow feedback to be gathered about the criteria proposed for the network.
7.6. Workshops for collections and relevant stakeholders.
Two workshops were organized during the Q-collect project.
The objective of the first Workshop (Kleinmachnow, DE) was to present the progress made after 12 months, and gather stakeholder expectations. A summary report of this first Workshop is available on the Q-Collect project website http://www.q-collect.eu/events/.
See 7.1 for details.
For these workshops all collections identified during the inventory organized in the framework of WP2 were invited to attend as well as all Heads of EPPO Plant Pest Diagnostic Laboratories.
The first Workshop took place at the Julius Kühn Institute in Kleinmachnow (DE) on 2014-11-27/28 and 45 participants from 16 countries attended.
The second Workshop was attended by 45 participants from 19 countries and including a representative of the International Plant Protection Convention Secretariat who stressed the importance of collection for official plant pest diagnostic.
Details on these Workshops are available on the Q-collect website.
Potential Impact:
In the Q-collect project an inventory was made on collections of phytosanitary importance within the EU and the EPPO region. Through answers on a questionnaire we got insight in the quality and the material available in those collections. Within the Q-collect consortium we identified gaps in those collections and a number of recommendations to fill these gaps were made. Priority needs and obstacles of the user/provider community with regard to the access to biological reference material and to the connected services were identified.
In proposing the creation of a sustainable network of reference collections and producing guidelines for quality criteria standards and access, Q-collect created a significant impact for collections in the near future as part of EU Reference Laboratories for plant health diagnostics (in line with the amendment of Regulations EC 882/2004). Furthermore, the inclusion of EPPO as partner within the consortium greatly strengthened the impact of this project. EPPO, as regional organization with 51 member countries, has a strong role in Plant Health and distributed by its network the outcome of the Q-collect project results most efficiently to all stakeholders interested in Plant Health.
A strong link has also been established with the MIRRI project. MIRRI (Microbial Resource Research Infrastructure) started in 2012 and is established on the European Strategy Forum for Research Infrastructures (ESFRI) road map with the goal to improve access to the microbial resources and services that are needed to accelerate research and discovery processes. The ESFRI Roadmap (2008) emphasises the evident need for improved availability of high quality materials and reagents for the study of species other than humans i.e. the animals, plants, bacteria - microorganisms. The objectives of MIRRI were completely in line with the objectives of Q-collect for microorganisms. Several partners of the Q-collect consortium were also participating in MIRRI and ensured most optimal cross exchange between both projects. Although MIRRI is only focusing on microbial collections and Q-collect is also including nematodes, arthropods and invasive plants, this collaboration helped Q-collect in obtaining its deliverables. A questionnaire which is developed within the first half year of the MIRRI project was used and adjusted to Q-collect needs and send to relevant collections and stakeholders .
The Q-collect project made an important first step to the harmonisation, interconnection and quality improvement of collections in the field of Plant Health, which is needed for a good infrastructure essential for the detection, interception and recognition of both established and new or emerging plant pathogens and pests. Plans for transnational access to the data of the established benchmark collections for quarantine pathogens and pests have been made by using existing state-of-the-art solutions for developing searchable networks of collected specimens in biodiversity informatics. With this implementation of a transnational accessible joint search info-portal for the establishment of databases and collection management systems, Q-collect provided the first step in improved services to the consortium partners and for the whole Plant Health scientific community.
The expected impact of Q-collect on the European Research Area of Plant Health will be improvement in the following areas:
- Models for sustainable collaboration, coordination and maintenance of trans-national reference collections
A key output from this project is the proposed establishment of initial networks with defined criteria of key international reference collections of quarantine plant pests and pathogens. In an initial phase, collections represented by the project partners will be involved, but this concept can be extended to all relevant collections through information posted on the project website, two international workshops involving the main stakeholders and also through on-going links through EPPO and the MIRRI project. The embryo networks and associated project outputs serve as models to catalyse on-going and more extensive collaborations amongst the other European reference collections. These collaborations will help to increase the diversity of reference materials and ensure that they are preserved under common standards, are easily located and made available to end-users across the whole community for the near future. The model system of transnational networks will also help to identify and safeguard specific reference materials which are in danger of being lost due to current lack of infrastructure, resources or taxonomic experience amongst the many informal (and often temporary) research (or working) collections that exist across the EU.
- Info-portal to improve sourcing of quality reference material as diagnostic tools.
The Q-collect project generated a pilot info-portal that will effectively catalogue in a simplified way all currently available reference materials of relevance to the plant health community, the locations where they are held under common quality standards and harmonised guidelines via which they can be obtained and used by end-users across the EU and wider EPPO region.
At the end of the Q-collect project only information was available for a few collections, but this needs to be extended to all collections included in the network. Once this information is available it will facilitate the procurement of standardised reference materials from a choice of reliable sources and guarantee their suitability for use in diagnosis, method validation, research and proficiency testing. Analyses of current gaps in the availability of particular quarantine reference organisms or important taxonomically or diagnostically similar organisms will similarly be made widely available, thus creating opportunities to extend the catalogue the holdings of the network either through deposition of key organisms via the reference collection networks or by incorporation of additional collections into the relevant networks.
- Harmonised guidelines to ensure reliability and sustainability of reference materials.
Within the Q-collect project, guidelines to standardise requirements of quality, maintenance, access, procurement and use of reference standards were produced. These quality criteria will be discussed in the different EPPO panels and once agreed they can be used as EPPO standards.
The further harmonisation and dissemination of those guidelines will also have impact far beyond the life of this project. The developed guidelines will help to increase the capacity of independent national reference collections thus enabling them to operate to the agreed international reference standards and either join the international collection networks or offer alternative independent sources of reference materials. In either way, the quality and diversity of these materials will be increased, sustaining and safeguarding their availability in the longer term.
- Training of staff involved in preservation, supply and correct use of reference materials.
Within the Q-collect project this part of collections was not discussed. However, it is expected that once the envisaged future network of important phytosanitary collections is established, training of staff members will be a particularly important task for such a network. Training should enable education of all persons involved in the preservation, supply and use of reference materials in the field of Plant Health. The long-term impact will be supporting networks of model reference collections of quarantine organisms with capacity to provide advice and training in:
- preservation methods,
- taxonomical verification of reference specimens or samples,
- minimum quality standards,
- diagnostic methods for detection and identification,
- correct use of reference materials, and
- regulations surrounding their safe movement and application.
In the questionnaire of the Q-collect project collections were asked to identify scientists with taxonomic expertise relating to key groups of quarantine pest and pathogens who will be highlighted as key contact persons for younger scientists wishing to work with those organisms. At the same time the project also identified those areas where expertise is currently lacking, and where future research and training needs to be focussed. This exercise in fully in line with the strategy that is also developed in the MIRRI research infrastructure.
- Relevance to creation of EU Reference Laboratories for plant health diagnostics, in line with Regulation (EC) 882/2004.
All of the above mentioned expected impacts is highly relevant towards the identification, strengthening, co-ordination and networking of pockets of national expertise on quarantine organisms and the possible creation of EU reference laboratories for plant health diagnostics in line with those that have been created for Regulation (EC) 882/2004. In this way, official controls performed to ensure the verification of compliance with feed and food law, animal health and animal welfare rules would also be applied to the verification of compliance with Plant Health law stipulated under Commission Directive 2000/29/EC.
Spreading excellence, exploiting results, disseminating knowledge
Q-collect disseminated the results during and at the end of the project in several ways to the stakeholders. Partner 13 (EPPO) is leader of WP7 Dissemination. They have disseminate the project and its results to the wider plant health stakeholder community in the following way:
- A dedicated website has been developed to show the objectives of the project,
- An electronic leaflet explaining the project has been made available via the website,
- Stakeholders have been contacted during the project with a questionnaire to guarantee that their wishes, in relation to relevant phytosanitary collections, are ensured,
- Two workshops have been organized: one after one year and the second at the end of the project to disseminate the results and discuss other collections, institutes, NPPOs within the EU and EPPO region, inspection services and other stakeholders the outcome of the different work packages.
Relevant targeted stakeholder groups (NPPOs within the EU and EPPO region, industrial sector, policy, end-users and other stakeholders were contacted by a questionnaire to ensure that their requirements are incorporated into the project. They have also been invited to attend the two workshops, which were organized within the project (year 1 and year 2).
Dissemination to laboratories of National Plant Protection Organisation was ensured through EPPO via different channels (direct contacts with Heads of NPPOs, dissemination thought EPPO Panels on Diagnostics, and workshops for heads of plant pest diagnostic laboratories).
Project results such as inventory results, quality standards, access criteria, reference criteria and other deliverables from the seven different work packages have been made available to participating organisations and in part to other interested groups by publication in guidance documents
Information about the content and location of the reference collections, service reference collections and working collections and the trans-national accessible info-portal will be made publicly available through the project website.
The external project website presents descriptions of Q-collect objectives, of the project consortium, reports of meetings, the project outputs and links to other appropriate websites of each participating organisation/country and other relevant organisations. Recipients of information will be EU Plant Health diagnostic laboratories, Regional Plant Protection Organisations (RPPOs), and key non-EU National Plant Protection Organisations (NPPOs). RPPOs and some key non-EU NPPOs who are active in relevant phytosanitary-related research, or key exporting countries to the EU, will be contacted early in the project. They have been informed of the project’s aims and objectives and were invited to discuss issues and explore possible interactions with the Q-collect network, including joint activities beyond the end of the project.
Publishing information materials (plus printable leaflet versions in English only) about Q-collect have been produced for the consortium members to be distributed at meetings and conferences.
Progress reports were produced for the EC. The outputs of the project have been presented to the participants of the Final Project Dissemination Workshop, such as research funders, research providers, Plant Health policy makers, ‘industry’ representatives and interested parties from across Europe, and from outside Europe (e.g. RPPO’s and, as appropriate, key non-EU NPPO’s).
The Q-collect project results can be exploited by the NPPOs and associated diagnostic laboratories. The guidelines on Quality Assurance for reference collections will be further developed with EPPO Panels for each group of organisms in order to prepare an EPPO Standard.
Additionally, the joint search portal of the connected databases of benchmark and reference collections will be used both by the consortium members and other NPPOs within Europe.
White Paper
During the project a white paper on phytosanitary important collections has been written and discussed at the second workshop in Rome (September 2015).
Phytosanitary diagnosis and collections
Introduction
International trade and movement of plants and plant products into and from Europe has increased tremendously in recent years leading to higher numbers of consignment imported. The type of commodities imported and the origins have also diversified. As an illustration; imports of woody plants from Asian origins have become more frequent than in the past where most woody plants were traded between European countries. As a result, the rate of introduction and establishment of new organisms in Europe has increased steadily as well as the phytosanitary risk of introducing such new organisms.
Organisms relevant in plant health include plant pathogens, arthropods and invasive plants. Some may have already been identified as posing an unacceptable risk to agricultural and horticultural crops, forests and the wider environment and currently approximately 250 organisms are included in the Annexes of the Directive 2000/29/EC as pests of the European Union (also called quarantine pest lists). However, it should be noted that some of the pests recently introduced in Europe had not been identified as posing an unacceptable risk before they established in Europe. Consequently the phytosanitary vigilance to detect unknown pests needs to become more and more efficient.
As plants may be latently infected, inspection of consignments and of places of production of plants and plant products often involves laboratory analysis of samples collected during these inspections. In outbreak situations the accurate identification of the causal agent relies on laboratory testing as well. In all these situations the capability of National Plant Protection Organizations (NPPOs) and the affiliated laboratories to quickly and reliably detect and identify organisms is critical for effective phytosanitary measures to be taken. Plant pest diagnostic is also essential to support the phytosanitary certification of consignments of plants and plant products exported from Europe.
In order to better ensure the reliability of diagnostics, laboratories are increasingly working under quality assurance systems (including accreditation, ISO 17025) and this is becoming a requirement of National Plant Protection Organizations for laboratories performing official tests.
Under such circumstances, laboratories need to have access to well characterised biological reference material for morphological identifications and the use for development and validation of tests. Moreover, in tests biological reference material is needed as a base for positive and negative controls.
Validation of tests is carried out to provide data on the performance of a test and in particular regarding its analytical sensitivity and specificity. Reproducibility of a test is also essential and is often determined in test performance studies. In order to be able to establish these performance characteristics, well-defined biological reference material is needed for the organism to be identified with the test but also for those organisms with which the target organism may be confused with (look-alikes). Availability of biological material coming from reliable, curated collections is thus essential for test development and validation. In order for laboratories to confirm its competence to correctly perform tests, participation in proficiency testing schemes is recommended. Although offers to participate in proficiency testing are currently still limited in the plant health sector, they are increasing. Laboratories organizing proficiency testing need to have access to well-defined biological material of the target organism but also material of look-alikes.
Finally biological material is also essential to ensure the quality of analyses at different levels: for each diagnosis as well as for global quality control of the laboratory. Although molecular tests are based on nucleic acid sequences, biological material is essential for the development, validation and quality assurance of these tests. Reliability of the sequences on which the tests are based depends on the correct identification of the original biological material.
The biological material also needs to be kept in collections as a current source of reference DNA. New molecular technologies like Next Generation Sequencing (whole genome sequencing) will increase new taxonomic insights in essence on the short term for bacteria, viruses (viroids) and fungi. Therefore it is essential to be able to re-examine the original biological material. Biological material is also needed for quality control of nucleic acid isolation. Biological material is kept in collections and these should provide appropriate guarantee regarding this material in term of quality.
New legislations
The Nagoya Protocol
The Nagoya Protocol on ‘Access to Genetic Resources and the Fair and Equitable Sharing for Their Utilization’ was adopted in 2014 and will have impact on all researchers working with biological resources1. It is a legal binding instrument for the implementation of the Convention on Biological Diversity (CBD). The CBD has three main goals i) the conservation of biological diversity; ii) the sustainable use of its components and iii) the fair and equitable sharing of benefits arising from its utilization. Basically the CBD recognises the sovereign rights of countries over their own biological resources and the so-called genetic resources contained therein. Access to genetic resources in a country that is party to the CBD (i.e. a country that has signed and ratified the CBD) requires prior informed content (PIC) from the competent authority in that country and a setting of mutually agreed terms (MAT) between provider and user. Parties are free to decide whether access to genetic resources is subject to such requirements or not. But the Party must assure that, within their territory, genetic resource, originating from other Parties (countries) are handled according the CBD and that benefits arising from the use of the genetic resources or traditional knowledge associated with these resources are shared fairly and equitable.
The Nagoya Protocol aims to provide guidance for the parties to implement the CBD’s fair and equitable sharing of benefits arising from the utilization of the resources by adopting their national access and benefit sharing (ABS) legislation. The biological material (including DNA extracts) held in collections is covered by the Nagoya Protocol. This Protocol is now going to be implemented in the EU 2 and guidelines are being prepared and are currently under consideration by different groups. The objective at European level (http://eur-lex.europa.eu/legal-content/FR/TXT/?uri=uriserv:OJ.L_.2015.275.01.0004.01.FRA ) is an implementation of the Nagoya Protocol on the 12th of October 2015. It should be noted that this legislation seems to create conflict with obligations under the IPPC, for example it is not clear if specimens isolated from imported consignments can be stored and used for diagnostic and research purposes. This needs to be clarified.
New EU control directive
For EU member states, a major change in the organization of plant pest diagnostic laboratories performing official diagnostic will happen with the revision of the EU Regulation No. 882/2004 on official controls. The new Regulation proposal of the European Commission will extend the scope of the above Regulation to plant health. One of the changes foreseen will be the establishment in the plant health sector of a network of official laboratories, National Reference Laboratories (NRL) and EU Reference Laboratories (EU-RL). For these laboratories performing tests the requirements will include accreditation and the use of standardised methods. The EU-RL will (among other tasks) play a dominant role in elaboration and harmonization of tests, analyses and diagnosis and providing reference methods, providing reference material, organisation of test performance studies and proficiency testing. The EU-RL therefore needs (the access to) a reference collection. Therefore the need of well-established reference collection will increase even more in the coming years.
Current situation
Results of Q-collect project
The survey organized during the Q-collect EU funded project confirmed that although there is a significant number of plant pathogens and pest collections still present within Europe, they are dispersed, widespread and of very variable quality. The main findings of the project are as follows:
- Most collections are working or research collections and only few of these collections are likely to be organized to provide services to outside users.
- There is a limited number of information on collection’s holdings available online.
- Many collections have no quality system in place, and accreditation of collections is scarce.
- Sharing of material between collections to ensure resilience is not common and can be considered as a high risk for loss of important biological material in case of incidents with buildings or equipment.
- Appropriate basic funding is not secured enough and there is a need for a common policy towards collection management throughout the region.
Achievements of the project
• Guidelines have been drafted on Quality assurance for reference collections and will be further developed with Panels for each group of organisms in order to prepare an EPPO Standard.
• The Project proposed criteria for the establishment of a sustainable network. This network will bring together previously dispersed information on biological material and stimulate collaboration. The criteria will be reviewed in the EPPO framework.
• The Project recommended that an online platform should be established and maintained to stimulate and facilitate networking and data sharing. This platform will improve accessibility and visibility of biological material (and related information) available in collections. A pilot platform will be established to include a deposit form for information on biological material, a search engine and links to additional relevant information available online.
Other initiatives
Online access to collections can facilitate the availability of collection. Since 2010 a database called Q-bank has been elaborated. This database links information, sequences and collections of the most important organisms (Q-organisms, look-alikes and other important organisms). The database can be used for diagnosis, but gives also the possibilities of finding organisms in collections. This initiative originally started as a Dutch project. The EU funded project QBOL has been using Q-bank to serve as a repository of DNA sequences. Nowadays this database is maintained by a group of international scientific curators responsible for their discipline. In the past 4 years the Dutch government has supported this group and the database was further elaborated. During the Q-collect project more work on this database has been done especially on quality criteria.
Future
Goal for the future: for every organism group/discipline there are at least at 2 locations official reference collections and through online catalogue(s) these reference collections can be accessed by interested users to search and order material.
All the initiatives of the past years (Q-bank, QBOL, Q-collect, etc.) have given a boost to the phytosanitary collections. Much energy, knowledge and hard work has been given to the collections. The challenge is to keep up the good work and follow this road. In the coming years it is unlikely collections will be supported with big additional budgets or project funding. However, a database like Q-bank has proved that it is possible to connect specialists and their collections on an online platform. Other projects have proved that the network of phytosanitary specialists is strong and people are willing to collaborate. In the framework of Euphresco there are many international co-operations especially between official NPPO related laboratories. The laboratories in the EPPO region do not need a reference collection in every country or at every laboratory, but they do need access to these collections. By connecting collections online and clustering collections an international coverage for reference materials can be achieved. With quality systems in place the collections can offer reliable, well defined reference material. The new EU regulation with extra demands on reference material and the forming of EU-RL’s can help to speed up this movement. Official collections as part of or related to an EU-RL and partly financed by the EU provide possibilities. Through co-operations like EUPHRESCO an even distribution of the reference collections should be possible.
Recommendations
To reach the above mentioned, first steps should be taken in the near future. The need to improve the infrastructure supporting phytosanitary collections and use them more efficiently and improve collaboration will be the main ingredients.
A: Priority to making/maintaining inventories
It is essential to be able to know which and where biological material is available. Collections should make an inventory of their holdings and provide this information in a format that could allow sharing on a platform.
B: Establish a long term sustainable online platform
Encourage and support the creation of a long term single platform to access the information. Choose the online platform to be used and assure a long time hosting.
C: Improvement of Quality systems for collections
The implementation of quality systems in collections is essential to ensure that proper reference material is used in the development and performance of tests. The upgrade of working collections should be a short term objective.
D: Establish networks for collections
Networks of collections should be established in order to share the responsibility of maintaining reference material and also for duplication purposes whenever necessary. When quarantine organisms are involved the network should have a link with Euphresco.
E: Establish a common policy for reference material
A common policy should be established for developing and maintaining reference material among member states as one of the basic requirements for a sustainable network of National Reference Laboratories and EU Reference Laboratories in the new EU control directive on official controls. Exchange of material and concentration of material in yet well-established collections will be a first step.
In case of outbreaks it is essential that not only information on the location of collections is accessible but also prompt and organised/regulated exchange of material is possible. Therefore a common policy for issuing of material and shipment in compliance with legislation should be developed.
F: Nagoya Protocol
Consequences for plant health related collections should be clarified and in case of conflict with plant health legislation, derogations should be sought.
The basis for the above steps originate from the different collection projects. Now there is a strong need for further implementation from within our field and our organisations.
List of Websites:
www.q-collect.eu