Guidelines for applicants within the One Health EJP for PhD Grants

TABLE OF CONTENTS

Call Background.................................................................................................................................2

PhD Grants..........................................................................................................................................2

2.1 Proposals and Assessments...................................................................................................2

2.2 Eligibility...................................................................................................................................3

2.3 Criteria and Process for selection........................................................................................4

2.4 Budget..................................................................................................................................4

2.5 Progress Monitoring...............................................................................................................5

2.6 Selection of Students...............................................................................................................5

Annexes...............................................................................................................................................6

3.1 Strategic Research Agenda 1: Key information..................................................................6

3.1.1 Prioritised research and integrative topics..........................................................................................6

3.1.2 Description of the Research Themes...................................................................................................7

3.1.3 Description of the integrative activities............................................................................................10

3.2 Updated list and descriptions of priority research topics and integrative topics : Key information...................................................................................................................................12

FINAL RANKING OF RESEARCH TOPICS............................................................................................12

Foodborne zoonoses (FBZ)..........................................................................................................................12

Antimicrobial resistance (AMR)...................................................................................................................13

Emerging threats (ET)..................................................................................................................................13

DESCRIPTIONS OF RESEARCH TOPICS..............................................................................................14

FINAL RANKING OF INTEGRATIVE ACTIVITIES..................................................................................14

DESCRIPTION OF INTEGRATIVE ACTIVITIES......................................................................................15

3.3 JRP and JIP information.......................................................................................................17

3.4 Frequently Asked Questions (FAQs)..................................................................................17

3.5 PhD Proposal Application Form.........................................................................................19

Lead Applicant Details............................................................................................................................19

Project Key Information.........................................................................................................................19

Supporting Information..........................................................................................................................19

3.6 One Health EJP Consortium Partners................................................................................20

1

CALL BACKGROUND

The One Health EJP is a Co-Fund action under the European Commission’s European Joint

Programme within the H2020 Framework Programme. The One Health concept recognizes that

human health is tightly connected to the health of animals and the environment.

Consistent with the “Prevent-Detect-Respond” concept, the One Health EJP aims at reinforcing

collaboration between institutes by enhancing transdisciplinary cooperation and integration of

activities by means of dedicated Joint Research Projects (JRP), Joint Integrative Projects (JIP) and

through education and training activities, including PhD projects. The programme includes alignment

and harmonization with on-going EC-funded research projects, and deliverables from the One Health

EJP will feed into evidence based risk assessment and response for national authorities.

PHD GRANTS

At the start of the Programme, up to twelve PhD grants were available, each funded 44% by the EU.

The remaining 56% will need to be funded by other non-EU sources. In the first call, four grants were

awarded. In this second call, the remaining eight grants will be awarded. The value added by these

grants includes:

1. Provide interdisciplinary (med-vet-environment) training for the next generation of One Health

researchers in Europe contributing to the sustainability of the One Health approach.

2. Allow greater flexibility in the PhD projects than Joint research projects to ensure innovative

hypothesis driven research.

3. Maximise international and interdisciplinary networking among One Health EJP partners in

addition to the interaction provided by the JIPs and JRPs that started in January 2018.

2.1 PROPOSALS AND ASSESSMENTS

Partners applying for PhD grants should submit a clear and succinct (adhere to word limits)

application by the 16:00 CET 28 Feb 2019, following the provided application form (see Annex 3.5).

Current state of the art in the chosen area, the knowledge gap being addressed and a

testable hypothesis

Proposed methods

Relevance of PhD topic to the One Health EJP SRA 1 or Updated List and Descriptions of

Priority Research and Integrative topics

2

Relevance to the general objectives of the EJP: prevent-detect-respond - improve integration

and societal preparedness to deal with foodborne zoonoses, antimicrobial resistance and

emerging threats within the mandate of EJP partner institutes

Principle and collaborative supervisor’s experience and suitability

Institutional PhD student support

Opportunities for student development

Opportunities for networking and partner involvement in addition to existing and planned

EJP activities (added value from this PhD project):

o International

o Interdisciplinary (med-vet-environment, other disciplines)

Budget

A named student is NOT required at the application stage.

2.2 ELIGIBILITY

The lead applicant must have relevant experience and hold a substantive position (at least

0.5FTE) at a One Health EJP Partner Institute

At least one co-supervisor must be at an academic institution able to award higher degrees

(does not need to be an OHEJP Partner Institute)

Minimum number of One Health EJP partners is two. Only linked third parties are also

eligible for PhD funding. Non One Health EJP partners may be included as collaborators, but

are not eligible for funding. However, these third party institutes are allowed to work within

the OHEJP under the umbrella of a beneficiary. If these beneficiaries are selected for a PhD

programme , it can be envisaged that they will use in-kind contribution provided by these

third party institutes

Topic of the PhD must be within scope of the SRA (Annex 3.1) or the Updated List and

Descriptions of Priority Research and Integrative topics (Annex 3.2)

PhD must reinforce the general objectives of the EJP: prevent-detect-respond, improve

integration and societal preparedness within the mandate of EJP partner institutes (Annex

3.1)

The PhD Project must be inter-disciplinary (for example disciplines may include at least two

of med-vet-environment and may include other disciplines such as food or social science).

3

A link with an existing JRP or JIP (Annex 3.3) is to be encouraged, but it is not required.

Three year or four year PhDs will be considered. As the One Health European Joint

Programme ends in Dec 2022, in the case of four year PhDs, any costs incurred in the final

year must be covered by 100% external sources of funding (see budget section 2.4)

Evidence of co-funding (a letter of support is considered ‘confirmed’, and absence of one is

considered ‘proposed’ )

2.3 CRITERIA AND PROCESS FOR SELECTION

Following an initial check for eligibility by the WP6 team, proposals will be sent out for anonymous

review by experts selected from within the EJP partner network according to their expertise and

independence from the proposed activity. Reviewers will be given detailed guidance including the

following criteria:

Quality of training support available (Institute support, supervisor’s expertise & track record)

Quality of the science (a testable hypothesis and likelihood of high-impact outputs)

Opportunities for student development and for integration among partners

Strengthen the general objectives of the EJP

Proposals will be ranked by the WP6 team in April 2019, this ranking will be based on the reviews

received in April 2019 and discussed with PMT. Project selection will be validated by the Scientific

Steering Board in May 2019 where a meeting to discuss the projects via tele or videoconference will

be held, and an online vote (with voting instructions) will be arranged by WP6 to validate the

projects selected to be funded. Only one vote from each institute will be allowed. Each institute will

be asked to vote whether they agree with the results. They will be given three options: yes / no /

abstain. Project selection will be announced in May 2019.

2.4 BUDGET

The total budget per partner institute(s) hosting the PhD and summary of allocation (stipend/salary,

registration fees (EU or international), laboratory consumables or bench fees, sufficient travel for

mobility) must be stipulated in the application. The total costs funded by the OHEJP (44% EU funds +

56% partner institutes co-funding) must not exceed €136,250. However, financial contributions

from other external sources can be added to cover additional costs induced by the PhD programme.

As the One Health European Joint Programme ends in Dec 2022, in the case of four year PhDs, any

costs incurred in the final year must be covered by 100% external sources of funding.

4

Evidence of co-funding will be required before the student is recruited, however at the application

stage co-funding can be pending.

2.5 PROGRESS MONITORING

PhD project progress will be monitored by the degree awarding body (University at which the

student is registered) according to their guidelines and integrating the requirements of all

collaborating One Health EJP and non-One-Health EJP partners.

In exceptional circumstances applicants may apply for a cost-neutral extension to a PhD project, up

to the maximum possible duration determined by the registering University. Criteria for extension

will include logistic or external constraints that have delayed aspects of the project beyond the

applicant’s control.

Copies of formal assessment documents (yearly reports, confirmation reports, publications and a

final report) will be submitted as appendices in the Annual EJP reports. All students will be required

to present at the Annual Scientific Meeting of the One Health EJP.

2.6 SELECTION OF STUDENTS

Once the project has been approved, student selection will be undertaken by the supervisory team

(lead applicant and co-supervisors) and the awarding institution (University that the student will be

registered at) according to local guidelines and eligibility, and to include the following criteria:

Demonstrated intention to pursue a career in at least one area of zoonotic disease: prevent-

detect-respond, improve integration and preparedness

Demonstrated enthusiasm for a One Health approach

Demonstrated experience or potential for international integration

Once a preferred candidate has been selected, the candidate’s details should be provided to the

WP6 Leaders. A summary of selected projects and candidates will then be circulated to all partners.

Individual contractual agreements will then be made for each student between the Lead Applicant’s

institution and the selected student.

5

ANNEXES

3.1 STRATEGIC RESEARCH AGENDA 1: KEY INFORMATION

A full copy of SRA 1 is available on the private space of the OHEJP website, or by contacting WP6 (p.basu@surrey.ac.uk )

3.1.1 PRIORITISED RESEARCH AND INTEGRATIVE TOPICSResearch topics domain Foodborne Zoonoses (FBZ)

1. Improved surveillance system and harmonized data analyses 2. Development and harmonisation of NGS-based methods for detection and tracing of FBZ agents,

emerging threats and AMR determinants 3. Biosecurity and other interventions 4. Source attribution and transmission routes 5. Epidemiological studies: risk factors and dynamics 6. Risk communication and consumer targeted intervention strategies 7. Optimizing options for risk management and enforcement in feed and food production and

processing 8. Model Systems (in vitro and in vivo) to study host/food – microbe interactions 9. Frameworks and systems for sharing tools and data for risk assessment and effective decision

making Research topics domain Antimicrobial Resistance (AMR)

1. Development and harmonisation of phenotypic methods 2. Epidemiological studies into the dynamics of AMR in human and animal populations and the

environment including horizontal gene transfer and selection of AMR 3. Risk Assessment AMR 4. Communication and stewardship AMR 5. Disease burden, socio-economic consequences and risk ranking 6. Metagenomics and bioinformatics for detection and surveillance of AMR pathogens and

determinants Research topics domain Emerging Threats (ET)

1. Development and harmonisation of non-NGS-based methods for detection of FBZ agents and emerging threats

2. Improving preparedness and response 3. Applying risk assessment/modelling methodologies to support decisions for the control of

emerging threats, foodborne zoonoses and antimicrobial resistance 4. Host factors associated with colonization, persistence and disease 5. Ecology of emerging pathogens

Integrative topics 1. Interpretation of surveillance data - Standardised data formats and ontologies, common tools

and procedures for data analyses, including interpretation of sequence data 2. Common reporting and signalling procedures, joint platform for sharing surveillance data and

their interpretation, incl. risk assessments 3. Joint databases of reference materials and data, incl. metadata 4. Harmonised protocols and common best practice 5. Mentoring (twinning) system for sharing of best intervention practice 6. Common frameworks for design and methods to assess equivalence between surveillance and

control activities 7. Aligned use of experimental facilities and models (of transmission, ecology, risk assessment etc.)

6

3.1.2 DESCRIPTION OF THE RESEARCH THEMES Theme: Analytical methods

Within the theme analytical methods, 4 topics are identified and prioritised: 1) Development and harmonization of phenotypic methods 2) Development and harmonisation of non-NGS-based methods for detection of FBZ agents and emerging threats 3) Development and harmonisation of NGS-based methods for detection and tracing of FBZ agents, emerging threats and AMR determinants and Metagenomics and bioinformatics for detection and surveillance of AMR pathogens and determinants. Even in the area of NGS techniques, phenotypic methods are of utmost importance in daily routine practice, both in veterinary and human medicine. The objective of this topic is to stimulate the development of new quick diagnostic phenotypic tests for the detection and/or identification of AMR bacteria in humans, animals, feed, food and the environment. There will be a strong link with integration activities around data management.

Development and harmonisation of non-NGS-based methods for detection of FBZ agents and emerging threats will fill the gaps in the knowledge of the methodologies alternative to standard PCR or cultural isolation applicable to food-borne zoonoses and emerging threats. Technology increasingly allows developing or re-directing analytical methodologies for the detection of pathogens, which are more rapid and reliable than the standard approaches based on cultural strategies and potentially can cover pathogens that are currently not identifiable or misdiagnosed. For example, by use of highly specific antibodies (mabs), recombinant proteins, and/or genetic probes novel methods can be developed. Such technologies have the potential to deliver rapid assays on platforms applicable to field use such as bed/farm/pen-side tests, as well as in the food production chain. It is the goal to validate the methods to be used in EU and seek to develop automated systems with electronic data collection.

Development and harmonisation of NGS-based methods for detection and tracing of FBZ agents, emerging threats and AMR determinants should resolve delayed responses to crises which negatively affect management of human infections, trade, food chain sustainability and food security. The rapid growth of the sequencing technologies potentially allows delivering analytical tools for rapid identification of pathogens and AMR determinants based on characterisation of the agents and their genomes, not only on isolates but also following culture-independent strategies. One of the foreseen outcomes is the establishment of standardized and validated pipelines to extract information from raw NGS data on the detection and typing of specific pathogens, and genomic traits in genomes including virulence genes and AMR determinants.

The topic Metagenomics and bioinformatics for detection and surveillance of AMR pathogens and determinants will enforce WGS metagenomics approaches in the monitoring of AMR development in complex microbiota recovered from relevant sites under selective pressure with antibiotics. This would include specific expected hotspots of AMR selection such as at hospital or farm level, or in the environment. Foreseen outcome is the production of quantitative WGS metagenomic data in geographical sites of human or veterinary (or combined) relevance as well as the correlation of metagenomic data with antibiotic usages and other risk factors

7

Theme: Epidemiology

Within the theme Epidemiology, 5 topics are prioritised: risk factors and dynamics, ecology of emerging pathogens, the dynamics of AMR in human and animal populations and the environment including horizontal gene transfer and selection of AMR, source attribution and transmission routes and improved surveillance system and harmonized data analyses.

Identification of risk factors and infection dynamics will serve to improve the effectiveness of surveillance systems and optimize the use of time and resources, both for foodborne zoonoses surveillance systems as well as for recognizing emerging threats. Verification of identified risk factors and optimal control points for foodborne and emerging threats will facilitate the development of models to predict pathogen transmission and dynamics related to the identified risk factors.

More insight in the ecology of emerging pathogens that are zoonotic and foodborne is needed for the prevention and control, including knowledge about pathogen transmission between human and animal populations and the environment. E.g. molecular epidemiology is needed to study host dynamics and to reconstruct high resolution transmission trees. An expected outcome is the identification of host-pathogen-ecology-combinations that constitute a higher risk if pathogens are introduced.

The dynamics of Antimicrobial Resistance attracts a lot of attention in recent times. Although multiple efforts have been undertaken, there are still knowledge gaps and inconsistencies in understanding of the epidemiology of antimicrobial resistance, i.e. its selection and spread under antimicrobial usage pressure in different ecological settings. Geographical differences, temporal trends, variable farming, environmental reservoirs, wildlife, farm and companion animals as well as human colonization, anthropogenic impact on the abundance of resistance in the environment, and factors promoting or mitigating resistance transmission need systematic studies. Foreseen outcome includes a better description of reservoirs and vectors of resistance as well as increased knowledge on environmental, geographical and demographic risk factors, drivers and catalysers of selection and trends in resistance.

The topic Improved surveillance system and harmonized data analyses is based on the observation that current EU surveillance systems on foodborne zoonoses, antimicrobial resistance and emerging threats are focused on selected threats and areas. Globalization however, requires broader and flexible actions to detect hazards, reservoirs, vectors, trends and routes of transmission as well as common approach and timely analysis and data sharing. For research in this area a strong interaction is foreseen with the integration activities in WP4.

Finally, source attribution and transmission route studies will improve knowledge on sources and transmission routes of pathogens and AMR determinants within ecosystems, including the food chain. Furthermore, it will provide sound methods and baseline information to guide risk assessment and management, including platforms for sharing new approaches to attribute cases of FBZ and AMR to their sources.

8

Theme: Host-microbe interactions

Within the theme Host Microbe interactions, 2 topics are identified and prioritised: 1) Host factors associated with colonization, persistence and disease and 2) Model Systems (in vitro and in vivo) to study host/food – microbe interactions.

The topic Host factors associated with colonization, persistence and disease will cover both foodborne zoonoses as well as emerging threats. The elements defining host specificity of microbes is poorly understood. Crossing of the species barriers represents a crucial event in emergence of known and novel diseases. Recent evidence suggests that the microbiota in combination with the host immune response and host tissue type, may be involved in host specificity. One of the objectives is to better understand humoral/cellular immune response and its implementation to control microbial infections and its role in latency/sub-clinical infections. A link with integration activities is foreseen as multi-microbial experts will share knowledge to create a multi-microbial hub to share and disseminate knowledge and techniques to study host specificity.

Model systems are crucial to understand the pathogenesis, emergence and spread of infectious diseases. One of the objectives is to develop novel in vivo models (both animal models and alternatives such as cellular systems) that reflect infection in the natural host that opens the door to understand the pathogenesis of infectious diseases. Since exposure does always lead to disease, studying the immune response by seroprevalence studies will reveal the burden of disease and exposure to microbes in each region. Also new mathematical approaches to dissect the behaviour of microbes within a host or their geographical dissemination will be developed. These mathematical models might describe and predict emergence and spread of food-borne pathogens from host, to food and in the food chain.

Theme: Risk Assessment

Within the theme Risk Assessment, 4 topics are identified and prioritised: 1) Frameworks and systems for sharing tools and data for risk assessment and effective decision making; 2) Disease burden, socio-economic consequences and risk ranking; 3) Applying risk assessment/modelling methodologies to support decisions for the control of emerging threats, foodborne zoonoses and antimicrobial resistance and 4) Risk Assessment AMR.

Rationale for the topic Frameworks and systems for sharing tools and data for risk assessment and effective decision making within and outside Europe is the fact that large number of predictive modelling and risk assessment models, software tools and databases have been developed in the past decades, but their maintenance is not always guaranteed and exchange of information between these resources is currently difficult and time consuming, which limits their application. An obvious next step is to combine the data and software tools that are available in Europe and facilitate the communication between them and the networks hosted by EFSA. Core results of the project are joint use of harmonized standards by EJP partner organisations and the joint infrastructure that provides resources that will be of immediate and future practical use when performing risk assessment to support decision making in Europe.

Disease burden is increasingly studied, particularly to inform risk management strategies. The recent publications on the global disease burden of foodborne disease have shown the relevance and potential of quantitative disease burden estimation, among others as a basis for risk prioritization. These latest developments also highlighted current challenges in estimating the burden of some foodborne diseases, particularly associated with AMR and other emerging threats. The need to extend current burden of disease estimations by incorporating socio economic consequences is widely recognized. By integrating health, economic and social impact assessments (applying e.g. multi-criteria decision analysis), and develop a method that can be applied in different countries, comparative risk rankings can be performed across the EU.

In the past decades, risk assessment modelling has been developed and applied in a number of European countries, mainly for microbial hazards like Salmonella, Campylobacter and Listeria. As a next step, it is important to further develop and apply risk assessment methods in the area of foodborne zoonoses and for a broader range of hazards, including emerging threats, antimicrobial resistant bacteria, viruses and parasites. These risk assessments should be aimed at decision support, including cost benefit analyses, cross- border animal movement and trade with feed and food. Expected outcomes are a.o. novel risk assessment methods

9

that allow the inclusion of NGS and metagenomic data and novel risk assessment tools for specific microbial hazards (e.g. Toxoplasma), emerging threats (e.g. models for their introduction and spread, and the impact of reactions to early detection) and the spread of antimicrobial resistance.

Risk Assessment of AMR is a dedicated topic due to constantly evolving nature of AMR. Therefore, risk assessments need to be regularly updated and adapted to new potential hazards. Projects in this field will address the relative and absolute contribution of animal and environmental sources to the public health burden of AMR, including variability between bacterial species, by using risk assessment. Expected results include increased understanding of the role of the environment in dissemination of antimicrobial resistance and human exposure.

Theme: Intervention

Within the theme Intervention, 5 topics are identified and prioritised: 1) Improving preparedness and response; 2) Communication and Stewardship AMR strategies 3) Risk communication and consumer targeted intervention 4) Biosecurity and other interventions, and 5) Optimizing options for risk management and enforcement in feed and food production and processing.

Natural disasters and microbiological threats are often unpredictable, nevertheless we want to try to reduce the effects they can cause by trying to detect and identify them and as much as possible eliminate or prevent them. Topic Improving preparedness and response aims at building an integrated capacity for European public health and veterinary laboratories to detect, control and prevent emerging diseases in Europe. Central point is the development of methods and tools to early identify, detect and control emerging threats, – including novel tools for data collection, analyses and data sharing - in cooperation with established networks like EMERGE, ENIVD, EWRS, IHR; focused on microbial, zoonotic, food-borne bacterial, viral and parasitic threats as well as on their emerging AMR mechanisms or virulence patterns.

Communication with stakeholders and stewardship of antimicrobial usage form an important component of the international strategy to combat antimicrobial resistance and preserve the effectiveness of antimicrobials in both man and animals. The impact of different prescribing practices in both animals and man on the development of antimicrobial resistance is a component of the evidence-base on which appropriate interventions may be recommended. As reduction of antibiotic usage might have side effects, one of the foreseen actions is to develop systems to monitor adverse consequences of adoption of antimicrobial stewardship guidelines including negative effects on animal productivity, welfare or costs of production.

Due to globalization and various selective pressures, pathogens on the European market are likely to have changed in recent years, and changing production systems create new challenges relating to pathogens in locally and globally produced food. The research focuses to give the European community (authorities, industry) a “toolbox” regarding communication and consumer targeted interventions.

Biosecurity (the sum of preventive measures to keep the unwanted microbes away from animals/humans/food/feed) is one of the key interventions as “prevention is better than cure”. Due to the large differences in production systems across Europe and changing husbandry and climate, the optimal solution in one area might not be optimal in another. It is important to validate promising practices in different countries and to perform robust, meaningful studies to provide sound evidence and avoid wasting funds on studies of insufficient power.

The international trade in feed, foods and breeding animals might constitute additional challenges when it comes to risk management options. In order to reduce the negative consequences of food borne pathogens, we aim at identification and evaluation of the cost benefit of various intervention methods, optimizing various processing steps, and evaluation of the efficacy of various communication strategies.

10

3.1.3 DESCRIPTION OF THE INTEGRATIVE ACTIVITIES

The core mission of partners in the One Health EJP is to provide expertise and services to appropriately prevent, detect and respond to societal challenges, i.e. foodborne zoonoses, antimicrobial resistance and emerging threats. The chain of actions from prevention via detection to response defines a series of capacities that need to be maintained and kept up to date by the expert institutes. These pertain to their capacity to design and implement surveillance activities, develop high quality laboratory methods, access reference materials and data, to their ability to timely and appropriately interpret and communicate surveillance information as well as provide guidance to risk managers about relevant actions, both for prevention and response.

Current state of the art More or less formalised collaborations and networks exist within the three domains of the EJP already today, both nationally and internationally, largely driven by the strong legislative framework on food safety and the corresponding dynamic policy environment that all institutes working within the field have to relate to. This includes, but is not limited to, networks set up by the European Commission, ECDC and EFSA such as the network of EU Reference Laboratories, the European Food- and Waterborne Diseases and Zoonoses Network, the European Antimicrobial Resistance Surveillance Network, the Emerging Viral Diseases-Expert Laboratory Network, VectorNet, the Animal Health and Welfare Network, and the networks for zoonoses monitoring data collection and analysis, as well as for BSE-TSE and microbiological risk assessment. Although most of these networks are established within their respective sectors (public health vs vet-food) the strategies of both EFSA and ECDC aim towards an improved inter-sectoral integration (ECDC strategic multi-annual programme 2014-2020). Examples are AMR surveillance in food-borne pathogens where an integrated EU system will be jointly developed, and the rapid detection and investigation of food- and waterborne outbreaks through linkage of strains through molecular typing data, with cluster analyses on anonymised data performed in a joint database. An ambition to link human data collection with baseline surveys in the food and animal sector with the aim to produce better public health risk assessments and broader scientific epidemiological overviews is also an area where the EU institutions can pave the way for an improved national integration of surveillance activities. Both EFSA and ECDC also have ambitions in the field of harmonised methodologies and in building capacity in scientific assessment, investigation and knowledge.

Another example of an international inter-institutional collaboration that serve integration across the public health-animal health interface is the Med-Vet-Net Association (www.medvetnet.org), an organisation established to maintain the collaborations developed as a result of the Med-Vet-Net network of excellence. There are also professional networks that are more tied to specific thematic expertise (microbiology, epidemiology, risk assessment), but even these tend to exist within sectors rather than across.

Nationally, the degree of methodological and operational integration between Med and Vet institutes across Europe varies, from formalised and well-established to informal and ad hoc (EU Workshop One Health Risk Analysis Structures, 2016, RIVM).

Challenge and progress beyond the state of the art

The ambition of the integrative activities of the One Health EJP is to develop structures, work processes and platforms that overcome any inter-sectoral division within the themes and domains defined by the EJP scope, resulting in ONE single European surveillance community. This integrative development should be aligned with European priorities, accommodate and be adapted to existing EU initiatives and support long-term sustainment in the improved joint capacity.

Operational integration will be promoted by means of several different instruments, with the primary being the implementation of joint integrative projects. Seven topics have been defined, to reflect the challenges along the prevent-detect-respond chain of actions. These challenges include the access to joint frameworks for cost-efficient design of surveillance activities, harmonisation of laboratory approaches, including access to well defined and relevant reference materials for proficiency testing and test development, as well as joint approaches for interpretation and communication of surveillance information to decision makers. With regards to means to prevention and joint outbreak investigations, there are also varying degree of challenges nationally, creating an opportunity for sharing expertise between EU member states. Resources such as

11

infrastructure and software, e.g. experimental facilities and simulation models (of transmission, ecology, risk assessment etc.) could also be used more efficiently across the sectors. A ranking reflecting the priorities of Programme Managers that contribute to the EJP has been made, initially highlighting two topics; standardised data formats and ontologies, common tools and procedures for data analyses, including interpretation of sequence data, as well as common reporting and signalling procedures, with a joint platform for sharing surveillance data and their interpretation, incl. risk assessments.

The remaining five areas for integration concern joint databases of reference materials and data, incl. metadata, harmonised protocols and common best practice for laboratory methods, development of mentoring (twinning) systems for sharing of best intervention practice, common frameworks for design and methods to assess equivalence between surveillance and control activities as well as the use of experimental facilities and models (of transmission, ecology, risk assessment etc.).

Clearly, since the joint EU capacity is a function of each member state’s capacity, the EJP integrative activities will aim to make the joint development accessible to all partners, ensure there is transfer of skills and knowledge and promote harmonised approaches wherever it is relevant.

3.2 UPDATED LIST AND DESCRIPTIONS OF PRIORITY RESEARCH TOPICS AND INTEGRATIVE TOPICS : KEY INFORMATION

The topic descriptions for all research topics and integrative activities can be found in Deliverable 2.6 Updated List and Descriptions of Priority Research and Integrative topics. A full copy is available on the private space of the OHEJP website, or by contacting WP6 (p.basu@surrey.ac.uk )

FINAL RANKING OF RESEARCH TOPICS

FOODBORNE ZOONOSES (FBZ)

1. FBZSH3: Source attribution of bacterial foodborne zoonoses and antimicrobial resistance considering also the environment and non-livestock reservoirs (e.g. pets and wildlife) as sources (Ranking score: 0.76).

2. FBZ3.1: Benchmarking biosecurity practices for pig farming across Europe using national surveillance data and management standards for identifying best practice to prevent biological hazards, particularly Salmonella and hepatitis E virus, from entering the food supply chain (Ranking score: 0.75).

3. FBZ4.1: Source attribution and transmission routes of foodborne pathogens other than bacteria, with emphasis on Toxoplasma gondii (Ranking score: 0.72, considering the highest of the two merged topics).

4. FBZSH5: Determinants of the reversal of the decreasing trend in Salmonella incidence in humans and poultry in the EU (Ranking score: 0.70).

5. FBZSH9: Better tools for detection and investigation of foodborne outbreaks, including antimicrobial resistant pathogens, as well as economic assessments of potentially increased cluster detection through whole genome sequencing (Ranking score: 0.67).

6. FBZSH8: Rapid risk assessment tools for introduction of zoonotic and foodborne diseases (Ranking score: 0.65).

7. FBZSH6: Intervention studies to determine the effectiveness of preventing exposure to risk factors for Toxoplasma gondii infection (Ranking score: 0.65).

8. FBZ7.1: Development of a risk assessment and management tool to prevent zoonotic bacteria, viruses and parasites in production and processing of pig meat (Ranking score: 0.63).

9. FBZSH7: Epidemiology of foodborne yersiniosis, including biotype and serotype data (Ranking score: 0.59).

12

10. FBZSH4: Global epidemiology of Shiga toxin-producing Escherichia coli (STEC): infections in humans and occurrence in foods and animals, as well as emergence of hybrid STEC strains (Ranking score: 0.59).

11. FBZSH1: Hepatitis E virus: Development of efficient and optimized cell culture methods and virus inactivation studies in food and food production/processing environments (Ranking score: 0.55).

12. FBZ9.1: Development of new tools, e.g. machine learning, to support risk assessment of STEC, (Salmonella, Listeria or Campylobacter) (Ranking score: 0.53).

13. FBZSH2: Hepatitis E virus: Determining the level of contamination in foods of animal origin other than pig liver products and risk of transmission from contaminated water to food (Ranking score: 0.53).

14. FBZ5.1: The impact of changing food consumption habits on the risk of transmission of foodborne zoonoses and AMR (Ranking score: 0.50).

15. FBZ6.1: Developing targeted and effective communication strategies to reduce risk behaviour and change attitudes of consumers concerning food borne zoonoses (Ranking score: 0.45).

16. ET3.1: Disease burden assessment of toxin producing bacteria (Ranking score: 0.43).

17. FBZ8.1: Development and validation of new in vivo models to study interactions between host, foodborne pathogens and the microbiota for investigating infection dynamics (Ranking score: 0.43).

ANTIMICROBIAL RESISTANCE (AMR)

1. AMRSH5: Development of new tools for early (real-time) detection of resistant pathogens in humans

and animals, as well as new diagnostic tools, in particular on-site tests for humans and animals (Ranking score: 0.66).

2. AMR2.1: Dynamics of AMR selection, clonal spread and horizontal gene transfer in humans, animals and the environment, including epidemiology of resistant microorganisms and antimicrobials in the environment and their (environment-mediated) spread (Ranking score: 0.62, considering the highest of the two merged topics).

3. AMR6.1: Development of NGS-based tools for surveillance of AMR in Enterobacteriaceae in animals, humans and the environment (Ranking score: 0.60).

4. AMRSH1: Strengthened infection prevention and control measures, including development and assessment of interventions that prevent the development and spread of AMR (Ranking score: 0.57).

5. AMR4.1: Evaluating the best practice for communication and stewardship of antibiotic prescribing in humans and animals (Ranking score: 0.57).

6. AMRSH3: Development of technologies that enable efficient and rapid degradation of antimicrobials in wastewater and the environment and reduce the spread of AMR (Ranking score: 0.52).

7. AMRSH2: Development of new economic models, exploring and analyzing incentives to boost the development of new therapeutics, alternatives, vaccines and diagnostics for AMR (Ranking score: 0.46).

8. AMR5.1: Risk assessment of ESBL transmission to humans from food and the environment (Ranking score: 0.43).

EMERGING THREATS (ET)

1. ET2.2: Development of a toolkit to characterize emerging threats by combining genomic and

phenotypic information (Ranking score: 0.78).

2. ET1.1: Development and harmonization of NGS and non-NGS methods (e.g. pheno-genotypic and histochemical methods) for the detection of foodborne parasites (Ranking score: 0.66).

13

3. ET5.2: Identification of key determinants of spread and persistence of foodborne zoonoses from wildlife (Ranking score: 0.63).

4. ET2.1: Evaluation of early detection methods for emerging threats (Ranking score: 0.62).

5. ETSH1: Factors associated with emergence of antimicrobial resistant strains in the food supply chain (Ranking score: 0.58).

6. ET5.1: The role of wildlife in the ecology of potentially zoonotic emerging threats (Ranking score: 0.54).

7. ET4.1: Host factors associated with increased susceptibility to infection and disease of emerging threats with undefined routes of transmission (Ranking score: 0.46).

DESCRIPTIONS OF RESEARCH TOPICS

The research topic descriptions here below have been developed by the OHEJP domain and theme secretaries in collaboration with WP2, and include input from the European stakeholders EFSA and ECDC (via WP5). After the OHEJP experts meeting held at RIVM on 4-5 June 2018 (see Deliverable D2.5 for more details), the PMT has decided to proceed with the development of research topic descriptions (one pagers) for the first (top ranked) 8 FBZ topics, the first 5 AMR topics, and the first 4 ET topics. A first rough draft description of these topics was initially predisposed by WP2 (based on the input from the experts meeting and later from the European stakeholders) and further developed by the secretaries. Specifically, each topic was developed jointly by the corresponding theme and domain secretary, as follows:

Foodborne zoonoses (FBZ) Solveig Jore

Antimicrobial resistance (AMR) Jean-Yves Madec

Emerging threats (ET) Dan Horton

Analytical methods Stefano Morabito

FBZSH9 AMR6.1 ET1.1

Host-microbe interactions Bruno Gonzalez-Zorn

Epidemiology Dariusz Wasyl

FBZSH3; FBZ4.1; FBZSH5 AMRSH5; AMR2.1 ET2.2; ET5.2; ET2.1

Risk assessment Maarten Nauta

FBZSH8; FBZ7.1

Intervention Marete Hofshagen

FBZ3.1; FBZSH6 AMRSH1; AMR4.1

The ID code of the topic identifies the domain (FBZ, AMR or ET) and the original topic number therein, but if the letters "SH" are present in the topic code, it means that the topic was originally proposed by a stakeholder. The final versions of the topic descriptions have been validated by the members of the Programme Management Team.

FINAL RANKING OF INTEGRATIVE ACTIVITIES

1. IA-3: Joint databases of reference materials and data, incl. metadata (Ranking score: 0.73)

14

2. IA-2: Harmonized protocols and common best practice (Ranking score: 0.72)

3. IA-1: Common frameworks for design and methods to assess equivalence between surveillance and control activities (Ranking score: 0.72)

4. IA-6: Mentoring (twinning) system for sharing of best intervention practice (Ranking score: 0.49)

5. IA-7: Aligned use of experimental facilities and models (of transmission, ecology, risk assessment etc.) (Ranking score: 0.43)

DESCRIPTION OF INTEGRATIVE ACTIVITIES

Background to integration - the One Health socio-political landscape

EJP integrative activities aim to strengthen preparedness and generate collaborative change. To understand the drivers for collaborative change in the public health and animal health sectors, it can be of interest to reflect on the current socio-political landscape in which One Health activities are prioritised and executed in Europe. In general, health priorities are largely determined within sectors, naturally influenced by the political system. In Europe, prioritised zoonotic infections are dominated by foodborne hazards, which is reflected through the comprehensive feed and food safety legislation. Still, for public health, the management of zoonotic infections, including those that are food-borne, have to compete with other important public health issues including not only other infectious diseases but also lifestyle health problems such as e.g. diabetes, cancer and cardiovascular diseases. Supra-national and national needs for preparedness for serious infectious diseases are driven by requirements to adhere to the International Health Regulations Decision 1082/2013/EU on serious crossborder threats to health.

For animal health, public management of zoonotic infectious diseases is highly influenced by economic decisions related to trade. Animal, food and feed issues that influence public health is of high regulatory importance, but the needs for preparedness for infectious diseases are also related to trade and to the regulatory framework on transboundary diseases of high priority (epizootic diseases).

In the food sector, the responsibility for producing safe food is on the food business operator. Public management of food hazards focus mainly on ensuring that the legislation is adhered to (through official controls). Thus, priorities in the food sector are linked to public health and, as indicated above, highly guided by EU level processes and legislation.

The ability to make trade-offs between EU level and national priorities also differ between the sectors. Where there is a high degree of independence between public health systems in different MS, animal health systems are under a great degree of EU level legislation and -coordination. Consequently, the mechanisms for prioritisation of investments in animal health and food surveillance are largely executed at EU level, which is in contrast to public health where priorities tend to be defined at the national level.

Simplistically put, one can say that the animal health-food sector puts major effort in preventing public health hazards, but the socio-political system always balances actions and restrictions against the consequences for free trade. In contrast, the public health sector deals with the consequences of breaches in feed-animal-food system. The focus is mainly on preventing further human illness and there is no obligation to consider trade and other economic consequences in the agri-food sector. These different perspectives, which are sometimes in conflict, also influence the landscape in which Med-Vet institutions are to collaborate.

It can be noted that in terms of responsibility for the EU Commission to coordinate crisis management, there is a link between Decision 1082/2013/EU on serious cross-border threats to health, implementing the International Health Regulations, and EU level food and feed crisis management as guided by Article 55-57 of

15

Regulation 178/2002, laying down the general principles and requirements of food law, establishing the EFSA and laying down procedures in matters of food safety. The above-mentioned differences in perspective come into play also at this level.

Approach to development of integrated preparedness

The purpose of integrative activities and projects within the OHEJP is to strengthen the joint preparedness of partners to prevent, detect and respond to hazards within their joint remit, both nationally and in collaboration within other EU institutes and -agencies. Due to the legislated landscape in which OHEJP partners operate, and due to the close relationship and collaboration with EFSA and ECDC, there are already many strategies, initiatives, activities and systems in place to develop the capacity to respond to joint hazards within the field of foodborne zoonoses, antimicrobial resistance and emerging threats. The objective of Joint Integrative Projects (JIP) is not to replicate, but to strengthen existing, well-functioning systems. The guidance and insight of EFSA and ECDC is of major importance to help such alignment. The objective of JIPs is also to bridge the gap between the sectors by successively focusing on the inter-sectoral mechanisms along the chain from preparedness to response, and to investigate and improve how the work processes of microbiologists, epidemiologists and information specialists function across the Med-Vet interface at the national level (Figure 1). Strengthening of inter-sectoral mechanisms at the national level will subsequently benefit the supra-national level.

A generic means to work systematically towards an overall higher institutional performance is to benchmark, identify best practice and to leverage the capacity through peer-to-peer twinning activities, through skills training and by development of supportive infrastructure. This is the approach of the integrative activities of the OHEJP, and the JIPs are one means to achieve that.

Two JIPs have been launched to date. COHESIVE focuses on the ability to pick up, share and communicate signals as well as the ability to conduct joint risk assessments. ORION focuses on the semantic and technical interoperability between the sectors, with focus on surveillance information.

For the second call of the OHEJP, call topics have been developed for steps in the prevent-detect-respond chain that were not covered in the first call. IA-1 is focusing on capacity to jointly design, adjust and optimise surveillance activities across the sectors. IA-2 and IA-3 targets ways to improve the joint laboratory capacity and IA-6 focuses on best intervention practice and outbreak response.

16

Figure 1. Schematic illustration of the preparedness and response systems within which OHEJP partners act, and the steps at which One Health integrative activities take place. Adapted from Iversen et al. (2018).

3.3 JRP AND JIP INFORMATION

There are currently 11 Joint Research Projects (JRP1-11) and 2 Joint Integrative Projects (JIP1-2) running. More information on each project can be found at https://onehealthejp.eu/research-projects/

3.4 FREQUENTLY ASKED QUESTIONS (FAQS)

Q: What is the maximum TOTAL calculated budget per grant?

A: €136’250 costs covered by 44% EU funds and 56% partner institute funds. Additional costs can be budgeted provided they are 100% funded by financial contributions from other external sources.

Total costs must be budgeted (costs funded by EU/partner institute as well as costs funded by financial contributions from other external third parties sources).

Total receipts must be budgeted (i.e. financial contributions from other external third parties sources).

Q: How many grants can a partner apply for?

A: There is no set limit.

Q: Will the money be transferred directly to the partner institute(s) hosting the PhD programme?

A: A budget will be set annually to provide authorisation for expenditure. Each year an amount equal to the share of the costs which are 44% funded by the EU will be transferred to the managing partner institute. Gathering the rest of the money (partner institute funding plus putatively financial contributions from other external third parties sources) will remain the responsibility of each of the partner institute(s) hosting a PhD programme.

Q: Is there any restriction on whether collaborating institutes (i.e. in the PhD programme) are to be from the same or a different country to the partner institute(s) hosting a PhD programme?

A: No

Q: How are collaborating institutes to be funded?

A: Only member partners of the OHEJP consortium may receive EU funds. The partner institute(s) hosting a PhD programme will be responsible for administering the financial arrangements of the project.

Q: Is there an indicative value for the PhD fellowship monthly allowance (salary), or will the value depend on a country’s own “rules”?

17

A: PhD funding should be in accordance with the local standards.

Q: Are tuition and bench fees subject to a maximum value?

A: Tuition and bench fees should comply with local standards.

Q: Does the fellowship cover a maximum value for living costs?

A: Living costs are to be paid out of the PhD salary which should be adequate for local living standards. The managing partner has control of the amount funded.

Q: When does the PhD need to start?

A: The PhD proposals selected must commence in October 2019. Three year or four year PhDs will

be considered. As the One Health European Joint Programme ends in Dec 2022, in the case of four

year PhDs, any costs incurred in the final year must be covered by 100% external sources of funding

(see budget section 2.4)

Q: Can proposals from the first OHEJP PhD call be re-submitted?

A: Yes, as long as they meet all the eligibility criteria

18

3.5 PHD PROPOSAL APPLICATION FORM

One Health European Joint Programme PhD Proposal Application Form

This application form should be filled out with reference to the One Health EJP Second PhD Call Guidelines, Supporting Information and FAQs. To access a copy, please contact WP6 Project Manager, Piyali Basu: p.basu@surrey.ac.uk

LEAD APPLICANT DETAILSTitle and Full Name

OHEJP Partner Address

Country

Email

Position in Institute

PROJECT KEY INFORMATIONApplication Number (to be filled out by WP6)

Title

Name of EJP Partners (min 2)

Name of collaborative non-EJP Partners

Main Supervisor Full Name

Main Supervisor EJP Institute and Country

Second Supervisor Full Name

Second Supervisor EJP Institute and Country

Other Supervisor(s) Full Name (s)

Other Supervisor(s) Institute and Country

Duration of PhD (years)

Total Calculated Costs (€)

EU funds ( max 44%, € 60’038)

Institutional funds ( max 56%, € 76’412)

Cost to be 100% funded by financial contributions from other external sources (€)

Status of Funds (Confirmed / Proposed)

SUPPORTING INFORMATION19

Fill the sections below providing as much information and evidence as possible (word limit: 600 words)

Current state of the art in the chosen area and the knowledge gap being addressed

Specify the topic(s) – Foodborne Zoonoses, Antimicrobial Resistance, Emerging Threats

Testable hypothesis and proposed methods

Inter-disciplinary nature (for example disciplines may include at least two of med-vet-environment and may include other disciplines such as food or social science)

Relevance of PhD topic to One Health EJP strategic research agenda and overarching objectives of the EJP (prevent-detect-respond, improve integration and societal preparedness). A full copy of SRA 1 and Updated List and Descriptions of Priority Research and Integrative topics can be found in the OHEJP Consortium Members group on the website or by contacting WP6. Key information from these documents can be found in the annexes of the PhD second call guidelines.

Principle and collaborative supervisor’s experience and suitability (track record in the subject area)

Institutional PhD student support ( lab and equipment facilities, development opportunities and pastoral support systems)

Opportunities for student development and networking in addition to existing and planned EJP activities (International and interdisciplinary (med-vet-environment))

Proposed scientific outputs

Title of linked EJP Joint Research Project or Joint Integrative Project (if applicable)

Indicate status of co-funding (confirmed, proposed)

Please return the completed form to wp6.onehealthejp@surrey.ac.uk by 16:00 CET 28 Feb 2019

3.6 ONE HEALTH EJP CONSORTIUM PARTNERS

Visit https://onehealthejp.eu/places/ for further information on all 39 OHEJP partners

20

1. AGENCE NATIONALE DE LA SECURITE SANITAIRE DE L ALIMENTATION DE L ENVIRONNEMENT ET DU TRAVAIL France

2. OSTERREICHISCHE AGENTUR FUR GESUNDHEIT UND ERNAHRUNGSSICHERHEIT GMBH Austria

3. SCIENSANOBelgium

4. BULGARIAN FOOD SAFETY AGENCY Bulgaria

5. STATNI ZDRAVOTNI USTAV Czech Republic

6. VYZKUMNY USTAV VETERINARNIHO LEKARSTVI Czech Republic

7. BUNDESINSTITUT FUER RISIKOBEWERTUNG Germany

8. FRIEDRICH LOEFFLER INSTITUT - BUNDESFORSCHUNGSINSTITUT FUER TIERGESUNDHEIT Germany

9. ROBERT KOCH-INSTITUT Germany

10. DANMARKS TEKNISKE UNIVERSITET Denmark

11. STATENS SERUM INSTITUT Denmark

12. TARTU ULIKOOL Estonia

13. Veterinary and Food Laboratory Estonia

14. INSTITUTO NACIONAL DE INVESTIGACION Y TECNOLOGIA AGRARIA Y ALIMENTARIA Spain

15. UNIVERSIDAD COMPLUTENSE DE MADRID Spain

21

16. Med-Vet-Net Association de recherche sur les zoonoses France

17. INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE France

18. INSTITUT PASTEUR France

19. THE SECRETARY OF STATE FOR ENVIRONMENT, FOOD AND RURAL AFFAIRS United Kingdom

20. Department of Health United Kingdom

21. UNIVERSITY OF SURREY United Kingdom

22. ORSZAGOS EPIDEMIOLOGIAI KOZPONT Hungary

23. NATIONAL UNIVERSITY OF IRELAND, GALWAY Ireland

24. TEAGASC - AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY Ireland

25. ISTITUTO SUPERIORE DI SANITA Italy

26. ISTITUTO ZOOPROFILATTICO SPERIMENTALE DELL'ABRUZZO E DEL MOLISE "G. CAPORALE" DI TERAMO Italy

27. ISTITUTO ZOOPROFILATTICO SPERIMENTALE DELLA LOMBARDIA E DELL'EMILIA ROMAGNA BRUNO UBERTINI Italy

28. RIJKSINSTITUUT VOOR VOLKSGEZONDHEID EN MILIEU Netherlands

29. STICHTING WAGENINGEN RESEARCH Netherlands

30. FOLKEHELSEINSTITUTTET Norway

22

31. VETERINAERINSTITUTTET - NORWEGIAN VETERINARY INSTITUTE Norway

32. PANSTWOWY INSTYTUT WETERYNARYJNY - PANSTWOWY INSTYTUT BADAWCZY Poland

33. INSTITUTO NACIONAL DE INVESTIGAÇAO AGRARIA E VETERINARIA Portugal

34. INSTITUTO NACIONAL DE SAUDE DR. RICARDO JORGE Portugal

35. Institutul de Igiena si Sanatate Publica Veterinara Romania

36. INSTITUTUL NATIONAL DE CERCETARE DEZVOLTARE PENTRU MICROBIOLOGIE SI IMUNOLOGIE Romania

37. LIVSMEDELS VERKET Sweden

38. FOLKHALSOMYNDIGHETEN Sweden

39. STATENS VETERINAERMEDICINSKA ANSTALT Sweden

23