One Health EJP

IMPART supports the development and harmonization of phenotypic methods for detection of antimicrobial resistant bacteria and susceptibility testing:

1. Selective isolation and detection of colistin resistant Enterobacteriaceae
2. Selective isolation and detection of carbapenemase resistant Enterobacteriaceae
3. Setting epidemiological cut-off values (ECOFFs) for veterinary pathogens
4. Improving susceptibility testing of Clostridium difficile

Kees Veldman from WBVR is the project manager.

Antimicrobial resistance is a growing European and global health problem in both humans and animals, leading to limited or poor treatment options for many diseases.

In RADAR, the impact on public health and the disease burden will be evaluated, when assessing potential mitigation measures.

WBVR focusses on two tasks. Firstly we collaborate with the Julius Institute (Utrecht University) in guiding a PhD student (located in Utrecht) who will develop and analyse methods for quantifying risk source attribution, specifically taking account of the variation within Europe, and the different focal points of transmission.

Secondly, we are tasked with the collaboration and synthesis of two modelling work packages, one focussing on modelling the dynamics of AMR in animal production systems and in a full system with all kinds of hosts (human and animal), and the other focussing on the flow of AMR from livestock and other sources, via food, environment and contact to humans, thus influencing public health.

In addition to cross-sectional data from the Netherlands, the UK, France, Germany, Spain and Norway, longitudinal data will be collected from hospitals and livestock farms in all countries. Longitudinal sampling means that multiple samples are taken at set intervals over time. During this period, data will also be collected for each company or hospital on the use of antibiotics. Combining these data will produce a better picture of the distribution of AMR over time.

Ultimately, it will be possible to determine the molecular background of the DNA elements that spread AMR between bacteria. These data will also be compared between the different countries in order to determine whether trends at national level also occur more widely in Europe.

METASTAVA aims to evaluate the potential use of metagenomic analysis to the public health reference laboratory by targeted collection of reference data and reference materials, by generating focused validation data, and by proposing criteria and tools for a robust quality assurance (QA) of metagenomic workflows from sample selection to interpretation of result .

Metagenomic analysis is increasingly used to identify possible causes of unexplained disease outbreaks, to complement routine diagnostic evaluation, and to study the role of the microbiome and virome in health and disease. Currently, standardisation of metagenomics data generation and analysis tools is  being sufficiently covered by other ongoing initiatives (including COMPARE). However, translating these promising technological developments into diagnostic tools for veterinary and public health laboratories requires careful validation, which is the focus of this project.

In order to use Metagenomic analysis for robust diagnostics,  METASTAVA identified several important gaps in our knowledge of NGS and metagenomics that must be filled:

1. Development of a set of reference data for the model pathogens, representing most common sample types
2. Development of harmonized workflows for the generation and analysis of metagenomic data fitting to a defined diagnostic scope for the model pathogens
3. Development of a validation protocol for metagenomic diagnostics (including quality assurance and robustness testing).

The METASTAVA project is addressing the identified gaps and using hepatitis E virus (HEV), norovirus (NoV), zoonotic pox viruses, antibiotic resistant bacteria and Shigatoxigenic Escherichia coli (STEC), as model pathogens in developing the methods and reference datasets.

T. gondii can infect any warm-blooded vertebrates. Cats are the definitive host, depositing oocysts into the environment through their faeces. Livestock can be exposed to these oocysts in their natural environment and become infected, leading to the development of tissue cysts in their meat. Humans can become infected through exposure to oocysts in their environment, or by consuming tissue cysts in infected meat that has not been thoroughly cooked.

The key outcomes of TOXOSOURCES will be quantitative estimates of the most important sources and transmission routes of T. gondii infection. In the Netherlands, the National Institute for Public Health and the Environment (RIVM) has calculated the extent of transmission through meat consumption, and these calculations will be further developed to a Europe-wide level. Environmental routes of transmission will now also be included in the calculations.

Expanding the calculations to a Europe-wide level with the inclusion of other routes and sources of transmission will improve their accuracy and applicability. As part of this, the consortium (including WBVR) will carry out a literature study into the prevalence of T. gondii in humans and animals in Europe.

The results of this will make it possible to determine the relative roles of the various transmission routes and specific meat products to human toxoplasmosis infection, and to develop preventative strategies.

Salmonella causes more than 90,000 infections and around 150 deaths annually in the EU. HEV causes several hundred deaths annually in the EU.

As part of a network of institutes both within the Netherlands and abroad, WBVR will contribute to prevalence studies, the development of hygiene protocols for pig production companies and abattoirs, and the development of specific tests to reveal the persistence of HEV on surfaces and the infectiousness of any virus in circulation.

The project’s outcomes will include:

• Quantitative microbial risk assessments for Salmonella and HEV
• A catalogue of effective hygiene measures relevant to Salmonella and HEV
• Workshops and training sessions to raise awareness of hygiene measures
• Specific tests to measure the persistence and infectiousness of Salmonella and HEV

The ultimate aim is to further develop the technology so that sequencing and the detection of resistant genes can be performed in hospital wards or on farms.

WBVR is already experienced in using this sequencing technology, but new protocols will need to be designed for on-site use. This is both to enable the technology to be used directly on clinical samples rather than on bacteria cultivated in laboratories, and also to reduce the need for technical laboratory equipment.

The Knowledge and Innovation Agenda identifies antimicrobial resistance as a core problem, and this project will deliver a practical instrument for the rapid detection of resistance so that appropriate treatments can be chosen more promptly. This will help improve public health as well as animal health and wellbeing.

Because antimicrobial resistance is located on elements of DNA where bacterial exchange occurs, data from current standard DNA sequencing are not suitable for this purpose.

National reference laboratories are working together to come up with a Europe-wide standardised protocol for performing long-read sequencing, and to develop analytical methods and set up methods for performing source attribution studies.

These methods can and will be applied to various parts of the supply chain. This international collaboration, and the collaboration between reference laboratories for food safety and human and animal health, will deliver a proactive contribution to improving the safety of the food supply chain, and will provide a tool that can be put directly into practice for managing food safety risks.

This will involve a cross-sectoral approach, investigating the possible causes at the levels of primary production, epidemiology and exposure, as well as the pathogen itself. All of these factors will be analysed collectively using a Multi-Criteria Decision Analysis (MCDA) model, which will deliver concrete results for industry and knowledge and insights for governments regarding the most effective intervention measures for the production sectors as well as for public health.

WBVR will focus specifically on primary production, pathogen characterisation, and modelling. Potential modifications to animal management will be evaluated, along with current control measures such as vaccination programmes and hygiene protocols, and the sensitivity of statutory sampling protocols. At the pathogen level we will investigate whether the recent stagnation in the decline of Salmonella incidence in Europe is related to genetic variation in the bacteria; for example, a clonal expansion of specific bacterial strains that are more robust due to accelerated cell division, greater virulence or antimicrobial resistance.

The project will draw on a wide variety of sources, including those that are not traditionally used in surveillance, such as domestic pets, wild fauna and environmental reservoirs.

WBVR will focus on the development and application of a risk attribution method for antimicrobial resistance (AMR) and will contribute data on Campylobacter and AMR. DiSCoVer will give WBVR access to international expertise and data, which will be valuable to on-going research into source attribution challenges in the Netherlands.

These new, Europe-wide harmonised and tailored tools will enable detection, identification and characterisation to be carried out rapidly and efficiently, thereby contributing to safe and sustainable food production.

The project will include:

• The detection of different Brucella strains from different sources and in different epidemiological contexts, such as natural landscapes/ecosystems, cattle and wild animal populations, and Mediterranean and Eastern, Northern and Western European locations
• Mapping emerging types of Brucella using genetic and phenotypical variation, using high throughput methods (NGS, molecular tests, proteomics, metabolomics)
• Creating a better understanding of virulence and zoonotic potential using in vivo and in vitro infection modelling
• Developing an approach for collecting information on emerging Brucella types, and using that harmonisation to enable more rapid recognition/characterisation of new strains

WBVR will focus on identifying the zoonotic potential of new strains of Brucella. WBVR will develop an in vitro model for testing the pathogenicity. This model could in future be expanded to include other existing or potential pathogenic micro-organisms. WBVR will also be working on the genomic characterisation.

The expected results of this project are:

1. An “OH Surveillance Codex” - a high level framework for harmonised, cross-sectional description and categorisation of surveillance data covering all surveillance phases and all knowledge types.
2. An “OHS Knowledge Hub” - a cross-domain inventory of currently available data sources, methods / algorithms / tools, that support OHS data generation, data analysis, modelling and decision support
3. “OHS Infrastructural Resources” - technical and infrastructural resources that form the basis for successful harmonization and integration of surveillance data and methods. These infrastructural resources include harmonized data standards, software libraries, ontologies, terminology mappings, software tools supporting the adoption of the “OHS Codex”.

The aims of the projects are:

• Stimulating sustainable One Health approaches at the national level within EU countries, focussing on strengthening human-veterinary collaboration with respect to early signalling and assessing zoonotic threats.
• Roadmap towards an EU zoonoses risk-assessment or risk-analysis structure
• Design of a common IT platform with associated easy-to-use tools for the collection and analysis of surveillance and outbreak data on (foodborne) zoonoses and harmonized risk assessment.
• Capacity building within and between EU countries at several levels within the area of zoonotic diseases

To achieve these aims the work is divided in four work packages of which WP1 is about the coordination, collaboration and communication of the project. WP2 aims to facilitate the implementation of early signalling forums in EU member states. In several countries these signalling forums already successfully exist and we want to extract best practises and give guidelines to start with these forums. In WP3 we want to go towards an EU One Health structure an come with a flexible risk assessment tool to quickly and thoroughly assess signals from either the public health domain and the veterinary domain. As a lot of data already exist although scattered between many databases with a national focus we want to assess the opportunities to come to a EU broad data platform together with EFSA and ECDC. This will highly facilitate risk-analysis and outbreak control.

WBVR participates in this project in all four work packages and is deputy project leader.

For WBVR this encompasses a large collection of food pathogen strains (such as Salmonella and Campylobacters) and their associated data, including data related to antimicrobial resistance, collected as part of the monitoring programme.

A repository of reference materials (bacterial strains and metadata) is being developed and will be made fully accessible with a view to future collaborations between partner institutes. This data bank will consist of metadata (source, origin etc), phenotypical data, epidemiological data, demographic data and genomic data. Methods for cross-sectoral Proficiency Tests (PTs) will also be established based on Whole Genome Sequencing (WGS) and pilots will be carried out to test the system in practice.

Establishing a One Health reference bank for food pathogens and zoonotic bacteria will lead to greater collaboration between European partner institutes in various sectors and will improve the quality and output of future research on food safety.

The key basic principles for MATRIX are:

1. The need for a problem-oriented approach drawing on existing case studies
2. An understanding of the different situations within different EU countries and of how this calls for specific solutions

WBVR is contributing to the evaluation of existing networks and programmes for the surveillance of microbial hazards in food, and the development of road maps for the implementation of One Health surveillance.

There have been a number of interventions over the past few years that have attempted to limit the spread of antimicrobial resistance in chickens. These have included banning growth promoters, reducing the use of antibiotics and increasing biosecurity in the supply chain. These efforts have not managed to eliminate resistance in chickens. Other possible interventions are therefore now being considered as a way of reducing resistant bacteria.

In the VIMOGUT project, a PhD student will measure the microbiome of chickens at processing businesses over a period of time and link this to ESBL carriers to determine the point at which interventions to the microbiome have the greatest chance of success.

The PhD student will also contribute to developing an in vitro model to simulate the chicken gut microbiome in the laboratory. This model will enable the measurement of the effects of feed interventions on the chicken microbiome, including pre- and probiotics and feed additives, as well as therapeutic interventions such as antibiotics and coccidiostatics.

The project is based on the One Health approach to antimicrobial resistance, including a focus on animal health.

To achieve this, hepatitis E viruses in pigs and humans will be characterised and their genetic characteristics will be closely compared. At its conclusion, the project will deliver a method for identifying dangerous hepatitis E viruses within the pig reservoir.

TRACE is a PhD project and as such will deliver support for both research and the training of co-workers. It will also strengthen collaboration between Wageningen’s research institutes and the University.