Topic: Diagnostics

Animal mycoplasmas are major bacterial pathogens causing various diseases in livestock and pets and also significant economic losses in herds. Their diagnostics and antimicrobial susceptibility testing (AST) are difficult because of their growth characteristics.

Ongoing project

Standard usual procedures for other bacteria don’t apply for mycoplasmas. As a consequence, their clinical impact and their contribution to antimicrobial use and resistance is often disregarded. Because of their intrinsic resistance to the broadly used ampicilins/penicilins family and the increasing number of acquired resistances to other antimicrobial families, mycoplasmas must be subjected to an improved antimicrobial resistance surveillance.

The MyMIC network is developed as a necessary first step towards this aim. It will allow sharing best practices and harmonised procedures between expert laboratories as well as proposing future new required developments. Furthermore, aggregation of AST data from different laboratories will permit first proposal of tentative epidemiological cut-offs as a surrogate to clinical breakpoints in order to help clinical interpretation of AST results.

Review on new alternative AST techniques, antimicrobial use across the different animal sectors and pharmacologic data will come as a complement to the diagnostic and AST guidelines expected from the MyMIC network. Lastly MycMIC is expected to be the basis for construction of future laboratories projects for animal mycoplasmas diagnostics and AST methods comparison and validation.

Expected outcomes:

Analysis of the answers to the questionnaire (on culture, identification and antimicrobial susceptibility testing) distributed to all partners.
Construction of a database to gather all MIC data obtained with the same (or a comparable) method for different Mycoplasma species (livestock and companion animals).
Contribution to MIC distribution open databases such as on the EUCAST site and participation to VetCAST (EUCAST subcommittee dealing with all aspects of AST of bacterial pathogens of animal origin).
Writing of guidelines in order to harmonize culture, identification and AST in livestock mycoplasmas.
Creation of a website for the network.
Drafting a project for a future JPI AMR call (or other calls on antimicrobial resistance) funding laboratory activities like ring trials, exchange of reference materials and methods comparison or validation, development of new rapid method for detection of resistance determinants (including WGAS).

Sharing and exchanging knowledge and expertise with developing countries in control of mycoplasmas in this part of the world.

Network partners

Tardy Florence, French Agency for Food, Environmental and Occupational Health and Safety, France (Coordinator)

This network includes 48 partners from 18 countries: Australia, Austria, Belgium, Cuba, Finland, France, Germany, Hungary, Israel, Italy, Nigeria, Pakistan, Poland, Spain, Sweden, Switzerland, the Netherlands and the United Kingdom.

Call

Diagnostics and Surveillance Networks

Design and implementation of effective cOmbination of Phages and Antibiotics for improved TheRApy protocols against KLEbsiella pneumoniae (KLEOPATRA)

The multidrug-resistant bacteria Klebsiella pneumoniae represents a critically emerging pathogen that confounds treatment in a clinical setting. This is due to their pan-resistance to antibiotics and specific biological traits, including a protective capsule, that makes it insensitive to the host immune system.

Bacterial viruses, also called (bacterio)phages are natural predators of bacteria. Our previous research has identified phages that overcome the capsule barrier by specific enzymes and resensitize bacteria to the innate immune system as well as to antibiotic treatment.

In this project, we introduce the concept of “K-sensitization” which uses these phages and their enzymes (capsule depolymerases) to strip the protective capsules from prevalent K. pneumoniae strains and provide a proof-of-concept of how phages/depolymerases act synergistically to antibiotic treatment. Besides the development of a protocol for compassionate phage therapy against these encapsulated pathogens, we will comprehensively analyze the prevalent K. pneumoniae circulating in human & animal reservoirs, as well as environmental ecosystems. This in turn will lead to the establishment of tailored phage banks & associated diagnostics tools, supported by computational models to ensure rationally designed phage therapy cocktails for antibiotic/phage/enzyme combination treatments.
In this manner, the KLEOPATRA consortium aims to contribute to improving the treatment of this critical WHO priority 1 pathogen within a ‘One Health’ setting.

Project partners

Zuzanna Drulis-Kawa, University of Wroclaw, Poland (Coordinator)
Rob Lavigne, KU Leuven, Belgium
Regis Tournebize, Sorbonne Université, France
Joachim J. Bugert, Bundeswehr Institute of Microbiology, Germany
Jens Andre Hammerl, German Federal Institute For Risk Assessment, Germany
Ronen Hazan, Hebrew University of Jerusalem, Israel
Kilian Vogele, INVITRIS SME, Germany

Call

Disrupting drug resistance using innovative design

Bench, Bedside, Business, and Beyond: innovative solutions for AMR diagnostics (B2B2B AMRDx)

With the growing threat of antimicrobial resistance (AMR) worldwide, and few novel antimicrobials being developed, it is becoming more and more important to quickly, accurately and inexpensively diagnose infections and the precise microbe causing them in order to treat them with the right antimicrobial and prevent the emergence of further resistance. However, the path to developing such diagnostics is full of challenges, so much that the space between developing a working prototype and getting a diagnostic used in patients is often called the “valley of death”.

Ongoing project

The network, B2B2B AMRDx, brings together a diverse group of researchers from universities (bench), hospitals (bedside), for-profits (business), governments and nonprofits (beyond), to tackle some of these challenges. We have expertise in human, animal, and environmental AMR, and come from 20 different countries. The networks goals are as follows.

First, the network creates a comprehensive online AMR Diagnostics Developer Directory (ADDD) to facilitate exchange of ideas in the field. Second, the network extends the JPIAMR Seq4AMR Virtual Benchmarking Platform (VBP) to allow diagnostics developers to systematically evaluate their diagnostics on a collection of high-quality genotypes (genomic data) and phenotypes (antimicrobial resistance data) and identify their strengths and weaknesses. Third, the network identifies new policy directions that can support diagnostics development and adoption by accounting for the public health benefits of using AMR diagnostics. These developments will help AMR diagnostics cross the “valley of death” and help patients.

Expected outcomes:

An open, curated online AMR diagnostics developer directory (ADDD), building on AMR Insights’ Technology Pages.
A workshop to develop the standards for genotypes, phenotypes, and metadata, as well as the accompanying bacterial isolates for the VBP, building on previous achievements of the Seq4AMR network (Raphenya et al, 2022)
A systematic approach for the management, selection and curation of gold standard NGS data, phenotype data, and metadata, as well as the corresponding bacterial isolates for the VBP.
Communication, dissemination and roadmap open-access publication describing the VBP contents, its format, and the benchmark set selection protocol. Possible journals: Microbial Genomics or similar.
A workshop to develop a proposal for a regulatory pathway to allow AMR diagnostics developers to benefit from incentives based on the public health benefits of their products.
An open-access roadmap publication describing the proposed policy.

Network partners

Leonid Chindelevitch, Imperial College London, United Kingdom (Coordinator)

This network includes 69 partners from 22 countries: Belgium, Canada, Denmark, Egypt, Estonia, France, Germany, Ireland, Italy, Lithuania, Macedonia, Mexico, Moldova, Norway, Poland, South Africa, Spain, Sweden, Switzerland, the Netherlands, the United Kingdom and United States of America.

Call

Diagnostics and Surveillance Networks

International Fungal Network for One-Health Resistance Surveillance: Antifungal Resistance (INFORM-AFR)

Information & application

Antifungal resistance (AFR) is an increasing concern in fungal pathogens, including Aspergillus fumigatus, yeasts and uncommon moulds that may cause breakthrough infection. There are currently no international AFR surveillance programs, as public health surveillance commonly focusses on bacterial resistance.

Ongoing project

Acquired AFR may develop through in host resistance selection and through exposure of fungi to fungicides in our environment, underscoring the requirement for a One Health approach to AFR surveillance. In this proposal we aim to provide a snap shot of current national AFR surveillance initiatives through an online survey, including identifying the stakeholders involved.

We subsequently will organize a start-up workshop aimed to design surveillance programs that involves clinical and environmental sampling, the use of genomics tools and data management. We aim to involve all relevant stakeholders, including public health institutes, mycology excellence centres and reference laboratories, and environmental and veterinary research groups. The outcome of this workshop will be a surveillance framework that enables systematic resistance surveillance in multiple countries, thus allowing inter-country comparisons.

To increase efficacy, we aim to develop standardized surveillance for multiple fungal pathogens including A. fumigatus, yeasts and non-fumigatus moulds. Laboratory protocols (clinical and environmental), culture collections, case record forms, data management and exchange, privacy and ethical approval issues, and communication plans will be developed. Using this framework, we will apply for funding to secure support to perform surveillance and scientific research associated with the network.

Expected outcomes:

Snap shot of current resistance surveillance activities for yeasts, Aspergillus and other moulds and involved stakeholders in various countries and organisations
AFR surveillance network designs: Involving the various stakeholders will help to determine how we can build the surveillance network, which information is to be collected (including patient groups and fungal disease entities), how environmental surveillance can be accommodated, how surveillance data can be collected and shared.
Alignment between the AFR networks: the network aims using a uniform surveillance network to monitor various pathogens, including A. fumigatus, yeasts and non-fumigatus moulds. This would increase the efficiency of the combined effort although differences in the epidemiology and One-Health aspects need to be addressed.
An AFR surveillance funding proposal

Network partners

Paul Verweij, Radboud University Medical Centre, The Netherlands (Coordinator)

This network includes 29 partners from 14 countries: Austria, Australia, Belgium, Denmark, France, Germany, Greece, India, Ireland, Norway, Spain, the United Kingdom, the Netherlands and the United States of America.

Call

Diagnostics and Surveillance Networks

Shadows of people on a colourful background.

Diagnostics and Surveillance Networks

Funders

Supported projects

JPIAMR is launching a transnational network call under the umbrella of the JPIAMR and within the framework of the ERA-NET JPIAMR-ACTION. The call Diagnostics and Surveillance Networks involves funding organisations from 11 countries to date. Networks can be funded with a maximum of 50,000 Euro each.

Call picture Diagnostics and Surveillance Networks 2022. Shadows of people on a colourful background.

This call is closed

The aim of this call is to assemble networks of leading experts and stakeholders with an intent to facilitate the development, optimisation and use of diagnostic and surveillance tools, technologies and systems. Networks should work towards the conceptualisation of ideas in order to provide white papers, guidance documents and/or best practices/roadmaps and evidence frameworks to identify key questions to be addressed and/or potential solutions to overcome barriers to enhanced surveillance and advanced diagnostics to reduce the burden of AMR.

Networks should connect experts from research performing organisations and/or establish clusters with different relevant stakeholders and end users in the AMR community. Networks may build upon new or existing global collaborations/partnerships.

Eleven (11) JPIAMR-ACTION members are participating in this network call. Each network coordinator will be able to apply for a maximum of 50,000 Euro for 12 or 24 months period for support of its activities. The total budget of the call is approximately 1 M Euro.

Please note that JPIAMR network calls do not fund research projects.

Topic of the call

Networks should design and implement ways to support AMR research considering at least one of the two JPIAMR Strategic Research and Innovation Agenda (SRIA) priority topics Diagnostics and Surveillance.

Networks should also aim to address one or more of the following topics:

Identify actions that will improve the diagnostics and surveillance of AMR (in humans and/or animals and/or agriculture and the environment).
Identify actions needed to support the development of new tools, technologies and systems for diagnosis and surveillance.
Identify novel or existing data platforms that can be developed or improved to aid international alignment and support the use of surveillance data and/or diagnostics to improve prescription of narrow-spectrum antimicrobials and support alignment with stewardship programmes.
Identify or assess user needs for tools, technologies, or systems for diagnostics and/or surveillance in appropriate One Health settings.
Identify the data collection needed to understand inequality in access to diagnostics and how socio-economic factors contribute to this inequality.
Extend or continue activities of previously funded JPIAMR networks within Surveillance.

Eligibility

Network should consist of a minimum of fifteen (15) partners (including coordinator) from at least ten (10) different countries. In addition, at least three (3) of the partners must come from three (3) different countries whose funding agencies are participating in the call. A network must include at least three (3) early career researchers.

Networks are encouraged to consider gender and geographical diversity among partners.

Information & application

Call text (pdf 1 MB). All specific information on the call “Diagnostics and Surveillance Networks”.
Proposal application form (Word file 0,1 MB). The application form must be attached to the application in the submission platform.
Submission platform. The proposal must be submitted by the coordinator before 14 June 2022, 14h CEST using the electronic submission platform.

Please contact the call secretariat if you have any questions about the call: jpiamr2022ncs@lmt.lt

Webinar for applicants

A live webinar for applicants was held on the 25^th of April 2022 presenting the call and the partner search tool. Representatives from funders participating in the call were available to answer questions.

The webinar was recorded and the videos are now available on the JPIAMR YouTube channel:

Questions and Answers:

Selection of Q&As from the webinar (pdf 0,1 MB)

Partner search tool

A match-making tool has been created for applicants to facilitate creation of networks. The tool can be used for:

Partner looking for the network: an individual searching for a network to join.
Network looking for partners: when somebody wants to build a network of experts for the implementation of a particular idea.

Partner search tool for the call Diagnostics and Surveillance Networks

Timeline

12 April 2022 (11.00) – Call opens

25 April 2022 (13.00 CEST) – Webinar for applicants

14 June 2022 (14.00 CEST) – Proposal deadline

Previous JPIAMR network calls

Learn more on the previous JPIAMR network calls:

Funders

Estonia
Estonian Research Council (ETAg)

France
Agence Nationale de la Recherche (ANR)

Italy
Ministero della Salute (It-MoH)

Ireland
Health Research Board (HRB)

Lithuania
Research Council of Lithuania (RCL)

Moldova
Agentia Nationala Pentru Cercetare Si Dezvoltare (ANCD)

Netherlands
Zorgonderzoek Nederland Zon (ZonMw)

Norway
Research Council of Norway (RCN)

Spain
Instituto de Salud Carlos III (ISCIII)

Sweden
Swedish Research Council (SRC)

United Kingdom
Medical Research Council (UKRI/MRC)

Supported projects

Six networks have been recommended for funding within the JPIAMR 15th transnational call: “Diagnostics and Surveillance Networks”. The networks include 228 partners from 40 countries and the total funding amount was 300 000 € plus up to 100 000 € fort start-up and final joint workshops. Click on the titles in the list below to learn more on each network.

Phage Therapy to Reduce AMR Enterobacteria Spread from a One Health Perspective (Phage-Stop-AMR)

The spread of multi-drug resistant (MDR) bacteria in food-producing animals including broilers is a global public health concern.

Controlling growth of MDR bacteria and limiting the transmission of antimicrobial resistance genes in broilers could be an effective mitigation strategy. To counteract the spread of MDR bacteria among zoonotic pathogens in food-producing animals and reduce the risk of their transmission to humans or the environment, antibiotic use in animal husbandry has to be reduced. Bacteriophage therapy is increasingly accepted as an environmentally-friendly antimicrobial intervention strategy, effective at specifically targeting bacterial pathogens, to prevent the transmission of resistant bacteria from foods to humans and vice versa.

We use MDR Salmonella and E. coli in broilers as a model and will first select the most efficient phage combinations to specifically reduce these bacteria and MDR plasmids in broilers. Using laboratory, an experimental chicken gut model and farm-level experiments, we will then establish the efficacy of phage formulations as feed additives within a commercial farming context to reduce bacterial numbers and progressively reduce MDR plasmid carriage in broilers. We will test the effect of phage therapy on intestinal parameters of the treated broilers and also on the broiler intestinal microbiome and resistome composition. We will investigate the transmission of AMR plasmids between different enterobacteria in the broiler gut and improve on-site detection of MDR foodborne pathogens as an early warning system at farm level.

Project partners

Ulrich Dobrindt, Universität Münster, Germany (Coordinator)
Clara Marín-Orenga, Universidad Cardenal Herrera – CEU, Spain
Muna Anjum, Animal and Plant Health Agency, United Kingdom
Raul Fernandez Lopez, Universidad de Cantabria, Spain
Danish Malik, Loughborough University, United Kingdom
Annamária Szmolka, Veterinary Medical Research Institute, Hungary
Eliora Ron, Tel Aviv University, Israel

Call

One Health interventions to prevent or reduce the development and transmission of AMR

Microbiota Intervention Strategies Limiting Selection and Transmission of Antibiotic Resistance burden in the One Health domain (MISTAR)

The central aim of MISTAR is to implement and quantify the effect of novel intervention strategies based on the preservation of the “healthy microbiota” to eradicate and control the spread of antimicrobial resistance (AMR).

We will do this using a One Health approach that involves hospitalized patients, healthy humans, pets, farm animals and the environment. In MISTAR we will follow three main approaches to control the spread of AMR. (i) Intervene with the gut microbiota either by prioritizing potential interventions based of microbiota composition indices/diagnostic tools or by using fecal microbiota transplantation (FMT) to modulate the gut microbiota to reduce and possibly avoid the colonization of and further infections by multidrug resistance pathogens. (ii) Intervene with airborne dust-bound spread of antibiotic resistant bacteria (ARB) between pets and humans in households, farm animals and hospitalized patients by applying air purifiers to remove these microorganisms from the air. Finally, we will (iii) develop novel innovative intervention approaches aimed at specifically targeting ARB in complex microbial communities, like the intestinal tract and sewage.

MISTAR will bring perspectives on novel interventions to reduce the emergence of antibiotic resistance that can readily be integrated into existing organisational structures that are also applicable in low-and-middle income countries, and innovative technologies, which needs investment.

Project partners

Marcel de Zoete, University Medical Centre Utrecht, Netherlands (Coordinator)
Teresa M. Coque, Instituto Ramón y Cajal de Investigación Sanitaria, Spain
Surbhi Malhotra- Kumar, University of Antwerp, Belgium
Stineke van Houte, University of Exeter, United Kingdom
Willem van Schaik, University of Birmingham, United Kingdom
Alex Bossers, Utrecht University, Netherlands
Ilana Lopes Baratella da Cunha Camargo, University of São Paulo, Brazil

Call

One Health interventions to prevent or reduce the development and transmission of AMR

Combating Antibiotic Resistance in Philippine Lakes: One Health upstream interventions to reduce the burden (ARPHILAKE)

Antimicrobial resistance (AMR) may lead to more deaths than cancer by 2050. Action is required now to avert this disaster.

This study aims to implement key interventions in Greater Manila, The Philippines to reduce AMR. Interventions will focus on hospitals, small farms, and the Laguna Lake, one of the largest freshwater lakes in Asia. Better antibiotic use, point of care testing in hospitals and farms, and novel solar-powered wastewater cleaning technologies will be implemented. Their impact will be assessed by state-of-the-art molecular surveillance for antibiotic resistance genes and bacteria in the water before and after interventions. The study will be the most comprehensive and systematic interventions to be introduced in Asia to reduce AMR in lakes.

Project partners

Dylan Pillai, University of Calgary, Canada (Coordinator)
Maria Pythias Espino, University of the Philippines Diliman, Philippines
Stefanos Giannakis, Polytechnic University of Madrid, Spain
Ana Pereira do Vale, University College Dublin, Ireland
Paul Wigley, University of Liverpool, United Kingdom

Call

One Health interventions to prevent or reduce the development and transmission of AMR

JPIAMR Network for Integrating Microbial Sequencing and Platforms for Antimicrobial Resistance (Seq4AMR)