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Diagnostics and Surveillance Networks

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.

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:

  1. Identify actions that will improve the diagnostics and surveillance of AMR (in humans and/or animals and/or agriculture and the environment). 
  2. Identify actions needed to support the development of new tools, technologies and systems for diagnosis and surveillance.  
  3. 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. 
  4. Identify or assess user needs for tools, technologies, or systems for diagnostics and/or surveillance in appropriate One Health settings.  
  5. Identify the data collection needed to understand inequality in access to diagnostics and how socio-economic factors contribute to this inequality.  
  6. 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

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 25th 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:

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

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

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

  • Fernanda Paganelli, 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

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

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

Main Questions/Approach: How can we best identify and promote collaboration and implementation between AMR NGS stakeholders that link the individual fields of (new) NGS technologies, algorithms, quality standards, teaching/training and sequence databanks?

Ongoing project

Answer – By establishing an international and interdisciplinary OneHealth network of public and private experts to take the lead in identifying potential knowledge gaps and solutions. Further, by developing AMR NGS-dedicated quality and teaching/training materials. Finally, by promoting discussion and interactions between AMR NGS stakeholders and other working groups with cross-cutting priorities – including extensive use of JPIAMR VRI.

Objectives:

  1. Promote active collaboration between interdisciplinary OneHealth AMR NGS stakeholders
  2. Identify knowledge gaps and provide solutions to current/future AMR NGS issues
  3. Formulate recommendations on quality and quality materials
  4. Educate AMR NGS stakeholders via interdisciplinary-directed AMR NGS teaching/training materials

Activities:

  1. Dedicated website and access to network materials
  2. Face-to-face network meetings and regular teleconferences (in collaboration with other relevant JPIAMR working groups)
  3. Open access publications and collation of a Seq4AMR Strategic Roadmap
  4. Dedicated interdisciplinary Seq4AMR webinar(s) and course(s)
  5. Dedicated Seq4AMR workshop at a relevant international meeting
  6. Promotion of Seq4AMR and JPIAMR during conferences.

Expected Results:

  1. Establish new OneHealth AMR synergies between international and interdisciplinary experts for knowledge exchange, joint publications grant writing etc.
  2. Identify current knowledge gaps and how to best fill these gaps
  3. Formulate quality recommendations and access to materials
  4. Develop new interdisciplinary AMR teaching/training/ materials
  5. To publish a Seq4AMR Strategic Roadmap
  6. To contribute and strengthen the activities of JPIAMR VRI

Network partners

  • John Hays, Erasmus MC University Medical Center, Netherlands (Coordinator)
  • A. Stubbs, Erasmus MC University Medical Center, Netherlands
  • A. Heikema, Erasmus MC University Medical Center, Netherlands
  • A. van Belkum, BioMérieu France, Craponne, France
  • W. A. Valdivia, Orion Integrated Biosciences (OIB), Kansas, USA
  • Liping Ma, East China Normal University, Shanghai, China
  • E. Kristiansson, University of Gothenburg, Gothenburg, Sweden
  • S. Bruchmann, Cambridge University, Cambridge, UK
  • A. McArthur, McMaster University, Hamilton, Canada (CARD Database)
  • S. Emler, SmartGene GmbH, Lausanne, Switzerland
  • E. Claas, Leiden University Hospital, Leiden, the Netherlands
  • S. Beisken, Ares Genetics GmbH, Vienna, Austria
  • R. Stabler, London School for Hygiene and Tropical Medicine, London, UK
  • A. Lebrand, Swiss Institute of Bioinformatics, Lausanne, Switzerland
  • M. Petrillo, European Commission, Joint Research Centre (JRC), Ispra, Italy
  • S. Capella-Gutierrez, Barcelona Supercomputing Centre (BSC), Barcelona, Spain
  • L. Portell, Barcelona Supercomputing Centre (BSC), Barcelona, Spain
  • B. Grüning, Freiburg Galaxy Team, Freiburg, Germany
  • G. Cuccuru, Freiburg Galaxy Team, Freiburg, Germany
  • C. Carrillo, Canadian Food Inspection Agency, Ottawa, Canada
  • B. Blais, Canadian Food Inspection Agency, Ottawa, Canada
  • B. Gruening, University of Freiburg, Freiburg, Germany
  • W. Meier, University of Freiburg, Freiburg, Germany
  • B. Batut, University of Freiburg, Freiburg, Germany
  • K. Vanneste, Sciensano, Brussels, Belgium
  • J. Bengtsson-Palme, University of Gothenburg, Gothenburg, Sweden
  • T. Naas, Hopital de Bicêtre, Paris, France
  • N. Strepis, Erasmus University Medical Centre (Erasmus MC), the Netherlands
  • A. Rhod Larsen, Statens Serum Institut, Copenhagen, Denmark
  • B. Helwigh, National Food Institute, Lyngby, Denmark
  • H. Hasman, National Food Institute, Lyngby, Denmark
  • R. Hendriksen, National Food Institute, Lyngby, Denmark
  • S. Forslund, Max Delbrück Center for Molecular Medicine, Berlin, Germany 
  • L. Pedro Coelho, Institute of Science and Technology, Fudan University, Shanghai, China
  • A. Patak, Molecular Biology and Genomics Unit, Institute for Health and Consumer Protection, Ispra, Italy
  • M. Querci, Deputy Head of Unit, Joint Research Centre European Commission, Brussels, Belgium
  • G. van den Eede, Head of Unit, Health, Consumer and Reference Materials, European Union, Brussels, Belgium

Call

Yeast-based biosensors for the specific and accessible detection of pathogens and antimicrobial resistance (AntiRYB)

Early and specific detection of microbial infections is crucial for the containment of diseases and for reducing the dependence on the use of antibiotics. There is however a lack of reliable, cheap and easy to use detection methods for day-to-day monitoring of infection and antimicrobial resistances in samples from patients, animals and the environment. This deficinecy is critical for the abuse of antibiotics and the diffusion of antimicrobial resistance.

Ongoing project

The aim of this project is establishing a method based on yeast biosensors that can detect with high specificity pathogens from different sources to develop a new, fast and specific diagnostic tool for resistant pathogens. We will achieve this by joining together strong research groups on antimicrobial resistance, systems biology, and strain engineering at SINTEF, Chalmers University and National Medicines Institute. Particular focus will be given to the detection of ESBL or carbapenemase-producing strains belonging to the emerging ESKAPE group of resistant pathogens.

The biosensor is developed using the yeast Saccharomyces cerevisiae as host, which will be engineered to express specific receptors able to recognise unique molecules produced by the pathogens. The ligand-receptor binding initiates a cascade mechanism that activates the genes for the production of a red pigment visible to the naked eye. Using the biosensors, we aim to identify molecular markers specific for resistant pathogen strains, to enable fast, easy and inexpensive point-of-use profiling of resistant pathogens.

Project partners

  • Geir Klinkenberg, SINTEF, Norway (Coordinator)
  • Verena Siewers, Chalmers University of Technology, Sweden
  • Alicja Kuch, National Medicines Institute, Poland

Call

Concomitant IDentification and Antibiotic REsistance profile of bacteria in one hour with an adaptive targeted single Mass Spectrometry analysis (IDAREMS)

Blood stream infection (BSI) is annually responsible of hundred thousand estimated deaths worlwide. The time frame for identification and antimicrobial susceptibility testing of the causative agent(s) of BSI directly impact the delay in the administration of appropriate antimicrobial therapy and, consequently, the clinical outcome of patients.

Ongoing project

MALDI-TOF mass spectrometry obviously revolutionized routine microbial identification by drastically shortening the delay of the identification (ID). There is however no consensus on a universal and affordable tool for shortening the characterization of putative antibiotic resistance mechanisms. IDAREMS aims to introduce a disruptive tool for clinical diagnosis of blood stream infection (BSI) based on targeted proteomics carried out by tandem mass spectrometry (MS) to achieve concomitant pathogen identification and antibiotic resistance profiling directly from an aliquot of positive blood culture in less than one hour.

IDAREMS project is structured over three main work packages: WP1) the development by partner 1 (France) of a prototype assay for concomitant identification and rapid diagnostics of antimicrobial resistance in Gram-negative bacteria using a limited number of antibiotic-resistant bacterial isolates provided by partner 2 (France), partner 3 (Poland) and partner 4 (Thailand); WP2) the validation of the assay through blind testing of new clinical strains; WP3) technician training and deployment of the validated assay in the respective partner’s clinical platforms.

Project partners

  • Jérôme Lemoine, Jérôme Lemoine, France (Coordinator)
  • Frederic Robin, Université Clermont Auvergne, France
  • Marek Gniadkowski, National Medicines Institute, Poland
  • Visanu Thamlikitkul, Mahidol University, Thailand
  • Susan M. Poutanen, University of Toronto, Canada

Call

IDx: An exploration of regulatory, corporate, relational, and technical barriers to uptake of diagnostics in the fight against AMR (IDx)

Greater availability of fast and accurate diagnostics for infections would greatly reduce the over-prescription of antibiotics and slow the growth of antibiotic resistance which limits treatment options. It would also help prescribe the right drug at the right time, thus reducing suffering and increasing survival.

Ongoing project

However, despite advances in technology, few useful diagnostics for bacterial infections have come to market and we are seeing a downward trend in innovation. This study proposes to identify the key barriers that remain once a new diagnostic has been developed, looking at recent technological advances that ultimately failed to be authorized, adopted, or able to change prescribing. It will also look at technologies that have helped in the fight against antimicrobial resistance. Are there any features or particularities that seem to have improved their chance of success?

Lessons from the failures and few successes will be used to assess chances for products in the pipeline, examining how regulation, reimbursement, technology transfer, and organizational characteristics might be improved to make them succeed within the clinical setting. The work will focus on each of these themes in developed world settings but also use them as a lens (in addition to a technical lens) to examine determinants of uptake in rural parts of South Africa, which are to some extent a proxy for LMIC.

Project partners

  • Olof Lindahl, Uppsala University, Sweden (Coordinator)
  • Marc Mendelson, University of Cape Town, South Africa
  • Eve Dubé, Université Laval, Canada
  • Volkan Özenci, Karolinska Institutet, Sweden
  • Florence Séjourné, BEAM Alliance, France

Call

Prevention of antibiotic resistance by TARGEted Treatment of pneumonia in children (TARGET)

Lower respiratory tract infections (LRTI), such as pneumonia, are a leading cause of death especially in children below the age of 5 years. Low and middle-income countries (LMIC) suffer the highest burden of childhood pneumonia.

Ongoing project

Most LRTIs are caused by viruses, but differentiating viral from bacterial causes is frequently impossible in LMIC due to lack of diagnostics. As a consequence, most cases are treated empirically with antibiotics leading to overuse and misuse of antibiotics, which is an important driver of the global epidemic of antimicrobial resistance.

Therefore, we propose to apply a newly developed diagnostic device, the modular breath sampler (MBS), which is based on the entrapment of aerosols from the lower respiratory tract to identify the etiological agent in children with LRTI. Because the MBS is a non-invasive, patient-friendly device and easy applicable for repeated measurements, it allows direct monitoring of the effect of antibiotic treatment. In addition, the identification of pathogens will not only be determined by PCR but also by loop-mediated isothermal amplification (LAMP) that amplifies DNA with high specificity, efficiency and rapidity in a single tube under isothermal conditions, and does not require a thermal cycler, which would make it easy to apply in LMICs.

Project partners

  • Marien de Jonge, Radboud University Medical Center, Netherlands (Coordinator)
  • Markéta Martinkova, Charles University, Czech Republic
  • Blandina Mmbaga, Kilimanjaro Christian Medical Centre, United Republic of Tanzania
  • Corne van den Kieboom, Xheal Diagnostics, Netherlands

Call

A K-mer Based Approach for Institutional AMR Surveillance, Transmission Monitoring, and Rapid Diagnostics (K-STaR)

Antibiotic resistant organisms (AROs) have become increasingly difficult to treat, with rising morbidity and mortality worldwide. Healthcare institutions are often the epicenter for outbreaks of these antibiotic resistant organisms, and are also windows into their circulation within the broader community.

Ongoing project

Transmission of antibiotic resistant organisms within hospitals is under appreciated. Moreover, identification of linked strains that may be causing occult outbreaks is often not systematically performed. Genomic approaches can provide a better understanding of within-hospital transmission of AROs, which can be used to guide infection control practices. Some institutions have augmented their ARO surveillance with whole genome sequencing, but this is both expensive and time consuming, making it unsuitable for routine use.

However, new approaches that use k-mer based algorithms along with genomic reference databases can provide rapid evaluation of pathogen lineage and potential for linked transmission. These same approaches can also be used to provide important rapid diagnostic information about the pathogen and likelihood of resistance to a given antibiotic. While there is much potential in these approaches, they need to be formally evaluated across care settings and geography before they can be trialled in the clinical setting. Here we propose a multi-continental prospective evaluation of the performance of a k-mer based approach for institutional surveillance of common multidrug resistant Gram-negative pathogens as well rapid prediction of antibiotic resistance patterns.

Project partners

  • Derek MacFadden, Ottawa Hospital Research Institute, Canada (Coordinator)
  • Allison McGeer, Mt. Sinai Hospital, University of Toronto, Canada
  • Hajo Grundmann, University of Freiberg, Germany
  • Martin Antonio, Medical Research Council Unit, The Gambia, Gambia
  • William Hanage, Harvard Chan School of Public Health, USA

Call