Standardization of diagnostics and antimicrobial susceptibility testing and clinical interpretation in animal mycoplasmas (MyMIC)

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.


Improving surveillance of antibiotic-resistant Pseudomonas aeruginosa in Europe (ISARPAE)

Pseudomonas aeruginosa is one of the top resistance threats world-wide, for which the situation is classified as critical by the World Health Organization. The growing prevalence of nosocomial infections produced by multidrug-resistant P. aeruginosa strains is indeed associated with significantly increased morbidity and mortality, since it compromises the available effective therapeutic options, even those recently introduce, due to emerging resistance mechanisms.

Ongoing project

In summary antibiotic resistance in P. aeruginosa is a severe, complex, continuously evolving threat in Europe and therefore coordinated efforts should be established to improve its surveillance and control.

The network Improving surveillance of antibiotic-resistant Pseudomonas aeruginosa in Europe (ISARPAE) gathers 37 researchers from 17 European countries, including multiple national reference centres on P. aeruginosa antibiotic resistance. Thus the specific objectives of this network will be:

  1. Create a forum of experts and researchers working on P. aeruginosa antimicrobial resistance to define the focus, procedures strategies and priorities for surveillance.
  2. Training clinical microbiologists, infectious diseases physicians and researchers across Europe: Hands on workshop on Pseudomonas aeruginosa resistance phenotypes and whole genome sequence resistome analysis.
  3. Provide advice, support and mentorship to less experienced or lower resources laboratories in Europe.
  4. Develop the basis for a coordinated action with relevant stakeholders at European level, including future EU research grants applications.

Expected outcomes:

  • Create a forum of experts and researchers working on P.  aeruginosa antimicrobial resistance
  • Publication of rational documents: Define the setting, variables, focus, strategies and priorities for surveillance of P. aeruginosa antimicrobial resistance in Europe
  • Publication of laboratory manuals: Define the procedures for appropriate surveillance of P. aeruginosa antimicrobial resistance Europe
  • Hands on workshops: Training clinical microbiologists, ID physicians and researchers across Europe will improve surveillance

Network partners

  • Antonio Oliver, Hospital Son Espases-IdISBa, Spain (Coordinator)

This network includes 38 partners from 17 countries: Belgium, Bulgaria, Croatia, France, Germany, Hungary, Italy, Lithuania, Luxembourg, Norway, Portugal, Slovenia, Spain, Sweden, Switzerland, the Netherlands and Turkey.


Bridging of Amicrobial resistance Surveillance systems In Community Settings across Europe (BASICS)

In 2019, 1.27 million deaths were directly attributable to antimicrobial resistance (AMR) globally. This makes AMR one of the leading causes of death worldwide. Among its determinant are the overuse and the misuse of antibiotics. For this reason, AMR surveillance is necessary to monitor its progression, improve our understanding of its diffusion and support local efforts to promote appropriate use of antibiotics.

Ongoing project

Actually, in Europe, AMR surveillance is mainly focused on invasive isolates reported for inpatients by hospitals or national agencies (EARS-net). The importance of AMR in primary care is scarcely documented in EU and its burden remains unclear today.

The aim of the proposed Network “BASICS” would be to map existing initiatives and identify needs for AMR Surveillance in Community Settings in Europe. It will rely on experts in AMR surveillance from several countries in Europe that will participate to physical and online workshops during 2 years in order to map the clinical labs structuring and the existing surveillance networks across Europe and to define the priority indicators needed to monitor AMR surveillance in the community.

It is expected that it will help to promote the convergence of national data of AMR surveillance in the community toward an existing or a future European online platform. Once data of AMR available, it would allow a Europe-wide benchmarking and could guide the elaboration of recommendations for appropriate use of antibiotics and serve as a tool for research on the understanding of AMR.

Expected outcomes:

  • Mapping of the existing national networks on AMR surveillance in community care across European countries/production of a report
  • Consensual list of indicators (i.e. bacterial species and resistance) to monitor through surveillance systems/production of a report
  • Definition of the most efficient feedback strategies of surveillance data to combat AMR in the community setting/recommendations on the formatting of data for publication on a platform

Network partners

  • Olivier Lemenand, Nantes University Hospital, France (Coordinator)

This network includes 18 partners from 11 countries: Austria, Cyprus, France, Germany, Greece, Ireland, Italy, Portugal, Spain, Switzerland and the United Kingdom.


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.


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

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.


Tools for the Epidemiology of AMR Plasmids, One-Health Transmission and Surveillance (TEAPOTS)

Disease-causing bacteria, such as E. coli, are becoming increasingly difficult to treat with antibiotics. This is because the bacteria are evolving by picking up genes that make them resistant to these drugs. This can happen very quickly, because the resistance genes responsible can hop from one bacterial cell to another by hitching a ride with small rings of DNA called plasmids.

Ongoing project

Because the plasmids, and the resistance genes they carry, can spread independently of the bacteria, it is very difficult to track and monitor how they are moving. This can pose a problem in hospitals, where plasmids can spread rapidly from one cell to another resulting in an ‘outbreak’ of infections resistant to antibiotics. It also makes it much more challenging to understand how resistance spreads in environmental settings like farms or rivers, where the presence of antibiotics might pose a risk to human and animal health by selecting for more resistant strains.

This network brings together experts from different disciplines with research expertise that addresses different aspects of this complex problem; this includes bioinformaticians and software developers, clinical and environmental epidemiologists, and evolutionary biologists.

The aims of this network are twofold; first to establish a conceptual ‘roadmap’ that presents possible solutions, whilst accounting for the rapid evolution of plasmids. Second, to provide proof-of-principal of novel approaches through the development of prototype software tools.

Expected outcomes:

  • Development of a proof-of-concept prototype linking with the bespoke database. This will inform on a new roadmap for plasmid epidemiology, and will be accompanied by a perspective article.
  • The network prepares a positional article outlining the requirements and utility of a plasmid typing system and how this might be used alongside standard strain typing. To include a consideration of how plasmid typing might impact on infection control strategies in health care settings.
  • Benchmarking and harmonisation to compare different tools and how each performs using short read (vs hybrid) assemblies.
  • The networks develop and validates novel typing approaches based on combining a plurality of ‘backbone’ and Mash distance methods, validated against complete plasmid assemblies. This is a pivotal step in enhancing AMR surveillance, and if validated successfully will be written up as short bioinformatics note.
  • Bioinformatic analysis on existing hybrid assemblies (from the JPI-AMR SpARK data and other partner projects) to determine plasmid transmission networks across different settings (informed by WS2). This will help to resolve the question as to extent to which AMR plasmids can transfer freely over complex One-Health landscapes.
  • Analysis of One-Health metagenomics data using tools developed by partners to ascertain the feasibility of applying typing tools to these data and thus aligning with evidence from single-colony WGS analysis.

Network partners

  • Edward Feil, University of Bath, United Kingdom (Coordinator)

This network includes 24 partners from 11 countries: Belgium, Brazil, France, Germany, Nigeria, Norway, Pakistan, Portugal, Spain, the Netherlands and the United Kingdom.


Shadows of people on a colourful background.

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.

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:

  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.


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:

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


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:


Estonian Research Council (ETAg)

Agence Nationale de la Recherche (ANR)

Ministero della Salute (It-MoH)

Health Research Board (HRB)

Research Council of Lithuania (RCL)

Agentia Nationala Pentru Cercetare Si Dezvoltare (ANCD)

Zorgonderzoek Nederland Zon (ZonMw)

Research Council of Norway (RCN)

Instituto de Salud Carlos III (ISCIII)

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.