Intensive Care Airway and Lung Microbiome Network ICALM Network (ICALM)

Hospital acquired pneumonia (HAP) is the most frequent infection acquired in the Intensive Care Unit (ICU). ICU-related respiratory infections arise as a consequence of the processes of ICU care. Mechanical ventilation (MV) is potentially lifesaving, but also carries microorganisms into the lower airways, changing the native flora, and increasing the risk of Ventilator-Associated Tracheobronchitis (VAT) and Ventilator-Associated Pneumonia (VAP).

Completed project

Data concerning the characteristics of respiratory microbiota and its alterations in illness are largely limited to the respiratory microbial flora of patients with cystic fibrosis, and little is known about airway microbiota alterations in critical illness. We published the most comprehensive study on this topic, and found that mechanical ventilation, but not antibiotic administration, was associated with changes in the respiratory microbiome.

With funding from JPIAMR, we will empower a multinational team to develop common surveillance methods and monitoring approaches to build a global study of the lung microbiome in critical illness, and its associations with modifiable environmental colonisation and pneumonia in the individual patient.

Network partners

  • Ignacio Martin-Loeches, Trinity College, Ireland (Coordinator)

This network includes 17 partners, please click on the following link to see complete network composition: Network composition Intensive Care Airway and Lung Microbiome Network ICALM Network (ICALM)

The current research needs a boost of open-source information to identify potential countries were healthcare problems are currently highly visible by government and non-government parties. The current network helped to become a tool for healthcare industry stakeholders in infection outbreaks for multi drug resistant pathogens. Stakeholders in the healthcare industry include customers/patients, employees/healthcare providers, creditors, shareholders and the government. The aim to have a multidisciplinary common field for primary stakeholders and end-users for the ICALM Network and members of InFACT networks. In addition, our findings were of relevance to translational research in critical care and clinical microbiologist, to public health decision-makers, and a partnership with academia and industry.

Our findings were disseminated using a twofold strategy:
– White paper on the scope of the problem under the JPIAMR acknowledgement, and the research agenda vision in the peer reviewed biomedical literature. Visibility was enhanced by publication in an open access journal such as Critical Care Journal
– World Federation of Societies of Intensive and Critical Care Medicine (the PI is part of the WFSICCM council), to present our awareness activities and meetings during the 2019 World Congress of Intensive and Critical Care Medicine in Melbourne Australia

Project resources



Wildlife, Agricultural soils, Water environments and antimicrobial resistance – what is known, needed and feasible for global Environmental Surveillance (WAWES)

The World Health Organisation (WHO), Food and Agriculture Organisation (FAO), and World organisation for Animal health (OIE), agree that surveillance of antibiotic/antimicrobial resistant bacteria (AMR) should be performed using a One Health multi-sectoral approach. Despite this, there is an overall lack of surveillance focusing on the environment and wildlife. Furthermore, there is unquestionably a lack of standardisation and synergy between projects and research efforts focusing on AMR in the environment and wildlife.

Completed project

The JPIAMR Strategic research agenda published in 2013 also highlighted the lack of data, comparable information and cross-sectoral studies on AMR in the environment. To amend this, we have initiated the WAWES network – Wildlife, Agricultural soils, Water environments and antimicrobial resistance – what is known, needed and feasible for global Environmental Surveillance, which consists of 27 partners from 16 countries from all over the globe representing low to high income settings.

The WAWES participants have a shared objective of finding a way to perform global comparative surveillance of AMR in the environment and wildlife, which is furthermore applicable in the majority of countries irrespective of economic resources. Due to the complexity of the environment WAWES will in the initial phase focus on wildlife, agricultural soils and water environments, including wastewater.

Network partners

  • Stefan Börjesson, National Veterinary Institute, Sweden (Coordinator)

This network includes 27 partners, please click on the following link to see complete network composition: Network composition Wildlife, Agricultural soils, Water environments and antimicrobial resistance – what is known, needed and feasible for global Environmental Surveillance (WAWES)

Antibiotic resistant bacteria (ARB) are one of the greatest challenges for both animal and human healthcare, this because the availability of antibiotics is the foundation for all modern medicine. To battle ARB surveillance plays an essential role to identify emergences of new or rare ARB, the continued transmission of more well-known ARB, and to assess if strategies and policies implemented to mitigate the spread has had an effect. In the endorsed action plans on antimicrobial resistance from The World Health Assembly (WHO), the Food and Agriculture Organization (FAO), and The World organization for Animal health (OIE) all agrees upon that surveillance should be performed in a one-health approach involving all sectors. Despite this, current national and international programs focus largely on the human and livestock sectors, in a limited number of countries companion animals is also included, but with the environment and wildlife generally overlooked. Furthermore, there is unquestionably a lack of standardization and synergy between projects and research efforts focusing on ABR in the environment and wildlife.

To amend this, we have initiated the WAWES network – “Wildlife, Agricultural soils, Water environments and antimicrobial resistance – what is known, needed and feasible for global Environmental Surveillance”, which consists of 27 partners from 16 countries from all over the globe representing low to high income settings. The WAWES participants have a shared objective of finding a way to perform global comparative surveillance of AMR in the environment and wildlife, which is furthermore applicable in most countries irrespective of economic resources. The work to focus on suggesting approaches to perform surveillance on ABR in the environment and wildlife is challenging mainly due to the complexity of the environment both on a macroscopic and microscopic scale, and the complexity of wildlife. In fact, one of the large hurdles, and the major ongoing discussion point of Wawes, is exactly defining what should be included in the definition of environment. Another major obstacle of suggesting approaches for surveillance on the environment and wildlife is that it preferably would be comparable to ongoing surveillance efforts in humans and livestock. However, the methods and chosen indicators for humans and livestock might not be suitable as indicators in the environment.

After initial discussions it was decided within Wawes to focus the efforts. First a white paper focusing on the suitability of using Escherichia coli, which is the major indicator bacteria for surveillance ARB efforts in human and livestock, as an indicator bacterium also in the environment. This work will define both the advantageous and primarily the weaknesses of using E. coli. In addition, the paper will also try to define the environment in the perspective of performing ABR surveillance. The second effort will be on an overview of ABR in wildlife with focus on other wildlife than birds since there already exist extensive studies and comprehensive reviews about ABR in wild birds. This work would also include on how wildlife should be defined in the perspective of performing ABR surveillance and highlight why wildlife is relevant when performing ABR surveillance.

Project resources



Towards Developing an International Environmental AMR Surveillance Strategy

There is an urgent and increasing need to fully understand the development and transmission of AMR both into and within the wider environment. However, at present, research into environmental aspects of AMR has been largely confined to individual institutions or academic laboratories.

Completed project

National governments and international bodies (EU, UN, WHO) have recognised that we must establish effective environmental surveillance systems to identify and monitor AMR in our waters, soils, air and wildlife in order to increase understanding of the natural environment’s role in emergence and spread of AMR and how the introduction of antimicrobials/resistant microorganisms from human/animal sources into the environment contribute to AMR.

A One Health approach promotes harmonised surveillance across human, veterinary and food sectors and the use of common outcome indicators to monitor AMR and antimicrobial use: several joint national reports publish AMR trends for key indicator bacteria and key antibiotics (for example UK One Health report, DANMAP and Scottish One Health Antimicrobial Usage and Antimicrobial Resistance Report (SONAAR). However, there is no clear consensus so far regarding which indicators to measure for the environmental sector.

Therefore, this network aims to identify robust, measurable surveillance indicators and methodologies for environmental AMR by:

  • Building on and transferring existing knowledge from clinical and animal AMR indicators and methodologies in the context of a multi-sectorial, One Health approach.
  • Bringing together key researchers with policy makers and regulators across the environmental, human health and veterinary sector and from countries with a wide range of economic settings.
  • Arrive at a standardised set of targets and reproducible, accessible methodologies allowing comparative data to be generated in a coordinated manner.

Setting out our findings in advice and briefings to governments and international bodies.

Network partners

  • William Gaze, University of Exeter, United Kingdom (Coordinator)

This network includes 23 partners, please click on the following link to see complete network composition: Network composition Towards Developing an International Environmental AMR Surveillance Strategy

Project resources

Final report: Towards developing an international environmental AMR surveillance strategy (pdf 0,6 MB)

Antimicrobial resistant (AMR) infections are predicted to be the leading cause of death by 2050, with a substantial proportion of these caused by AMR bacterial pathogens. The JPIAMR environmental AMR surveillance network brought together 23 partners from 15 countries to discuss the need for, and necessary approaches to implement a surveillance programme. The network included cross sectoral involvement spanning human, animal and environmental regulators and policy makers.

Why is the environment important when considering AMR human infections when there is so much focus on reducing antimicrobial usage and improving infection control in hospitals? The answer is because AMR is not a modern phenomenon, and it is much more complex than many people believe. Firstly, it must be recognised that for most of life on earth, the only life was microbial. This means that bacteria are hugely diverse having evolved over billions of years, producing millions of species resulting in a biomass many times greater than all the animals on earth. Just as we obtained our first antimicrobial drugs, such as penicillin, from environmental microorganisms, diverse AMR mechanisms have evolved in environmental bacteria over evolutionary time. Now, antimicrobial usage for treating infections in humans and for treating and preventing disease in livestock has accelerated the rate of AMR evolution in human and animal microbiomes. This has led to the discharge of AMR bacteria and antimicrobial residues to the natural environment through human and animal waste, where they mix with environmental bacteria allowing transfer of resistance mechanisms through a process known as horizontal gene transfer.

This network has produced a report highlighting why environmental AMR surveillance is important and which methods are appropriate to generate data on AMR in the complex microbial communities present in soil and aquatic ecosystems. Current understanding of AMR in human bacterial pathogens is largely based on methods which are unable to capture the “gene flow” of antimicrobial resistance genes between bacteria and between environmental, animal and human microbiomes. Comprehensive environmental surveillance data can be used to better understand, and mitigate, the emergence of new resistance mechanisms in human pathogens that originate in environmental microbial communities. It can also be used to inform risk of human exposure to, and transmission of, AMR bacteria from the environment to humans. Appropriate environmental AMR surveillance is an integral part of tackling the global rise in AMR bacterial (and fungal) infections as the data can be used to underpin changes in policy and regulation driving interventions to mitigate the rate at which AMR evolves and spreads across the


Convergence in evaluation frameworks for integrated surveillance of AMR (CoEval-AMR)

An integrated approach to surveillance spanning different sectors has been promoted by international organisations for more than a decade and constitutes a central recommendation of the WHO action plan on AMR. The objective of the network is to develop guidance for a harmonised evaluation framework that will address the specific needs of integrated surveillance systems for AMR.

Completed project

Two main scientific workshops will be used to build on researchers’ experience and expertise and harmonise existing evaluation frameworks and approaches. Protocols and written guidance will be developed and made publicly available through an existing online website used for surveillance evaluation (SurvTools). Results will allow understanding of the potential value of integrated surveillance for AMR, and comparing integrated surveillance strategies across countries in order to identify the most cost-effective approaches.

Network partners

  • Barbara Haesler, Royal Veterinary College, United Kingdom (Coordinator)

This network includes 19 partners, please click on the following link to see complete network composition: Network composition Convergence in evaluation frameworks for integrated surveillance of AMR (CoEval-AMR)

Antimicrobial resistance refers to the ability of a microorganism (such as bacteria, viruses and fungi) to resist the effects of a drug. Consequently, common medicines used to treat infections may no longer be effective. Antimicrobial-resistant microorganisms can be found in people, animals, food and the environment and may spread from one to the other. These linkages need to be considered when designing surveillance strategies to monitor existing resistance, identify new resistance, understand how resistance evolves, and plan and evaluate policies for resistance reduction. International organisations have called for collaboration across public, animal and environmental health sectors. Several surveillance strategies exist that span multiple sectors, but their effectiveness and economic efficiency remain ambiguous.

Therefore, we created the network CoEvalAMR, which stands for “Convergence in evaluation frameworks for integrated surveillance of antimicrobial usage and antimicrobial resistance”. The network brought together more than 30 international experts (researchers and other stakeholders) in surveillance, evaluation and antimicrobial resistance to develop guidance for the evaluation of integrated surveillance for antimicrobial use and antimicrobial resistance. We were particularly interested in researching the cross-sectoral dimensions of such integrated surveillance.

We formed 5 working groups (WGs) and compiled a list of existing evaluation tools for surveillance (some were general tools and some targeted specifically antimicrobial usage and antimicrobial resistance). WG1 characterised these existing evaluation tools and categorised them based on defined attributes. WG2 conducted interviews among surveillance stakeholders to determine their most pressing needs for conducting surveillance evaluations in the future. WG3 conducted case studies of a range of existing evaluation tools and documented the experiences of users. Finally, WG4 assembled all aspects to create a publicly available online guidance that also includes an interactive decision-support tool. WG5 was responsible for dissemination, communication and engagement.

The guidance is publicly accessible. It helps users (e.g. personnel working to protect the health of humans, animals, plants and the environment) to gain a better understanding of what needs to be considered when planning an evaluation of integrated surveillance of antimicrobial usage and antimicrobial resistance and what the benefits of such surveillance may be. Moreover, it supports the user in choosing the most appropriate evaluation tool to fulfil their specific evaluation goals and gives them access to the experiences of other users. Ultimately, the guidance helps people to conduct evaluations of their surveillance systems for antimicrobial usage and antimicrobial resistance. The results of such evaluations will allow stakeholders to identify how surveillance effectiveness and efficiency could be improved.



Providing a Roadmap for Automated Infection Surveillance in Europe (PRAISE)

Surveillance of healthcare-associated infections (HAI), including surgical site infections (SSI) and central line associated bloodstream infections (CLABSI), is a key component of national surveillance programs. Identifying infections – as opposed to colonisation – allows for the quantification of the burden of infections by antimicrobial-resistant (AMR) pathogens and evaluation of the effectiveness of interventions.

Completed project

Traditional surveillance by manual chart review is time-consuming and prone to error, making large-scale standardised surveillance unachievable in many European countries. In recent years automated HAI surveillance systems using data routinely stored in hospital electronic health records have been developed for among others SSI and CLABSI. Advantages of (semi-)automated surveillance include higher quality of surveillance through better standardisation and a 75-95% reduction of manual chart review workload.

Automated surveillance is promising, but most of the currently available systems were developed in individual hospitals, and are hence heterogeneous in design, aims, methods and definitions used. In addition, within each centre, many similar challenges and barriers are encountered, but knowledge on how to address them is not widely disseminated, thus making inefficient use of resources and repeatedly requiring considerable investments.

Within the PRAISE network, we aim to design a shared roadmap to move automated surveillance from the research setting to large-scale implementation.

PRAISE will deliver:

  1. A roadmap to automated HAI surveillance, describing requirements of automated surveillance systems and one or more possible trajectories towards their design.
  2. A research agenda to support future development efforts.
  3. Guidance documents regarding regulatory and governance barriers, IT and data management solutions and training needs.

PRAISE will organise two workshops and divide tasks among subgroups.

The PRAISE network uniquely brings together experts working in the field of surveillance, with representatives from hospitals as well as public health institutes. The output of the network will improve AMR surveillance by providing the guidance necessary to develop high-quality automated surveillance tools for HAI, caused by AMR and susceptible pathogens.

Network partners

  • Maaike Van Mourik, University Medical Center Utrecht, Netherlands (Coordinator)

This network includes 32 partners, please click on the following link to see complete network composition: Network composition Providing a Roadmap for Automated Infection Surveillance in Europe (PRAISE)

Healthcare-associated infections (HAI) are infections that arise during the process of medical care, for example surgical site infections or central line-associated bloodstream infections. Such infections can be caused by both antimicrobial resistant (AMR) and non-AMR pathogens. Surveillance of HAI, systematically monitoring their incidence, is a cornerstone of infection prevention programmes and allows for the assessment of the effect of interventions. Conventional surveillance is performed by manually reviewing patient charts; this process is cumbersome and prone to error. These limitations, along with the increasing adoption of electronic health records, has driven the development of automated HAI surveillance. However, these initiatives have often been limited to individual hospitals and are mainly used in the research setting. This stand-alone development of systems makes inefficient use of resources and brings the risk of losing comparability across surveillance networks. Implementing large-scale automated surveillance requires a coordinated effort and redesign of surveillance methods.

The PRAISE network brings together 30 experts with HAI surveillance or IT expertise from 10 Western European countries and aims to provide guidance for large-scale implementation of reliable automated HAI surveillance. The main product of the network is a roadmap for large-scale implementation of automated surveillance. It does not provide a point-by-point checklist, but aims provide high-level guidance and outline the underlying principles. The roadmap discusses the selection of surveillance targets (what infections to detect), different organisational and methodological approaches to large-scale automation of surveillance and their advantages, disadvantages and risks. It defines key performance requirements of automated surveillance systems and suggestions for their design and provides guidance on how to achieve successful implementation, including the involvement of all relevant stakeholders. The roadmap also addresses areas of future research and lists training requirements for the infection control community and related disciplines.

The roadmap is supported by two accompanying papers. In the Governance Guidance document, the governance and data protection aspects are explored in more depth. The document aims to support collaboration between surveillance experts and legal and/or governance specialists. The IT Guidance document, serves to explain the basics of medical informatics and to outline the steps required to technically implement automated surveillance within healthcare facilities. It provides more in-depth information on among others data sources, interoperability, data storage, and communication. In all, the roadmap and guidance documents can be used by surveillance networks together with individual healthcare facilities to develop a strategy for implementing automated surveillance in line with the possibilities within their local setting.


National health care infrastructures, health care utilization and patient movements between hospitals: Networks working to improve surveillance (NeWIS)

There is a worldwide concern about the emergence, and widespread dissemination, of AMR “high risk” clones that carry the genomic determinants for enhanced virulence and resistance.


Regional, national and international surveillance is considered an important component in a strategy to control these strains. However, current surveillance systems are not fit for this purpose and there is still no good evidence base for deciding which and how many sentinel hospitals should be included in surveillance programs.

Previous work coordinated by the coordinator has shown that AMR “high-risk” clones spread between health care institutions as a result of patient movements. Hospitals thus become connected by patients. Taken together, all connections create a nexus of institutions that can be described as national health care referral networks. Despite their apparent complexity, these networks reveal a simple scaffolding and remarkably consistent properties that lie at the core of national health care infrastructures. These show many of the typical hallmarks of hierarchically distributed networks, with regionality, centrality, scale-freeness and small world properties. Hence a quantitative understanding of the network dynamics offers the means for purpose-designed surveillance and better targeted interventions.

The current proposal will bring together a critical mass of public health microbiologists, health systems researchers, and social network analysts from Europe and beyond. These experts will define the data needs, data sources, algorithms and analysis tools with the aim to identify a heuristic optimisation approach to sentinel site selection. In this way the suggested network activities will provide recommendations for the development of surveillance structures that are more parsimonious, cost- and time effective and provide—through the selection of sampling sites for genomic surveillance by whole genome sequencing (WGS)—the genetic signatures for early, next generation diagnostics of recently emerging clones. The focus on site selection means that WGS will not be part of this initiative.

Network partners

  • Hajo Grundmann, University of Freiberg, Germany (Coordinator)

This network includes 17 partners, please click on the following link to see complete network composition: Network composition National health care infrastructures, health care utilization and patient movements between hospitals: Networks working to improve surveillance (NeWIS)


KlebNet: a One Health network bridging science and surveillance on antimicrobial resistant Klebsiella (KlebNet)

Klebsiella, particularly Klebsiella pneumoniae (hereafter, collectively called Kp) is an opportunistic pathogen of humans and animals that now tops the ‘urgent threat’ lists of CDC, ECDC and WHO due to high rates of multidrug resistance.

Completed project

Kp can also play a pioneer role in the amplification of novel AMR mechanisms acquired from environmental microbes, which can then spread to other important bacterial pathogens, as exemplified with KPC-2 or NDM-1 carbapenemases. Despite this, Kp does not currently feature as a target of surveillance efforts. Although Kp is generally viewed as ‘ubiquitous’, data on its distribution in healthy people, the environment, animals and the food chain are scarce, and the transmission of Kp and its AMR gene cargo between these potential sectors and hospitalised individuals is poorly understood.

The KlebNet network is dedicated to identifying key knowledge gaps relating to Kp ecology and transmission, and to developing a One Health strategy for Kp surveillance. Strategy: Research on ecological distribution of Kp and on its transmission routes should, to be actionable, be guided by expected impact on implementation into surveillance and control programs. An optimal Kp surveillance strategy must be defined based on (1) Most advanced knowledge on the ecology, population biology and epidemiology of the pathogen, combined with (2) Actionability and practical aspects of the implementation of surveillance, in high-income as well as in low- and medium income countries (LMIC), and across sectors (clinical, animal, food).

Objectives: (1) To review current knowledge on Kp reservoirs, population biology and transmission dynamics, and to identify and prioritise gaps where further research is required; and (2) To issue recommendations on how Kp surveillance should be implemented and harmonised across environment, animals, food and hospitals, including both technical and strategic considerations.

Network partners

  • Sylvain Brise, Pasteur Institute, France (Coordinator)

This network includes 31 partners, please click on the following link to see complete network composition: Network composition KlebNet: a One Health network bridging science and surveillance on antimicrobial resistant Klebsiella (KlebNet)


Surveillance Of mobiLome meDiated aNtibiotic rEsiStance Spread (SOLIDNESS)

Mobile genetic elements (MGEs) are DNA molecules that often carry important genes for the fitness of microorganisms, such as resistance and virulence genes, which may confer an adaptive advantage to recipient bacteria. Hence, they play a pivotal role in horizontal gene transfer.

Completed project

MGEs are one of the main players in antibiotic resistance dissemination and can be shared by different bacterial strains, species or even genera, which makes them one of the biggest concerns to healthcare stakeholders. MGEs are challenging to characterise through sequencing, due to their chimeric, modular and repetitive nature. Our main objective is to establish a network of excellence for surveillance of MGE-mediated antibiotic resistance spread. This network will improve the access to high-quality and curated MGEs sequencing data that will be shared at the international level. It will result in the production of documents (standard operating procedures, SOPs) by the network detailing 1) harmonisation of high-quality sequencing standards and protocols for MGEs detection; 2) definition of a bioinformatics workflow for MGEs sequence analysis from next-generation sequencing data; 3) definition of new sequence-based typing methods of plasmids for both Gram-positive and Gram-negative bacteria.

Since the network includes a wide range of stakeholders with diverse expertise, including expertise in classical typing methods, “-omics”, bioinformatics and plasmid-detection, the combination of backgrounds will contribute to the creation of the high-quality and curated MGEs database from different sources. This proposal aims to track the evolution and spread of antimicrobial resistance and virulence in bacteria, mediated by MGEs, and in the future, find ways to prevent it.

Network partners

  • John Rossen, University of Groningen, Netherlands (Coordinator)

This network includes 21 partners, please click on the following link to see complete network composition: Network composition Surveillance Of mobiLome meDiated aNtibiotic rEsiStance Spread (SOLIDNESS)

Mobile genetic elements (MGEs) are DNA molecules containing genes that are important for a microorganism’s fitness. These include resistance and virulence genes, which can provide the
bacteria with an adaptive advantage over other bacteria. MGEs play a central role in horizontal gene transfer and are among the main drivers of antibiotic resistance and virulence spread. Such
dissemination is a significant concern for healthcare stakeholders and a challenge for those concerned with preventing the dissemination of antibiotic-resistant and / or virulent bacteria,
such as carbapenemase-producing Enterobacteriaceae and Shiga-toxin-producing Escherichia coli (STEC). Molecular characterization of MGEs is essential for a better understanding of these
molecules and their dissemination. Both are required for optimal surveillance of bacteria containing resistance and virulence genes. Sequence analysis techniques are often used for this
purpose. The sequencing protocols and subsequent bioinformatics tools used to characterize MGEs may significantly influence the final results and their interpretation.

To map this out, several studies were performed within the consortium, including a proficiency test. Significant differences were found in the quality of the sequences obtained from different
laboratories, in which the sequencing process and the sequencing technique played an important role. This had an impact on the subsequent data analysis, leading to variable results.
Small MGEs, abundant in Gram-positive bacteria, could be characterized by using a technique that generates short sequence fragments (≤ 300 base pairs). This method was not suitable for the
characterization of larger MGEs, typical for Gram-negative bacteria. Using a sequencing technology that produces longer sequencing fragments facilitated the characterization of large
MGEs, but some smaller MGEs could not be analyzed. Besides, this technology resulted in lower accuracy, which could be partially overcome by using additional polishing steps. The best results were obtained by combining the data generated by the two different sequencing technologies, which resulted in the correct characterization of small and large MGEs.

In summary, when characterizing MGEs, researchers must weigh the costs/turnaround time and the accuracy of the results. However, only by combined analyzes of the data generated by both short- and long fragment sequencing technologies will they produce results that will include all the MGEs of a specific strain.

Project resources



Bridging the gap between humAn and animal suRveillance data, antibiotic poliCy, and stewardsHip (ARCH)

Surveillance is essential to all aspects of the clinical management of antimicrobial resistance. It provides necessary information to develop empiric therapy guidelines, antibiotic formularies, and stewardship programmes. However, the value of surveillance as a critical component of antimicrobial stewardship is not fully established and the majority of the guidance documents focuses either on laboratory surveillance or antibiotic guidelines.

Completed project

The ARCH Network uniquely brings together multisectoral specialists and networks in the field of animal and human surveillance to bridge the gap between surveillance data and antibiotic stewardship in both compartments. The group will finalise four white papers (“Bridge the Gap: Survey to Treat”) tailored to: hospitals (medical and surgical wards, paediatric clinic, intensive care units), long term care facilities, out-patients ambulatory, and veterinary care. The white papers will be developed in the form of checklists (App and paper forms) summarising the kind of microbiological and antimicrobial use data that are essential for antibiotic prescribing, and how these data relate to antibiotic guidance and stewardship interventions. The multidisciplinary group will integrate recommendations for the checklist implementation in heterogeneous economic settings and where expertise in surveillance is limited.

The ARCH Network will organise two one day workshops and will be operating through Webex meetings and conference calls. During the first workshop, the group will discuss opportunities for data sharing, other networks involvement, website features, and define the milestones and tasks´ timeline. The drafts of the white papers will be available for open consultation to ARCH members and through the associated networks (EUCIC, EPI-Net, ResistanceMap, LOTTA, EUCAST, LAB-Net, KISS, HANNET, Global PPS, AMCLI-COSA, SWISS-NOSO, CLEO) and international stakeholders (ECDC, WHO, Wellcome, EMA).

The ARCH experts will also develop a strategic research agenda to identify critical areas and gaps in clinical surveillance. In the second workshop white papers and the strategic research agenda will be reviewed and approved. The dissemination will be pursued in the dedicated website, quarterly newsletter, national and international conferences, publications in open scientific peer reviewed journals and though relevant national societies in the field. The ARCH Network will also develop a plan for the sustainability of the network after the funding period.

Network partners

  • Evelina Tacconelli, University Hospital Tübingen, Germany (Coordinator)

This network includes 23 partners, please click on the following link to see complete network composition: Network composition Bridging the gap between humAn and animal suRveillance data, antibiotic poliCy, and stewardsHip (ARCH)

Among the factors that play a role in the alarming increase of antimicrobial resistance (AMR), misuse of antibiotics in both human and veterinary sectors is the most important catalyst. Prescribing antibiotics for viral infections, usage of antibiotics in meat production, self-medication, etc., are some examples of inappropriate use of these life-saving drugs. Once a bacterium develops resistance to an antibiotic, it loses its potential to kill the bacterium; hence infections caused by the bacterium cannot be treated. Considering that it is very difficult to develop new antibiotics, it is crucial to preserve the efficacy of antibiotics by promoting their prudent use through education and strong regulations.

Antimicrobial stewardship (AMS) is a regulatory program, which if performed in places where antibiotics are prescribed, can ensure their sustainability. AMS involves tracking the amount of antibiotics used (AMU) and frequency of occurrence of AMR (how many patients had a bacterium resistant to an antibiotic) to define a set of actions to improve the standards of AMU and bring down AMR and to educate staff (clinicians, nurses, pharmacists, etc.) performances. Although AMS has been in practice for over 20 years, guidance on how to perform AMS has been tailored to hospitals mostly and lacks details on surveillance of AMU and AMR for stewardship purposes. But with the recognition that AMR can only be tackled by addressing the antibiotic misuse in multiple sectors, including veterinary, a need for more comprehensive practical “One Health” recommendations has risen.

JPIMAR’s ARCH Network brought together multidisciplinary experts in the field with the aim of developing easy-to-use recommendations (checklists) to promote and help customize AMS programs in four highly relevant settings: hospitals, general practices, elderly homes and veterinary clinics. The checklists would indicate detailed answers to three primary questions: “how to build and lead a team to oversee and execute actions under the AMS program?”, “how to perform surveillance of AMR?”, and “how to perform surveillance of AMU?” To develop the four checklists, an extensive search of current literature was performed to generate “evidence” with which a draft of answers in the form of action items were developed by a research team.

The evidence and the draft were presented to the experts who evaluated the action items via an online survey followed by a two-day face-to-face meeting. Through this consensus process the checklists were finalized. For those questions for which no answers could be generated or those answers for which no consensus was achieved indicated serious gaps in the current scientific knowledge and were deemed as “research priorities” in need of immediate attention. We thus developed a very flexible, practical One Health tool with the potential to drive implementation of AMS and improve surveillance of AMR and AMU for a holistic strategy to preserve antibiotics.

Project resources



Network for Enhancing Tricycle ESBL Surveillance Efficiency (NETESE)

The extended-spectrum beta-lactamase (ESBL)-Escherichia coli Tricycle surveillance program has been developed by WHO to obtain a global picture of antimicrobial resistance (AMR) in humans, animals and the environment in all countries, especially in those with limited surveillance capacities.

Completed project

Basically, Tricycle proposes countries to implement a similar technical protocol to generate yearly rates of ESBL-E.coli in the three sectors of interest. Repetition of harmonised protocol every year should allow determination of trends as well as inter- and intra-regional comparisons and provide a dynamic dashboard of antibacterial resistance for decision makers.

Tricycle is currently in its implementation phase in a small number of pilot countries, sponsored by the Fleming Fund (United Kingdom). Other countries are preparing to initiate the process in the coming years with other sources of funding. However, at this stage, no formal system has been developed to assist all countries that will ultimately participate to Tricycle to be linked together for exchange, mutual support and experience sharing. The lack of such system could weaken the efficiency and sustainability of the whole project. Therefore, we take advantage of the 7th JPIAMR call to fulfil this gap by submitting the “Network for Enhancing Tricycle ESBL Surveillance Efficiency” (NETESE) proposal described here. NETESE gathers 15 institutions from nine low and middle income countries at different stages of implementation of Tricycle and three EU countries that have been strongly instrumental in its development. Effective networking will be obtained through the organisation of two face-to-face meetings that will gather all participants, at the beginning and at the end of the project. In between, they will exchange through trimonthly web-conferences on dedicated topics of interest.

The outputs of NETESE will be to synergise the experience of the countries that are implementing Tricycle. NETESE will also establish contacts to ensure on its own sustainability in order to become the nest where additional countries that will have the will to enter Tricycle in the coming years will find support and experience, before helping themselves and others with similar difficulties to enter the surveillance program. Altogether NETESE should be a key element to draw a global dynamic picture of AMR.

Network partners

  • Etienne Ruppé, INSERM, Francey (Coordinator)

This network includes 15 partners, please click on the following link to see complete network composition: Network composition Network for Enhancing Tricycle ESBL Surveillance Efficiency (NETESE)