Surveillance for Emerging Antimicrobial Resistance through Characterization of the uncharted Environmental Resistome
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Environment

Surveillance

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Research Project: 2024-04-01 - 2027-03-31
Total sum awarded: €1 463 915

Antimicrobial resistance (AMR) is a major healthcare challenge that, unless controlled, will cause millions of deaths annually in just a couple of decades. A major issue in curbing AMR is that we rarely know which newly emerged forms of AMR may be become significant threats to human health until these antibiotic resistance genes (ARGs) are already widespread in pathogenic bacteria. Therefore, it is difficult to employ surveillance to preventively identify emerging risks. In this project, we will characterize emergent ARGs in the environment, allowing their inclusion into AMR surveillance and detection before they become clinical problems. To achieve this, we will: 1) Identify novel ARGs using functional metagenomics, shotgun metagenomic sequencing and exposure experiments enriching relevant ARGs 2) Investigate the mobility of novel ARGs and their potential for transfer to pathogens 3) Pinpoint specific early warning indicators for emerging ARGs 4) Improve monitoring protocols for AMR so that they can be quickly updated with novel ARGs 5) Define important settings where humans interact with environmental bacteria, carrying novel ARGs, by sampling locations at the interface of humans, animals and the environment 6) Provide resources for the integration of emerging ARGs in routine AMR surveillance The project will result in an early warning system for emerging AMR threats. The system will be implementable in real-world surveillance in human, animal and environmental settings targeting applicability, affordability, and high information content.

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  • Johan Bengtsson-Palme, Chalmers University of Technology, Sweden (Coordinator)
  • Thomas Berendonk, Technische Universität Dresden, Germany (Partner)
  • Sofia Forslund, Max Delbrück Center for Molecular Medicine, Germany (Partner)
  • Etienne Ruppé, Université Paris Cité, France (Partner)
  • Luis Pedro Coelho, Queensland University of Technology, Australia (Partner)
  • Nnaemeka Emmanuel Nnadi, Plateau State University, Bokkos, Nigeria (Observer)
  • Rabaab Zahra, Quaid-i-Azam University, Pakistan (Observer)

Antibiotic resistance is threatening to kill millions of people every year in just a couple of decades and is already jeopardizing previously routine medical procedures, such as surgery and cancer treatment. A major problem in stopping the increasing resistance is that we don’t know what the new forms of resistance that emerge in bacteria look like. Therefore, we cannot use surveillance methods to identify them in the places where we typically try to find resistant bacteria of concern, such as in clinics, in animals, in sewage or in the environment. In this project, we want to create a system to detect these new types of resistance before they become a big problem in healthcare settings. To do this, we have come up with a set of methods to identify such new forms of resistance in environmental bacteria, which we will refine and utilize in this project. After identifying these novel forms of resistance, we can determine the risk that they spread from harmless environmental bacteria to the bacteria that cause diseases in humans and animals. We will also look for these new forms of resistance in settings where humans come into contact with bacteria from the environment and from animals, to see if there are particular environments where the risks for spread are high. All of this information will be used to create a system for surveillance of novel forms of resistance in clinics, animals, sewage and the environment, allowing us to prevent or delay their spread into bacteria that cause human diseases.