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

Surveillance

Research Network: 2023-04-01 - 2024-03-31
Total sum awarded: €50 000

Antimicrobial resistance (AMR) is spreading rapidly across the globe, and much of this is driven by plasmids harbouring AMR genes. The ability of AMR plasmids to transfer independently presents a serious challenge for epidemiologists attempting to monitor the prevalence and spread of AMR using genomics approaches, because the patterns of transmission of AMR plasmids, and AMR genes, might be distinct from those of the host bacteria. There is thus a requirement at the core of One-Health AMR management strategies to tease apart the transmission of strains, plasmids (and even AMR genes carried in transposons), to implement effective monitoring and risk assessments. Currently, however, our capacity for effective plasmid molecular surveillance in both clinical and non-clinical settings is limited due to the diversity and speed of evolutionary change of plasmids. This poses both bioinformatic and conceptual problems, and current plasmid typing schemes lack the resolution to infer transmission links. This network brings together experts who have made critical contributions to this problem through the development of bioinformatics tools, clinical and non-clinical AMR surveillance, and plasmid biology. The network has two key aims:i) design and implement a novel platform (plasmid.watch) that incorporates WGS data from plasmids and their host strains (allowing easy cross-referencing between the two), and ii) identify the optimum rapid plasmid typing methods for surveillance. The network includes partners from LMICs and will place an emphasis on ECR training and stakeholder engagement.

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  • Edward Feil, University of Bath, United Kingdom (Coordinator)
  • Harry Thorpe, University of Oslo, Norway (Observer)
  • Sergio Alonso, University of Oslo, Norway (Observer)
  • Mario Ramirez, University of Lisbon, Portugal (Observer)
  • Tjibbe Donke, Institute for Infection Prevention and Hospital Epidemiology, University of Freiburg, Germany (Observer)
  • Carla Rodrigues, Institut Pasteur, France (Observer)
  • Hajo Grundman, Institute for Infection Prevention and Hospital Epidemiology, University of Freiburg, Germany (Observer)
  • Iruka Okeke, University of Ibadan, Nigeria (Observer)
  • John Rossen, University Medical Center Groningen, Netherlands (Observer)
  • David Aanensen, University of Oxford, United Kingdom (Observer)
  • Barbara Kasprzyk-Hordern, University of Bath, United Kingdom (Observer)
  • Pieter-Jan Ceyssens, Sciensano, Belgium (Observer)
  • Mashkoor Mohsin, University of Agriculture Faisalabad, Pakistan (Observer)
  • Rob Willems, University Medical Centre Utrecht, Netherlands (Observer)
  • Teresa Coque, Ramón y Cajal Institute for Health Research (IRYCIS), Spain (Observer)
  • Kristen Reyher, University of Bristol, United Kingdom (Observer)
  • Val Lanza, Ramón y Cajal Institute for Health Research (IRYCIS), Spain (Observer)
  • Jukka Corander, University of Oslo, Norway (Observer)
  • Ilana Camargo, University of São Paulo, Brazil (Observer)
  • Rachel Kwiatkowska, University of Bristol, United Kingdom (Observer)
  • Sandra Reuter, Institute for Infection Prevention and Hospital Epidemiology, University of Freiburg, Germany (Observer)
  • Anita Schurch, University Medical Centre Utrecht, Netherlands (Observer)
  • Lauren Cowley, University of Bath, United Kingdom (Observer)
  • Zamin Iqbal, European Molecular Biology Laboratory - European Bioinformatics Institute, United Kingdom (Observer)
  • Natacha Couto, Big Data Institute, University of Oxford, United Kingdom (Observer)

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. 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.

Call

2022 - Diagnostics and Surveillance Networks