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Microbial Genomics logo Microbial Genomics

Volume 10, Issue 10

AMRColab – a user-friendly antimicrobial resistance detection and visualization tool Open Access

Abstract

Antimicrobial resistance (AMR) poses a significant threat to global public health, with the potential to cause millions of deaths annually by 2050. Effective surveillance of AMR pathogens is crucial for monitoring and predicting their behaviour in response to antibiotics. However, many public health professionals lack the necessary bioinformatics skills and resources to analyse pathogen genomes effectively. To address this challenge, we developed AMRColab, an open-access bioinformatics analysis suite hosted on Google Colaboratory. AMRColab enables users with limited or no bioinformatics training to detect and visualize AMR determinants in pathogen genomes using a ‘plug-and-play’ approach. The platform integrates established bioinformatics tools such as AMRFinderPlus and hAMRonization, allowing users to analyse, compare and visualize trends in AMR pathogens easily. A trial run using methicillin-resistant (MRSA) strains demonstrated AMRColab’s effectiveness in identifying AMR determinants and facilitating comparative analysis across strains. A workshop was conducted and feedback from participants indicated high confidence in using AMRColab and a willingness to incorporate it into their research. AMRColab’s user-friendly interface and modular design make it accessible to a diverse audience, including medical laboratory technologists, medical doctors and public health scientists, regardless of their bioinformatics expertise. Future improvements to AMRColab will include enhanced visualization tools, multilingual support and the establishment of an online community platform. AMRColab represents a significant step towards democratizing AMR surveillance and empowering public health professionals to combat AMR effectively.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antimicrobial resistance (AMR) , bioinformatics , genomic surveillance and Google Colaboratory
Funding
This study was supported by the:
  • Ministry of Higher Education, Malaysia (Award TRGS/1/2022/UKM/02/8/1)
    • Principle Award Recipient: NeohHui-min
  • Public Health Alliance for Genomic Epidemiology (Award AMR-SG-02 (UKM code: JJ-2021-006))
    • Principle Award Recipient: NeohHui-min
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2024-10-21
2025-07-16
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/content/journal/mgen/10.1099/mgen.0.001308
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AMRColab – a user-friendly antimicrobial resistance detection and visualization tool
M Gen 10, 001308 (2024); https://doi.org/10.1099/mgen.0.001308
/content/journal/mgen/10.1099/mgen.0.001308
/content/journal/mgen/10.1099/mgen.0.001308
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