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


Citation

Lam, Su Datt and Di Gregorio, Sabrina and Ang, Mia Yang and Griffiths, Emma and Tengku Jamaluddin, Tengku Zetty Maztura and Nathan, Sheila and Neoh, Hui-min (2024) AMRColab – a user-friendly antimicrobial resistance detection and visualization tool. Microbial Genomics, 10 (10). art. no. 001308. ISSN 2057-5858; eISSN: 2057-5858

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 Staphylococcus aureus (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. AMR-Colab’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. © 2024 The Authors.


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Additional Metadata

Item Type: Article
Divisions: Faculty of Medicine and Health Science
DOI Number: https://doi.org/10.1099/mgen.0.001308
Publisher: Microbiology Society
Keywords: Antimicrobial resistance (amr); Bioinformatics; Genomic surveillance; Google colaboratory
Depositing User: Ms. Azian Edawati Zakaria
Date Deposited: 27 Mar 2025 01:52
Last Modified: 27 Mar 2025 01:52
Altmetrics: http://www.altmetric.com/details.php?domain=psasir.upm.edu.my&doi=10.1099/mgen.0.001308
URI: http://psasir.upm.edu.my/id/eprint/116368
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