AMRColab – a user-friendly antimicrobial resistance detection and visualization tool
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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Microbiology Society
2024
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| Online Access: | http://psasir.upm.edu.my/id/eprint/116368/ http://psasir.upm.edu.my/id/eprint/116368/1/116368.pdf |
| _version_ | 1848866987263918080 |
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| author | Lam, Su Datt Di Gregorio, Sabrina Ang, Mia Yang Griffiths, Emma Tengku Jamaluddin, Tengku Zetty Maztura Nathan, Sheila Neoh, Hui-min |
| author_facet | Lam, Su Datt Di Gregorio, Sabrina Ang, Mia Yang Griffiths, Emma Tengku Jamaluddin, Tengku Zetty Maztura Nathan, Sheila Neoh, Hui-min |
| author_sort | Lam, Su Datt |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-15T14:29:20Z |
| format | Article |
| id | upm-116368 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T14:29:20Z |
| publishDate | 2024 |
| publisher | Microbiology Society |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-1163682025-03-27T01:52:18Z http://psasir.upm.edu.my/id/eprint/116368/ AMRColab – a user-friendly antimicrobial resistance detection and visualization tool Lam, Su Datt Di Gregorio, Sabrina Ang, Mia Yang Griffiths, Emma Tengku Jamaluddin, Tengku Zetty Maztura Nathan, Sheila Neoh, Hui-min 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. Microbiology Society 2024 Article PeerReviewed text en cc_by_4 http://psasir.upm.edu.my/id/eprint/116368/1/116368.pdf 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 https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001308 10.1099/mgen.0.001308 |
| spellingShingle | Lam, Su Datt Di Gregorio, Sabrina Ang, Mia Yang Griffiths, Emma Tengku Jamaluddin, Tengku Zetty Maztura Nathan, Sheila Neoh, Hui-min AMRColab – a user-friendly antimicrobial resistance detection and visualization tool |
| title | AMRColab – a user-friendly antimicrobial resistance detection and visualization tool |
| title_full | AMRColab – a user-friendly antimicrobial resistance detection and visualization tool |
| title_fullStr | AMRColab – a user-friendly antimicrobial resistance detection and visualization tool |
| title_full_unstemmed | AMRColab – a user-friendly antimicrobial resistance detection and visualization tool |
| title_short | AMRColab – a user-friendly antimicrobial resistance detection and visualization tool |
| title_sort | amrcolab – a user-friendly antimicrobial resistance detection and visualization tool |
| url | http://psasir.upm.edu.my/id/eprint/116368/ http://psasir.upm.edu.my/id/eprint/116368/ http://psasir.upm.edu.my/id/eprint/116368/ http://psasir.upm.edu.my/id/eprint/116368/1/116368.pdf |