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

Autores
Lam, Su Datt; Di Gregorio, Sabrina Noelia; Ang, Mia Yang; Griffiths, Emma; Jamaluddin, Tengku Zetty Maztura Tengku; Nathan, Sheila; Neoh, Hu Min
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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. 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.
Fil: Lam, Su Datt. Universiti Kebangsaan Malaysia; Malasia
Fil: Di Gregorio, Sabrina Noelia. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; Argentina
Fil: Ang, Mia Yang. Management & Science University; Malasia
Fil: Griffiths, Emma. University Fraser Simon; Canadá
Fil: Jamaluddin, Tengku Zetty Maztura Tengku. Universiti Putra Malaysia; Malasia
Fil: Nathan, Sheila. Universiti Kebangsaan Malaysia; Malasia
Fil: Neoh, Hu Min. Universiti Kebangsaan Malaysia; Malasia
Materia
Google Colaboratory
antimicrobial resistance (AMR)
bioinformatics
genomic surveillance
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/248153
Acceder
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network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling AMRColab – a user-friendly antimicrobial resistance detection and visualization toolLam, Su DattDi Gregorio, Sabrina NoeliaAng, Mia YangGriffiths, EmmaJamaluddin, Tengku Zetty Maztura TengkuNathan, SheilaNeoh, Hu MinGoogle Colaboratoryantimicrobial resistance (AMR)bioinformaticsgenomic surveillancehttps://purl.org/becyt/ford/3.3https://purl.org/becyt/ford/3Antimicrobial 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. 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.Fil: Lam, Su Datt. Universiti Kebangsaan Malaysia; MalasiaFil: Di Gregorio, Sabrina Noelia. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; ArgentinaFil: Ang, Mia Yang. Management & Science University; MalasiaFil: Griffiths, Emma. University Fraser Simon; CanadáFil: Jamaluddin, Tengku Zetty Maztura Tengku. Universiti Putra Malaysia; MalasiaFil: Nathan, Sheila. Universiti Kebangsaan Malaysia; MalasiaFil: Neoh, Hu Min. Universiti Kebangsaan Malaysia; MalasiaMicrobiology Society2024-10info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/248153Lam, Su Datt; Di Gregorio, Sabrina Noelia; Ang, Mia Yang; Griffiths, Emma; Jamaluddin, Tengku Zetty Maztura Tengku; et al.; AMRColab – a user-friendly antimicrobial resistance detection and visualization tool; Microbiology Society; Microbial Genomics; 10; 10; 10-2024; 1-112057-5858CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001308info:eu-repo/semantics/altIdentifier/doi/10.1099/mgen.0.001308info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T11:23:42Zoai:ri.conicet.gov.ar:11336/248153instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-22 11:23:42.437CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv AMRColab – a user-friendly antimicrobial resistance detection and visualization tool
title AMRColab – a user-friendly antimicrobial resistance detection and visualization tool
spellingShingle AMRColab – a user-friendly antimicrobial resistance detection and visualization tool
Lam, Su Datt
Google Colaboratory
antimicrobial resistance (AMR)
bioinformatics
genomic surveillance
title_short 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_sort AMRColab – a user-friendly antimicrobial resistance detection and visualization tool
dc.creator.none.fl_str_mv Lam, Su Datt
Di Gregorio, Sabrina Noelia
Ang, Mia Yang
Griffiths, Emma
Jamaluddin, Tengku Zetty Maztura Tengku
Nathan, Sheila
Neoh, Hu Min
author Lam, Su Datt
author_facet Lam, Su Datt
Di Gregorio, Sabrina Noelia
Ang, Mia Yang
Griffiths, Emma
Jamaluddin, Tengku Zetty Maztura Tengku
Nathan, Sheila
Neoh, Hu Min
author_role author
author2 Di Gregorio, Sabrina Noelia
Ang, Mia Yang
Griffiths, Emma
Jamaluddin, Tengku Zetty Maztura Tengku
Nathan, Sheila
Neoh, Hu Min
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Google Colaboratory
antimicrobial resistance (AMR)
bioinformatics
genomic surveillance
topic Google Colaboratory
antimicrobial resistance (AMR)
bioinformatics
genomic surveillance
purl_subject.fl_str_mv https://purl.org/becyt/ford/3.3
https://purl.org/becyt/ford/3
dc.description.none.fl_txt_mv 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. 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.
Fil: Lam, Su Datt. Universiti Kebangsaan Malaysia; Malasia
Fil: Di Gregorio, Sabrina Noelia. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Microbiología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; Argentina
Fil: Ang, Mia Yang. Management & Science University; Malasia
Fil: Griffiths, Emma. University Fraser Simon; Canadá
Fil: Jamaluddin, Tengku Zetty Maztura Tengku. Universiti Putra Malaysia; Malasia
Fil: Nathan, Sheila. Universiti Kebangsaan Malaysia; Malasia
Fil: Neoh, Hu Min. Universiti Kebangsaan Malaysia; Malasia
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. 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.
publishDate 2024
dc.date.none.fl_str_mv 2024-10
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/248153
Lam, Su Datt; Di Gregorio, Sabrina Noelia; Ang, Mia Yang; Griffiths, Emma; Jamaluddin, Tengku Zetty Maztura Tengku; et al.; AMRColab – a user-friendly antimicrobial resistance detection and visualization tool; Microbiology Society; Microbial Genomics; 10; 10; 10-2024; 1-11
2057-5858
CONICET Digital
CONICET
url http://hdl.handle.net/11336/248153
identifier_str_mv Lam, Su Datt; Di Gregorio, Sabrina Noelia; Ang, Mia Yang; Griffiths, Emma; Jamaluddin, Tengku Zetty Maztura Tengku; et al.; AMRColab – a user-friendly antimicrobial resistance detection and visualization tool; Microbiology Society; Microbial Genomics; 10; 10; 10-2024; 1-11
2057-5858
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001308
info:eu-repo/semantics/altIdentifier/doi/10.1099/mgen.0.001308
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Microbiology Society
publisher.none.fl_str_mv Microbiology Society
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 12.982451

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