CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database

Brian P. Alcock; William Huynh; Romeo Chalil; Keaton W. Smith; Amogelang R. Raphenya; Mateusz A. Wlodarski; Arman Edalatmand; Aaron Petkau; Sohaib A. Syed; Kara K. Tsang; Sheridan J.C. Baker; Mugdha Dave; Madeline C. McCarthy; Karyn M. Mukiri; Jalees A. Nasir; Bahar Golbon; Hamna Imtiaz; Xingjian Jiang; Komal Kaur; Megan Kwong; Zi Cheng Liang; Keyu C. Niu; Prabakar Shan; Jasmine Y.J. Yang; Kristen L. Gray; Gemma R. Hoad; Baofeng Jia; Timsy Bhando; Lindsey A. Carfrae; Maya A. Farha; Shawn French; Rodion Gordzevich; Kenneth Rachwalski; Megan M. Tu; Emily Bordeleau; Damion Dooley; Emma Griffiths; Haley L. Zubyk; Eric D. Brown; Finlay Maguire; Robert G. Beiko; William W.L. Hsiao; Fiona S.L. Brinkman; Gary Van Domselaar; Andrew G. McArthur

doi:10.1093/nar/gkac920

CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database

Brian P. Alcock, William Huynh, Romeo Chalil, Keaton W. Smith, Amogelang R. Raphenya, Mateusz A. Wlodarski, Arman Edalatmand, Aaron Petkau, Sohaib A. Syed, Kara K. Tsang, Sheridan J.C. Baker, Mugdha Dave, Madeline C. McCarthy, Karyn M. Mukiri, Jalees A. Nasir, Bahar Golbon, Hamna Imtiaz, Xingjian Jiang, Komal Kaur, Megan KwongZi Cheng Liang, Keyu C. Niu, Prabakar Shan, Jasmine Y.J. Yang, Kristen L. Gray, Gemma R. Hoad, Baofeng Jia, Timsy Bhando, Lindsey A. Carfrae, Maya A. Farha, Shawn French, Rodion Gordzevich, Kenneth Rachwalski, Megan M. Tu, Emily Bordeleau, Damion Dooley, Emma Griffiths, Haley L. Zubyk, Eric D. Brown, Finlay Maguire, Robert G. Beiko, William W.L. Hsiao, Fiona S.L. Brinkman, Gary Van Domselaar, Andrew G. McArthur

Producción científica: Contribución a una revista › Artículo › revisión exhaustiva

761 Citas (Scopus)

Resumen

The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation and interpretation of resistomes. As of version 3.2.4, CARD encompasses 6627 ontology terms, 5010 reference sequences, 1933 mutations, 3004 publications, and 5057 AMR detection models that can be used by the accompanying Resistance Gene Identifier (RGI) software to annotate genomic or metagenomic sequences. Focused curation enhancements since 2020 include expanded β-lactamase curation, incorporation of likelihood-based AMR mutations for Mycobacterium tuberculosis, addition of disinfectants and antiseptics plus their associated ARGs, and systematic curation of resistance-modifying agents. This expanded curation includes 180 new AMR gene families, 15 new drug classes, 1 new resistance mechanism, and two new ontological relationships: evolutionary_variant_of and is_small_molecule_inhibitor. In silico prediction of resistomes and prevalence statistics of ARGs has been expanded to 377 pathogens, 21,079 chromosomes, 2,662 genomic islands, 41,828 plasmids and 155,606 whole-genome shotgun assemblies, resulting in collation of 322,710 unique ARG allele sequences. New features include the CARD:Live collection of community submitted isolate resistome data and the introduction of standardized 15 character CARD Short Names for ARGs to support machine learning efforts.

Idioma original	English
Páginas (desde-hasta)	D690-D699
Publicación	Nucleic Acids Research
Volumen	51
N.º	D1
DOI	https://doi.org/10.1093/nar/gkac920
Estado	Published - ene. 6 2023

Nota bibliográfica

Publisher Copyright:
© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.

ASJC Scopus Subject Areas

Genetics

PubMed: MeSH publication types

Journal Article
Research Support, Non-U.S. Gov't

ODS de las Naciones Unidas

Este resultado contribuye a los siguientes Objetivos de Desarrollo Sostenible

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10.1093/nar/gkac920

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Alcock, B. P., Huynh, W., Chalil, R., Smith, K. W., Raphenya, A. R., Wlodarski, M. A., Edalatmand, A., Petkau, A., Syed, S. A., Tsang, K. K., Baker, S. J. C., Dave, M., McCarthy, M. C., Mukiri, K. M., Nasir, J. A., Golbon, B., Imtiaz, H., Jiang, X., Kaur, K., ... McArthur, A. G. (2023). CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research, 51(D1), D690-D699. https://doi.org/10.1093/nar/gkac920

Alcock, BP, Huynh, W, Chalil, R, Smith, KW, Raphenya, AR, Wlodarski, MA, Edalatmand, A, Petkau, A, Syed, SA, Tsang, KK, Baker, SJC, Dave, M, McCarthy, MC, Mukiri, KM, Nasir, JA, Golbon, B, Imtiaz, H, Jiang, X, Kaur, K, Kwong, M, Liang, ZC, Niu, KC, Shan, P, Yang, JYJ, Gray, KL, Hoad, GR, Jia, B, Bhando, T, Carfrae, LA, Farha, MA, French, S, Gordzevich, R, Rachwalski, K, Tu, MM, Bordeleau, E, Dooley, D, Griffiths, E, Zubyk, HL, Brown, ED, Maguire, F, Beiko, RG, Hsiao, WWL, Brinkman, FSL, Van Domselaar, G & McArthur, AG 2023, 'CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database', Nucleic Acids Research, vol. 51, n.º D1, pp. D690-D699. https://doi.org/10.1093/nar/gkac920

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title = "CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database",

abstract = "The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation and interpretation of resistomes. As of version 3.2.4, CARD encompasses 6627 ontology terms, 5010 reference sequences, 1933 mutations, 3004 publications, and 5057 AMR detection models that can be used by the accompanying Resistance Gene Identifier (RGI) software to annotate genomic or metagenomic sequences. Focused curation enhancements since 2020 include expanded β-lactamase curation, incorporation of likelihood-based AMR mutations for Mycobacterium tuberculosis, addition of disinfectants and antiseptics plus their associated ARGs, and systematic curation of resistance-modifying agents. This expanded curation includes 180 new AMR gene families, 15 new drug classes, 1 new resistance mechanism, and two new ontological relationships: evolutionary_variant_of and is_small_molecule_inhibitor. In silico prediction of resistomes and prevalence statistics of ARGs has been expanded to 377 pathogens, 21,079 chromosomes, 2,662 genomic islands, 41,828 plasmids and 155,606 whole-genome shotgun assemblies, resulting in collation of 322,710 unique ARG allele sequences. New features include the CARD:Live collection of community submitted isolate resistome data and the introduction of standardized 15 character CARD Short Names for ARGs to support machine learning efforts.",

author = "Alcock, {Brian P.} and William Huynh and Romeo Chalil and Smith, {Keaton W.} and Raphenya, {Amogelang R.} and Wlodarski, {Mateusz A.} and Arman Edalatmand and Aaron Petkau and Syed, {Sohaib A.} and Tsang, {Kara K.} and Baker, {Sheridan J.C.} and Mugdha Dave and McCarthy, {Madeline C.} and Mukiri, {Karyn M.} and Nasir, {Jalees A.} and Bahar Golbon and Hamna Imtiaz and Xingjian Jiang and Komal Kaur and Megan Kwong and Liang, {Zi Cheng} and Niu, {Keyu C.} and Prabakar Shan and Yang, {Jasmine Y.J.} and Gray, {Kristen L.} and Hoad, {Gemma R.} and Baofeng Jia and Timsy Bhando and Carfrae, {Lindsey A.} and Farha, {Maya A.} and Shawn French and Rodion Gordzevich and Kenneth Rachwalski and Tu, {Megan M.} and Emily Bordeleau and Damion Dooley and Emma Griffiths and Zubyk, {Haley L.} and Brown, {Eric D.} and Finlay Maguire and Beiko, {Robert G.} and Hsiao, {William W.L.} and Brinkman, {Fiona S.L.} and {Van Domselaar}, Gary and McArthur, {Andrew G.}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.",

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AU - Alcock, Brian P.

AU - Huynh, William

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AU - Smith, Keaton W.

AU - Raphenya, Amogelang R.

AU - Wlodarski, Mateusz A.

AU - Edalatmand, Arman

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AU - Syed, Sohaib A.

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AU - Imtiaz, Hamna

AU - Jiang, Xingjian

AU - Kaur, Komal

AU - Kwong, Megan

AU - Liang, Zi Cheng

AU - Niu, Keyu C.

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AU - Dooley, Damion

AU - Griffiths, Emma

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AU - Brown, Eric D.

AU - Maguire, Finlay

AU - Beiko, Robert G.

AU - Hsiao, William W.L.

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AU - Van Domselaar, Gary

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