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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 and 35 more
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.
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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., Dave, M., McCarthy, M. C., Mukiri, K. M., Nasir, J. A., Golbon, B., Imtiaz, H., Jiang, X., Kaur, K., … McArthur, A. G. (2022). 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, Brian P., et al. "CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database." Nucleic Acids Research, vol. 51, no. D1, 2022, pp. D690–D699, https://doi.org/10.1093/nar/gkac920.
Alcock, Brian P., William Huynh, Romeo Chalil, Keaton W Smith, Amogelang R. Raphenya, Mateusz A. Wlodarski, Arman Edalatmand, et al. "CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database." Nucleic Acids Research 51, no. D1 (2022): D690–D699. https://doi.org/10.1093/nar/gkac920.
Alcock B. P., Huynh W., Chalil R. [и др.] CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database // Nucleic Acids Research. — 2022. — Vol. 51, № D1. — P. D690–D699. — URL: https://doi.org/10.1093/nar/gkac920
@article{alcock2022card,
title = {{CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database}},
author = {Brian P. Alcock and William Huynh and Romeo Chalil and Keaton W Smith and Amogelang R. Raphenya and Mateusz A. Wlodarski and Arman Edalatmand and Aaron Petkau and Sohaib A Syed and Kara K. Tsang and Sheridan J.C. Baker and Mugdha Dave and Madeline C. McCarthy and Karyn M Mukiri and Jalees A. Nasir and Bahar Golbon and Hamna Imtiaz and Xingjian Jiang and Komal Kaur and Megan W‐L Kwong and Zi Cheng Liang and Keyu C Niu and Prabakar Shan and Jasmine Y J Yang and Kristen L. Gray and Gemma R Hoad and Baofeng Jia and Timsy Bhando and Lindsey A. Carfrae and Maya A. Farha and Shawn French and Rodion Gordzevich and Kenneth Rachwalski and Megan M. Tu and Emily Bordeleau and Damion Dooley and Emma Griffiths and Haley L. Zubyk and Eric D. Brown and Finlay Maguire and Robert Gerald Beiko and William Hsiao and Fiona S. L. Brinkman and Gary Van Domselaar and Andrew G. McArthur},
journal = {Nucleic Acids Research},
year = {2022},
volume = {51},
number = {D1},
pages = {D690--D699},
doi = {10.1093/nar/gkac920},
url = {https://doi.org/10.1093/nar/gkac920}
}TY - JOUR AU - Alcock, Brian P. AU - Huynh, William AU - Chalil, Romeo AU - Smith, Keaton W AU - Raphenya, Amogelang R. AU - Wlodarski, Mateusz A. AU - Edalatmand, Arman AU - Petkau, Aaron AU - Syed, Sohaib A AU - Tsang, Kara K. AU - Baker, Sheridan J.C. AU - Dave, Mugdha AU - McCarthy, Madeline C. AU - Mukiri, Karyn M AU - Nasir, Jalees A. AU - Golbon, Bahar AU - Imtiaz, Hamna AU - Jiang, Xingjian AU - Kaur, Komal AU - Kwong, Megan W‐L AU - Liang, Zi Cheng AU - Niu, Keyu C AU - Shan, Prabakar AU - Yang, Jasmine Y J AU - Gray, Kristen L. AU - Hoad, Gemma R AU - Jia, Baofeng AU - Bhando, Timsy AU - Carfrae, Lindsey A. AU - Farha, Maya A. AU - French, Shawn AU - Gordzevich, Rodion AU - Rachwalski, Kenneth AU - Tu, Megan M. AU - Bordeleau, Emily AU - Dooley, Damion AU - Griffiths, Emma AU - Zubyk, Haley L. AU - Brown, Eric D. AU - Maguire, Finlay AU - Beiko, Robert Gerald AU - Hsiao, William AU - Brinkman, Fiona S. L. AU - Domselaar, Gary Van AU - McArthur, Andrew G. TI - CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database JO - Nucleic Acids Research VL - 51 IS - D1 SP - D690 EP - D699 PY - 2022 DA - 2022/10/11 DO - 10.1093/nar/gkac920 UR - https://doi.org/10.1093/nar/gkac920 ER -
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