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

被引：787

作者：

Alcock, Brian P. ^{[1
,2
,3
]}

Huynh, William ^{[1
,2
,3
]}

Chalil, Romeo ^{[1
,2
,3
]}

Smith, Keaton W. ^{[1
,2
,3
]}

Raphenya, Amogelang R. ^{[1
,2
,3
]}

Wlodarski, Mateusz A. ^{[1
,2
,3
]}

Edalatmand, Arman ^{[1
,2
,3
]}

Petkau, Aaron ^{[4
,5
]}

Syed, Sohaib A. ^{[1
,2
,3
]}

Tsang, Kara K. ^{[1
,2
,3
,13
]}

Baker, Sheridan J. C. ^{[1
,2
,3
]}

Dave, Mugdha ^{[1
,2
,3
]}

McCarthy, Madeline C. ^{[1
,2
,3
]}

Mukiri, Karyn M. ^{[1
,2
,3
]}

Nasir, Jalees A. ^{[1
,2
,3
]}

Golbon, Bahar ^{[1
,2
,3
]}

Imtiaz, Hamna ^{[1
,2
,3
]}

Jiang, Xingjian ^{[1
,2
,3
]}

Kaur, Komal ^{[1
,2
,3
]}

Kwong, Megan ^{[1
,2
,3
]}

Liang, Zi Cheng ^{[1
,2
,3
]}

Niu, Keyu C. ^{[1
,2
,3
]}

Shan, Prabakar ^{[1
,2
,3
]}

Yang, Jasmine Y. J. ^{[1
,2
,3
]}

Gray, Kristen L. ^{[6
]}

Hoad, Gemma R. ^{[7
]}

Jia, Baofeng ^{[6
]}

Bhando, Timsy ^{[1
,2
,3
]}

Carfrae, Lindsey A. ^{[1
,2
,3
]}

Farha, Maya A. ^{[1
,2
,3
]}

French, Shawn ^{[1
,2
,3
]}

Gordzevich, Rodion ^{[1
,2
,3
]}

Rachwalski, Kenneth ^{[1
,2
,3
]}

Tu, Megan M. ^{[1
,2
,3
]}

Bordeleau, Emily ^{[1
,2
,3
]}

Dooley, Damion ^{[8
]}

Griffiths, Emma ^{[8
]}

Zubyk, Haley L. ^{[1
,2
,3
]}

Brown, Eric D. ^{[1
,2
,3
]}

Maguire, Finlay ^{[9
,10
,11
]}

Beiko, Robert G. ^{[9
,10
]}

Hsiao, William W. L. ^{[6
,8
]}

Brinkman, Fiona S. L. ^{[6
]}

Van Domselaar, Gary ^{[5
,12
]}

McArthur, Andrew G. ^{[1
,2
,3
]}

机构：

[1] McMaster Univ, David Braley Ctr Antibiot Discovery, Hamilton, ON, Canada

[2] McMaster Univ, Michael G DeGroote Inst Infect Dis Res, Hamilton, ON, Canada

[3] McMaster Univ, Dept Biochem & Biomed Sci, Hamilton, ON, Canada

[4] Univ Manitoba, Dept Comp Sci, Winnipeg, MB, Canada

[5] Publ Hlth Agcy Canada, Natl Microbiol Lab, Winnipeg, MB, Canada

[6] Simon Fraser Univ, Dept Mol Biol & Biochem, Burnaby, BC, Canada

[7] Simon Fraser Univ, Res Comp Grp, Burnaby, BC, Canada

[8] Simon Fraser Univ, Fac Hlth Sci, Burnaby, BC, Canada

[9] Dalhousie Univ, Fac Comp Sci, Halifax, NS, Canada

[10] Dalhousie Univ, Inst Comparat Genom, Halifax, NS, Canada

[11] Dalhousie Univ, Dept Community Hlth & Epidemiol, Halifax, NS, Canada

[12] Univ Manitoba, Max Rady Coll Med, Dept Med Microbiol & Infect Dis, Winnipeg, MB, Canada

[13] London Sch Hyg & Trop Med, Dept Infect Biol, London, England

来源：

NUCLEIC ACIDS RESEARCH | 2023年 / 51卷 / D1期

基金：

加拿大健康研究院; 加拿大自然科学与工程研究理事会; 加拿大创新基金会;

关键词：

EXPANSION;

D O I：

10.1093/nar/gkac920

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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 beta-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.

引用

页码：D690 / D699

页数：10

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