CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database.
CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database.
复制标题
DOI：
10.1093/nar/gkac920
复制
发表时间：
2023-01-06
影响因子：
14.9
通讯作者：
McArthur, Andrew G.
中科院分区：
文献类型：
--
作者：
Alcock, Brian P.;Huynh, William;Chalil, Romeo;Smith, Keaton W.;Raphenya, Amogelang R.;Wlodarski, Mateusz A.;Edalatmand, Arman;Petkau, Aaron;Syed, Sohaib A.;Tsang, Kara K.;Baker, Sheridan J. C.;Dave, Mugdha;McCarthy, Madeline C.;Mukiri, Karyn M.;Nasir, Jalees A.;Golbon, Bahar;Imtiaz, Hamna;Jiang, Xingjian;Kaur, Komal;Kwong, Megan;Liang, Zi Cheng;Niu, Keyu C.;Shan, Prabakar;Yang, Jasmine Y. J.;Gray, Kristen L.;Hoad, Gemma R.;Jia, Baofeng;Bhando, Timsy;Carfrae, Lindsey A.;Farha, Maya A.;French, Shawn;Gordzevich, Rodion;Rachwalski, Kenneth;Tu, Megan M.;Bordeleau, Emily;Dooley, Damion;Griffiths, Emma;Zubyk, Haley L.;Brown, Eric D.;Maguire, Finlay;Beiko, Robert G.;Hsiao, William W. L.;Brinkman, Fiona S. L.;Van Domselaar, Gary;McArthur, Andrew G.
综合抗生素耐药性数据库（CARD; card.mcmaster.ca）将抗生素耐药性本体（ARO）与策划的AMR基因（ARG）序列和赋予耐药性的突变相结合，以提供用于耐药基因的注释和解释的信息学框架。截至3.2.4版，CARD包含6627个本体术语、5010个参考序列、1933个突变、3004个出版物和5057个AMR检测模型，这些模型可由随附的抗性基因标识符（RGI）软件用于注释基因组或宏基因组序列。自2020年以来，重点加强的治疗包括扩大β-内酰胺酶治疗，纳入结核分枝杆菌基于可能性的AMR突变，添加消毒剂和防腐剂及其相关的ARG，以及耐药性修饰剂的系统治疗。这个扩展的策展包括180个新的AMR基因家族，15个新的药物类别，1个新的耐药机制，以及两个新的本体关系：evolutionary_variant_of和is_small_molecule_inhibitor。耐药基因的计算机预测和ARG的流行率统计数据已扩展到377种病原体、21，079条染色体、2，662个基因组岛、41，828个质粒和155，606个全基因组鸟枪组装，从而整理出322，710个独特的ARG等位基因序列。新功能包括CARD：社区提交的分离耐药基因组数据的实时收集，以及为ARG引入标准化的15个字符的CARD简称，以支持机器学习工作。
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.
登录
查看更多内容
影响因子：
16.6
作者：
Zhang AN;Gaston JM;Dai CL;Zhao S;Poyet M;Groussin M;Yin X;Li LG;van Loosdrecht MCM;Topp E;Gillings MR;Hanage WP;Tiedje JM;Moniz K;Alm EJ;Zhang T
通讯作者：
Zhang T
影响因子：
15.5
作者：
Berglund F;Marathe NP;Österlund T;Bengtsson-Palme J;Kotsakis S;Flach CF;Larsson DGJ;Kristiansson E
通讯作者：
Kristiansson E
Islandviewer 4：扩展了大规模数据集基因组岛的预测。
影响因子：
14.9
作者：
Bertelli C;Laird MR;Williams KP;Simon Fraser University Research Computing Group;Lau BY;Hoad G;Winsor GL;Brinkman FSL
通讯作者：
Brinkman FSL
影响因子：
9.8
作者：
Rodrigues, Camilla;Moore, David;Crook, Derrick W.;Cirillo, Daniela M.;Fowler, Philip W.;Iqbal, Zamin;Ismail, Nazir A.;Mistry, Nerges;Niemann, Stefan;Peto, Tim E. A.;Thwaites, Guy;Walker, A. Sarah;MWalker, Timothy;Wilson, Daniel J.;Earle, Sarah G.;Wilson, Daniel J.;Grazian, Clara;Walker, A. Sarah;Hunt, Martin;Knaggs, Jeff;Iqbal, Zamin
通讯作者：
Iqbal, Zamin
影响因子：
7.7
作者：
Knight GM;Glover RE;McQuaid CF;Olaru ID;Gallandat K;Leclerc QJ;Fuller NM;Willcocks SJ;Hasan R;van Kleef E;Chandler CI
通讯作者：
Chandler CI