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CARD 2023:在全面抗生素耐药性数据库中进行扩展的策展、对机器学习的支持以及耐药组预测。

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

机构信息

David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.

Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.

出版信息

Nucleic Acids Res. 2023 Jan 6;51(D1):D690-D699. doi: 10.1093/nar/gkac920.


DOI:10.1093/nar/gkac920
PMID:36263822
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9825576/
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.

摘要

综合抗生素耐药性数据库(CARD;card.mcmaster.ca)将抗生素耐药性本体论(ARO)与经过精心整理的 AMR 基因(ARG)序列和耐药性赋予突变相结合,为耐药组学的注释和解释提供了信息学框架。截至 3.2.4 版本,CARD 包含 6627 个本体论术语、5010 个参考序列、1933 个突变、3004 篇出版物和 5057 个 AMR 检测模型,这些模型可由随附的耐药基因标识符(RGI)软件用于注释基因组或宏基因组序列。自 2020 年以来,重点进行了 curated 增强,包括扩展了β-内酰胺酶 curated,纳入了基于可能性的结核分枝杆菌 AMR 突变,增加了消毒剂和防腐剂及其相关的 ARG,以及系统 curated 耐药修饰剂。这种扩展的 curated 包括 180 个新的 AMR 基因家族、15 种新的药物类别、1 种新的耐药机制和两种新的本体论关系:evolutionary_variant_of 和 is_small_molecule_inhibitor。耐药组的计算机预测和 ARG 的流行率统计已扩展到 377 种病原体、21079 条染色体、2662 个基因组岛、41828 个质粒和 155606 个全基因组鸟枪法组装体,共整理了 322710 个独特的 ARG 等位基因序列。新功能包括 CARD:社区提交的分离物耐药组数据的 Live 集合以及引入标准化的 15 个字符的 CARD 短名称,以支持机器学习工作。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d10/9825576/9345c82c150f/gkac920fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d10/9825576/0bf459851895/gkac920fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d10/9825576/9345c82c150f/gkac920fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d10/9825576/0bf459851895/gkac920fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d10/9825576/9345c82c150f/gkac920fig2.jpg

相似文献

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本文引用的文献

[1]
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PLoS Biol. 2022-8

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PLoS Biol. 2022-8

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AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence.

Sci Rep. 2021-6-16

[10]
Antimicrobial Resistance Threats in the emerging COVID-19 pandemic: Where do we stand?

J Infect Public Health. 2021-5

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