CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
复制标题
DOI：
10.1093/nar/gkz935
复制
发表时间：
2020-01-08
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.;Raphenya, Amogelang R.;McArthur, Andrew G.
全面的抗生素耐药性数据库(CARD；https://card.mcmaster.ca))是一个精选的资源，提供关于细菌抗菌素耐药性的分子基础的参考DNA和蛋白质序列、检测模型和生物信息学工具。CARD专注于在受控词汇表中提供高质量的参考数据和分子序列，即由CARD生物处理团队设计的抗生素耐药性本体论(ARO)，以与CARD的耐药性基因识别器(RGI)软件等用于耐药性分析和预测的软件开发工作相结合。自2017年以来，CARD通过广泛精选参考序列、修订本体论结构、精选500多个新的AMR检测模型、开发新的分类范式和扩展分析工具进行了扩展。最值得注意的是，一个新的耐药组和变异体模块提供了对82种病原体和超过10万个基因组的计算机预测抗药性变异体的分析和统计汇总。通过将这些耐药性变体添加到CARD中，我们能够使用CARD中包含的信息来总结预测的耐药性，识别AMR移动性的趋势，并确定以前未描述的和新的耐药性变体。在这里，我们描述了CARD及其生物聚集过程的更新和最新扩展，包括AMR分子参考数据的群落生物聚集的新资源。
The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models and bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses on providing high-quality reference data and molecular sequences within a controlled vocabulary, the Antibiotic Resistance Ontology (ARO), designed by the CARD biocuration team to integrate with software development efforts for resistome analysis and prediction, such as CARD's Resistance Gene Identifier (RGI) software. Since 2017, CARD has expanded through extensive curation of reference sequences, revision of the ontological structure, curation of over 500 new AMR detection models, development of a new classification paradigm and expansion of analytical tools. Most notably, a new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes. By adding these resistance variants to CARD, we are able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants. Here, we describe updates and recent expansions to CARD and its biocuration process, including new resources for community biocuration of AMR molecular reference data.