Wallace James C, Port Jesse A, Smith Marissa N, Faustman Elaine M
Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA.
Database (Oxford). 2017 Jan 10;2017. doi: 10.1093/database/baw165. Print 2017.
Antibiotic resistance (AR) is a major global public health threat but few resources exist that catalog AR genes outside of a clinical context. Current AR sequence databases are assembled almost exclusively from genomic sequences derived from clinical bacterial isolates and thus do not include many microbial sequences derived from environmental samples that confer resistance in functional metagenomic studies. These environmental metagenomic sequences often show little or no similarity to AR sequences from clinical isolates using standard classification criteria. In addition, existing AR databases provide no information about flanking sequences containing regulatory or mobile genetic elements. To help address this issue, we created an annotated database of DNA and protein sequences derived exclusively from environmental metagenomic sequences showing AR in laboratory experiments. Our Functional Antibiotic Resistant Metagenomic Element (FARME) database is a compilation of publically available DNA sequences and predicted protein sequences conferring AR as well as regulatory elements, mobile genetic elements and predicted proteins flanking antibiotic resistant genes. FARME is the first database to focus on functional metagenomic AR gene elements and provides a resource to better understand AR in the 99% of bacteria which cannot be cultured and the relationship between environmental AR sequences and antibiotic resistant genes derived from cultured isolates.Database URL: http://staff.washington.edu/jwallace/farme.
抗生素耐药性（AR）是全球主要的公共卫生威胁，但在临床背景之外，几乎没有资源对AR基因进行编目。当前的AR序列数据库几乎完全由临床细菌分离株的基因组序列组装而成，因此不包括许多在功能宏基因组研究中赋予抗性的环境样本来源的微生物序列。使用标准分类标准，这些环境宏基因组序列与临床分离株的AR序列往往很少或没有相似性。此外，现有的AR数据库没有提供有关包含调控或可移动遗传元件的侧翼序列的信息。为了帮助解决这个问题，我们创建了一个注释数据库，其DNA和蛋白质序列专门来自在实验室实验中显示出AR的环境宏基因组序列。我们的功能性抗生素抗性宏基因组元件（FARME）数据库是公开可用的DNA序列、预测的赋予AR的蛋白质序列以及调控元件、可移动遗传元件和抗生素抗性基因侧翼的预测蛋白质的汇编。FARME是第一个专注于功能性宏基因组AR基因元件的数据库，它提供了一个资源，有助于更好地了解99%无法培养的细菌中的AR，以及环境AR序列与培养分离株来源的抗生素抗性基因之间的关系。数据库网址：http://staff.washington.edu/jwallace/farme 。
