摘要
      宏基因组学可以用来监测抗生素耐药性基因（ARGs）的传播。在ResFinder和CARD等数据库中发现的ARG主要来源于可培养和致病细菌，而来自非可培养和非致病细菌的ARG仍然研究不足。功能宏基因组学基于表型基因选择，可以从与已知ARGs具有潜在低同一性的不可培养细菌中鉴定ARGs。2016年，创建了ResFinderFG v1.0数据库，用于收集功能宏基因组学研究中的ARG。在这里，我们展示了数据库的第二个版本，ResFinderFG v2.0，它可以在基因组流行病学中心的网络服务器上获得(https://cge.food.dtu.dk/services/ResFinderFG/). 它包括通过功能宏基因组学从50个精心策划的数据集中鉴定的3913个ARG。与肠道、土壤和水（海洋+淡水）全球微生物基因目录中的其他流行数据库相比，我们评估了其检测ARGs的潜力(https://gmgc.embl.de). ResFinderFG v2.0允许检测未使用其他数据库检测到的ARG。其中包括对β-内酰胺类、四环素、氯霉素、糖肽/环丝氨酸和甲氧苄啶/磺酰胺具有耐药性的ARGs。因此，ResFinderFG v2.0可用于识别与传统数据库中发现的ARG不同的ARG，从而改进对耐药性的描述。
ABSTRACT
Metagenomics can be used to monitor the spread of antibiotic resistance genes (ARGs). ARGs found in databases such as ResFinder and CARD primarily originate from culturable and pathogenic bacteria, while ARGs from non-culturable and non-pathogenic bacteria remain understudied. Functional metagenomics is based on phenotypic gene selection and can identify ARGs from non-culturable bacteria with a potentially low identity shared with known ARGs. In 2016, the ResFinderFG v1.0 database was created to collect ARGs from functional metagenomics studies. Here, we present the second version of the database, ResFinderFG v2.0, which is available on the Center of Genomic Epidemiology web server (https://cge.food.dtu.dk/services/ResFinderFG/). It comprises 3,913 ARGs identified by functional metagenomics from 50 carefully curated datasets. We assessed its potential to detect ARGs in comparison to other popular databases in gut, soil and water (marine + freshwater) Global Microbial Gene Catalogues (https://gmgc.embl.de). ResFinderFG v2.0 allowed for the detection of ARGs that were not detected using other databases. These included ARGs conferring resistance to beta-lactams, cycline, phenicol, glycopeptide/cycloserine and trimethoprim/sulfonamide. Thus, ResFinderFG v2.0 can be used to identify ARGs differing from those found in conventional databases and therefore improve the description of resistomes.

https://www.biorxiv.org/content/10.1101/2022.10.19.512667v2.abstract