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. However, ARGs composing the resistome of the human gut microbiota or the environment 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 database second version, ResFinderFG v2.0. Functional metagenomics studies were analyzed and DNA sequences described were retrieved, deduplicated and annotated. Sequences were curated to include only ARG sequences. ResFinderFG v2.0 was then compared to other databases for their relative sensitivity in searches for ARGs in subcatalogs from the Global Microbial Gene Catalog (GMGC). Fifty publications were considered, for a total of 23,764 ARGs identified from different environments. After deduplication, annotation and curation, 3,913 ARGs were included. New ARGs included are mainly glycopeptides/cycloserine or beta-lactams resistance genes identified mostly in human-associated samples. Results of GMGC gene subcatalogs annotation showed that ResFinderFG v2.0 detected comparable or higher ARG numbers than those detected with other databases. Most of the unigene hits obtained were database-specific and ResFinderFG v2.0 specific unigene hits included among others: glycopeptides/cycloserine, sulofnamides/trimethoprim resistance genes and beta-lactamases encoding genes. ResFinderFG v2.0 can be used to identify ARGs differing from those found in conventional databases and therefore improve the description of resistomes.

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 3913 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.