ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics

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. 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.

Inter-phylum circulation of a beta-lactamase - encoding gene: a rare but observable event

“…Analyzing 70,301 E. coli genomes available from the Enterobase, one was identified as possessing a beta-lactamase - encoding gene which was only found in the ResFinderFG and Mustard databases (6, 10, 11). The strain of interest was an E. coli strain belonging to the A phylogroup, sequence type (ST) 744/2 according to the Warwick University/Pasteur Institut schemes, respectively, serotype Onovel132:H10, fimH allele 54.…”

“…Analyzing 70,301 E. coli genomes available from the Enterobase, one was identified as possessing a betalactamase -encoding gene which was only found in the ResFinderFG and Mustard databases (6,10,11).…”

Peptostreptococcus equinus sp. nov., isolated from horse faeces

“…The quality of the sequenced genomes was checked based on their completeness and contamination rates using the CheckM software (version 1.1.3) [24]. The complete genome sequence was annotated using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline [25], eggNOG 5.0 [26], ResFinderFG version 2.0 [27], and the Virulence Factor Database [28]. The DNA G+C content of strain CBA3647 T was calculated based on its complete genome sequence.…”

Draft genome sequence of Enterobacter cloacae ST473 harbouring blaCMH-3 isolated from a human patient diagnosed with recurrent bacteriuria in Nigeria

“…Sequence type was defined using MLST v 2.0.9 and multi locus sequence typing (MLST) allele sequences and profile data obtained from PubMLST.org [13, 14]. ResFinderFG v 2.0 was used to identify antibiotic resistance determinants [15]. MobileElementFinder v 1.0.3 and ISfinder were used to identify insertion sequences and mobile genetic elements and their relation to antimicrobial resistance genes and virulence factors [16, 17].…”

“…org [13,14]. ResFinderFG v 2.0 was used to identify antibiotic resistance determinants [15]. MobileElementFinder v 1.0.3 and ISfinder were used to identify insertion sequences and mobile genetic elements and their relation to antimicrobial resistance genes and virulence factors [16,17].…”