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

Gschwind, Rémi; Perović, Svetlana Ugarčina; Weiss, Maja; Petitjean, Marie; Lao, Julie; Coelho, Luís Pedro

doi:10.1093/nar/gkad384

Cited by 18 publications

(8 citation statements)

References 69 publications

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“…An E. coli genome was identified as possessing a beta-lactamase-encoding gene which was only found in the ResFinderFG and Mustard databases ( 6 , 9 – 11 ). The strain of interest belonged to the A phylogroup, sequence type 744/2 according to the Warwick University/Pasteur Institute schemes, respectively, and serotype Onovel132:H10, fimH allele 54.…”

Section: Resultsmentioning

confidence: 99%

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

Gschwind,

Petitjean,

Fournier

et al. 2024

Antimicrob Agents Chemother

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Beta-lactamase-mediated degradation of beta-lactams is the most common mechanism of beta-lactam resistance in Gram-negative bacteria. Beta-lactamase-encoding genes can be transferred between closely related bacteria, but spontaneous inter-phylum transfers (between distantly related bacteria) have never been reported. Here, we describe an extended-spectrum beta-lactamase (ESBL)-encoding gene ( bla MUN-1 ) shared between the Pseudomonadota and Bacteroidota phyla. An Escherichia coli strain was isolated from a patient in Münster (Germany). Its genome was sequenced. The ESBL-encoding gene (named bla MUN-1 ) was cloned, and the corresponding enzyme was characterized. The distribution of the gene among bacteria was investigated using the RefSeq Genomes database. The frequency and relative abundance of its closest homolog in the global microbial gene catalog (GMGC) were analyzed. The E. coli strain exhibited two distinct morphotypes. Each morphotype possessed two chromosomal copies of the bla MUN-1 gene, with one morphotype having two additional copies located on a phage-plasmid p0111. Each copy was located within a 7.6-kb genomic island associated with mobility. bla MUN-1 encoded for an extended-spectrum Ambler subclass A2 beta-lactamase with 43.0% amino acid identity to TLA-1. bla MUN-1 was found in species among the Bacteroidales order and in Sutterella wadsworthensis (Pseudomonadota). Its closest homolog in GMGC was detected frequently in human fecal samples. This is, to our knowledge, the first reported instance of inter-phylum transfer of an ESBL-encoding gene, between the Bacteroidota and Pseudomonadota phyla. Although the gene was frequently detected in the human gut, inter-phylum transfer was rare, indicating that inter-phylum barriers are effective in impeding the spread of ESBL-encoding genes, but not entirely impenetrable.

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Section: Resultsmentioning

confidence: 99%

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

Gschwind,

Petitjean,

Fournier

et al. 2024

Antimicrob Agents Chemother

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“…Bacterial genes that encode resistance to antibiotic drugs, heavy metals, and biocides have been previously identified and compiled into several databases ( Alcock et al 2023 , Bonin et al 2023 , Bortolaia et al 2020 , Feldgarden et al 2021 , Gupta et al 2014 , Gschwind et al 2023 ) . We sought to collect these genes of interest into a single unique collection that we named PanRes; short for the pan resistance, as having a single, although highly redundant collection is computationally more efficient to search through.…”

Section: Methodsmentioning

confidence: 99%

“…The following gene databases were identified and used as seeds for the selection of genes for the PanRes collection: ResFinder (downloaded 20 January 2023, Bortolaia et al 2020 ), ResFinderFG (version 2.0, Gschwind et al 2023 ), CARD (version 3.2.5, Alcock et al 2023 ), MegaRes (version 3.0.0, Bonin et al 2023 ), AMRFinderPlus (version 3.11/2022-12-19.1, Feldgarden et al 2021 ), and ARGANNOT (V6_July2019, Gupta et al 2014 ). In addition to these collections, we used a set of cloned, functionally determined ARGs from environmental and clinical samples tested for resistance to antibiotics not yet on the market ( Daruka et al 2023 ).…”

Section: Methodsmentioning

confidence: 99%

ARGprofiler—a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets

Martiny,

Pyrounakis,

Petersen

et al. 2024

Bioinformatics

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Motivation Analyzing metagenomic data can be highly valuable for understanding the function and distribution of antimicrobial resistance genes (ARGs). However, there is a need for standardized and reproducible workflows to ensure the comparability of studies, as the current options involve various tools and reference databases, each designed with a specific purpose in mind. Results In this work, we have created the workflow ARGprofiler to process large amounts of raw sequencing reads for studying the composition, distribution, and function of ARGs. ARGprofiler tackles the challenge of deciding which reference database to use by providing the PanRes database of 14,078 unique ARGs that combines several existing collections into one. Our pipeline is designed to not only produce abundance tables of genes and microbes but also to reconstruct the flanking regions of ARGs with ARGextender. ARGextender is a bioinformatic approach combining KMA and SPAdes to recruit reads for a targeted de novo assembly. While our aim is on ARGs, the pipeline also creates Mash sketches for fast searching and comparisons of sequencing runs. Availability The ARGprofiler pipeline is a Snakemake workflow that supports the reuse of metagenomic sequencing data and is easily installable and maintained at https://github.com/genomicepidemiology/ARGprofiler.

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“…We checked CB-01 for such traits, scrutinizing its assembled draft genome 7 in Pathogenfinder (v1.1) 93 and ResFinderFG (v2.0) 94 , using standard settings. This revealed no evidence of human pathogenicity or antimicrobial resistance genes.…”

Section: Methodsmentioning

confidence: 99%

Unlocking bacterial potential to reduce farmland N2O emissions

Hiis,

Vick,

Molstad

et al. 2024

Nature

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Farmed soils contribute substantially to global warming by emitting N2O (ref. 1), and mitigation has proved difficult2. Several microbial nitrogen transformations produce N2O, but the only biological sink for N2O is the enzyme NosZ, catalysing the reduction of N2O to N2 (ref. 3). Although strengthening the NosZ activity in soils would reduce N2O emissions, such bioengineering of the soil microbiota is considered challenging4,5. However, we have developed a technology to achieve this, using organic waste as a substrate and vector for N2O-respiring bacteria selected for their capacity to thrive in soil6–8. Here we have analysed the biokinetics of N2O reduction by our most promising N2O-respiring bacterium, Cloacibacterium sp. CB-01, its survival in soil and its effect on N2O emissions in field experiments. Fertilization with waste from biogas production, in which CB-01 had grown aerobically to about 6 × 109 cells per millilitre, reduced N2O emissions by 50–95%, depending on soil type. The strong and long-lasting effect of CB-01 is ascribed to its tenacity in soil, rather than its biokinetic parameters, which were inferior to those of other strains of N2O-respiring bacteria. Scaling our data up to the European level, we find that national anthropogenic N2O emissions could be reduced by 5–20%, and more if including other organic wastes. This opens an avenue for cost-effective reduction of N2O emissions for which other mitigation options are lacking at present.

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

Cited by 18 publications

References 69 publications

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

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

ARGprofiler—a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets

Unlocking bacterial potential to reduce farmland N2O emissions

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