ArticlePLoS biology2022
A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome.
Article in PLoS biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper.Nature biotechnology · 2026Article
- Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns.mSystems · 2026Article
- pH regulates gut bacterial tryptophan metabolism.NPJ biofilms and microbiomes · 2026Article
- National antibiotic consumption is strongly related to the prevalence of antibiotic resistance across bacterial clades.iScience · 2025Article
- Utilizing co-abundances of antimicrobial resistance genes to identify potential co-selection in the resistome.Microbiology spectrum · 2024Article
- ARGprofiler-a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets.Bioinformatics (Oxford, England) · 2024Article
- Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa.PloS one · 2024Article
- Evidence for wastewaters as environments where mobile antibiotic resistance genes emerge.Communications biology · 2023Article
- The antimicrobial resistance crisis needs action now.PLoS biology · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The growing threat of antimicrobial resistance (AMR) calls for new epidemiological surveillance methods, as well as a deeper understanding of how antimicrobial resistance genes (ARGs) have been transmitted around the world. The large pool of sequencing data available in public repositories provides an excellent resource for monitoring the temporal and spatial dissemination of AMR in different ecological settings. However, only a limited number of research groups globally have the computational resources to analyze such data. We retrieved 442 Tbp of sequencing reads from 214,095 metagenomic samples from the European Nucleotide Archive (ENA) and aligned them using a uniform approach against ARGs and 16S/18S rRNA genes. Here, we present the results of this extensive computational analysis and share the counts of reads aligned. Over 6.76∙108 read fragments were assigned to ARGs and 3.21∙109 to rRNA genes, where we observed distinct differences in both the abundance of ARGs and the link between microbiome and resistome compositions across various sampling types. This collection is another step towards establishing global surveillance of AMR and can serve as a resource for further research into the environmental spread and dynamic changes of ARGs.
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Registered trials
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