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A curated data resource of 214K metagenomes for characterization of the global resistome

View ORCID ProfileHannah-Marie Martiny, View ORCID ProfilePatrick Munk, View ORCID ProfileChristian Brinch, View ORCID ProfileFrank M. Aarestrup, View ORCID ProfileThomas N. Petersen
doi: https://doi.org/10.1101/2022.05.06.490940
Hannah-Marie Martiny
1Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
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  • For correspondence: hanmar@food.dtu.dk
Patrick Munk
1Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
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Christian Brinch
1Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
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Frank M. Aarestrup
1Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
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Thomas N. Petersen
1Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
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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 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 allowing analyses of 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 a global surveillance of AMR and can serve as a resource for further research into the environmental spread and dynamic changes of ARGs.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://doi.org/10.5281/zenodo.6519843

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 06, 2022.
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A curated data resource of 214K metagenomes for characterization of the global resistome
Hannah-Marie Martiny, Patrick Munk, Christian Brinch, Frank M. Aarestrup, Thomas N. Petersen
bioRxiv 2022.05.06.490940; doi: https://doi.org/10.1101/2022.05.06.490940
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A curated data resource of 214K metagenomes for characterization of the global resistome
Hannah-Marie Martiny, Patrick Munk, Christian Brinch, Frank M. Aarestrup, Thomas N. Petersen
bioRxiv 2022.05.06.490940; doi: https://doi.org/10.1101/2022.05.06.490940

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