RT Journal Article
SR Electronic
T1 A curated data resource of 214K metagenomes for characterization of the global resistome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.05.06.490940
DO 10.1101/2022.05.06.490940
A1 Hannah-Marie Martiny
A1 Patrick Munk
A1 Christian Brinch
A1 Frank M. Aarestrup
A1 Thomas N. Petersen
YR 2022
UL http://biorxiv.org/content/early/2022/05/06/2022.05.06.490940.abstract
AB 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 StatementThe authors have declared no competing interest.