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

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 6.76.10(8) read fragments were assigned to ARGs and 3.21.10(9) 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.

Automated summary

Given the increasing threat of antimicrobial resistance (AMR), it is important to develop new surveillance methods and deepen our understanding of how antimicrobial resistance genes (ARGs) are transmitted worldwide. This study retrieved sequencing data from public repositories and analyzed them using a uniform approach to monitor the temporal and spatial dissemination of AMR. The results showed distinct differences in the abundance of ARGs and the composition of the resistome across different sampling types. This research provides valuable insights into the global surveillance of AMR and the environmental spread of ARGs.