摘要
      抗微生物耐药性（AMR）的威胁越来越大，这需要新的流行病学监测方法，以及更深入地了解抗微生物耐药性基因（ARGs）是如何在世界各地传播的。公共存储库中可用的大量测序数据为监测AMR在不同生态环境中的时间和空间传播提供了极好的资源。然而，全球只有有限数量的研究小组拥有分析此类数据的计算资源。我们从欧洲核苷酸档案馆（ENA）的214095个宏基因组样本中检索到442 Tbp的测序读数，并使用针对ARGs和16S/18S rRNA基因的统一方法对其进行比对。在这里，我们展示了这一广泛计算分析的结果，并分享了对齐的读取计数。超过6.76∙108个读取片段被分配给ARGs，3.21∙109个被分配给rRNA基因，在这些基因中，我们观察到不同采样类型的ARGs丰度以及微生物组和抗性组组成之间的联系存在明显差异。这一收集是建立全球AMR监测的又一步，可以作为进一步研究ARGs的环境传播和动态变化的资源。
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.

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001792