National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
PLoS One. 2023 Oct 19;18(10):e0293169. doi: 10.1371/journal.pone.0293169. eCollection 2023.
We are facing an ever-growing threat from increasing antimicrobial resistance (AMR) in bacteria. To mitigate this, we need a better understanding of the global spread of antimicrobial resistance genes (ARGs). ARGs are often spread among bacteria by horizontal gene transfer facilitated by mobile genetic elements (MGE). Here we use a dataset consisting of 677 metagenomic sequenced sewage samples from 97 countries or regions to study how MGEs are geographically distributed and how they disseminate ARGs worldwide. The ARGs, MGEs, and bacterial abundance were calculated by reference-based read mapping. We found systematic differences in the abundance of MGEs and ARGs, where some elements were prevalent on all continents while others had higher abundance in separate geographic areas. Different MGEs tended to be localized to temperate or tropical climate zones, while different ARGs tended to separate according to continents. This suggests that the climate is an important factor influencing the local flora of MGEs. MGEs were also found to be more geographically confined than ARGs. We identified several integrated MGEs whose abundance correlated with the abundance of ARGs and bacterial genera, indicating the ability to mobilize and disseminate these genes. Some MGEs seemed to be more able to mobilize ARGs and spread to more bacterial species. The host ranges of MGEs seemed to differ between elements, where most were associated with bacteria of the same family. We believe that our method could be used to investigate the population dynamics of MGEs in complex bacterial populations.
我们正面临着细菌中日益增加的抗生素耐药性（AMR）的威胁。为了减轻这种威胁，我们需要更好地了解抗生素耐药基因（ARGs）在全球的传播。ARGs 通常通过移动遗传元件（MGE）促进的水平基因转移在细菌之间传播。在这里，我们使用包含来自 97 个国家或地区的 677 个宏基因组测序污水样本的数据集，研究 MGE 如何在地理上分布以及它们如何在全球传播 ARGs。通过基于参考的读取映射计算 ARGs、MGE 和细菌丰度。我们发现 MGE 和 ARGs 的丰度存在系统差异，其中一些元素在所有大陆都很普遍，而另一些则在不同的地理区域中丰度更高。不同的 MGE 往往局限于温带或热带气候带，而不同的 ARGs 则往往根据大陆分开。这表明气候是影响 MGE 局部植物区系的重要因素。MGE 也被发现比 ARGs 更具地理限制。我们确定了几种具有与 ARG 和细菌属丰度相关的丰度的整合 MGE，表明它们具有移动和传播这些基因的能力。一些 MGE 似乎更能够移动 ARGs 并传播到更多的细菌物种。MGE 的宿主范围似乎在元素之间有所不同，其中大多数与同一科的细菌有关。我们相信，我们的方法可用于研究复杂细菌种群中 MGE 的种群动态。
