摘要

       了解抗生素抗性基因 (ARG) 的传播对人类健康至关重要。为此，有必要确定哪种类型的移动遗传元件能够将它们从动物宿主传播到人类病原体中。先前的研究表明，在猪粪便中，ARGs 可能由噬菌体编码。然而，由于细菌 DNA 污染问题，仍然缺乏猪病毒组中噬菌体编码的 ARGs 的令人信服的证据。我们收集了 14 份猪粪便样本，并对高度纯化的病毒部分和总微生物群进行了深度测序，以研究噬菌体和原噬菌体编码的 ARG。我们表明，ARG 不存在于活跃的、形成病毒的噬菌体的基因组中（低于来自病毒组的病毒重叠群的 0.02%），但存在于三个原噬菌体中，代表微生物数据集中确定的病毒重叠群的 0.02%。然而，在病毒组中没有检测到相应的噬菌体，它们的遗传图谱表明它们可能有缺陷。此外，我们的数据集首次允许全面了解原噬菌体和病毒颗粒之间的相互作用。

       Understanding the transmission of antibiotic resistance genes (ARGs) is critical for human health. For this, it is necessary to identify which type of mobile genetic elements is able to spread them from animal reservoirs into human pathogens. Previous research suggests that in pig feces, ARGs may be encoded by bacteriophages. However, convincing proof for phage-encoded ARGs in pig viromes is still lacking, because of bacterial DNA contaminating issues. We collected 14 pig fecal samples and performed deep sequencing on both highly purified viral fractions and total microbiota, in order to investigate phage and prophage-encoded ARGs. We show that ARGs are absent from the genomes of active, virion-forming phages (below 0.02% of viral contigs from viromes), but present in three prophages, representing 0.02% of the viral contigs identified in the microbial dataset. However, the corresponding phages were not detected in the viromes, and their genetic maps suggest they might be defective. Furthermore, our dataset allows for the first time a comprehensive view of the interplay between prophages and viral particles.

https://www.biorxiv.org/content/10.1101/2021.05.20.444921v1.abstract