Huge number of antibiotic resistance genes (ARGs) have been widely detected in phage genomes from anthropogenic environment or animal farms, whereas little is known about the dynamic changes of phage contribution to resistance under a feedlot wastewater treatment facility (WTF) pressure. Here, a metagenomics method was used to characterize the sewage phageome and identifies the antibiotic resistome. The results showed that the phage families of Siphoviridae, Myoviridae, and Podoviridae were always the most dominant. Analysis of ARGs carried by bacterial and phages showed that MLS and tetracycline resistance genes always had the highest abundances and the other ARG types also have a fixed hierarchy, showing that there is no significant change in overall ARGs abundance distribution. However, an extensively cored antibiotic resistome were specifically identified in aerobic environment. ARGs encoding ribosomal protection proteins, especially for the ARG subtypes lsaE, tet44, tetM, tetP, macB, MdlB and rpoB2, were more inclined to be selected by phages, suggesting that a more refined mechanism, such as specialized transduction and lateral transduction, was probably involved. In all, these results suggest that monitoring of dynamic changes of phage contribution to resistance should be given more attention and ARGs-carrying phage management should focus on using technologies for controlling cored ARGs rather than only the overall distribution of ARGs in phages.

在来自人为环境或动物农场的噬菌体基因组中广泛检测到大量抗生素抗性基因 (ARG)，而在饲养场废水处理设施 (WTF) 压力下，噬菌体对抗性的贡献的动态变化知之甚少。在这里，宏基因组学方法用于表征污水噬菌体并鉴定抗生素抗性组。结果表明，丝状病毒科、肌状病毒科和豆状病毒科的噬菌体科一直是最占优势的。对细菌和噬菌体携带的ARGs的分析表明，MLS和四环素抗性基因的丰度一直最高，其他ARG类型也有固定的等级，表明整体ARGs丰度分布没有显着变化。然而，在有氧环境中专门鉴定了一个广泛核心的抗生素抗性组。编码核糖体保护蛋白的 ARG，尤其是 ARG 亚型lsaE、tet44、tetM、tetP、macB、MdlB和rpoB2，更倾向于被噬菌体选择，这表明可能涉及更精细的机制，例如专门的转导和横向转导。总之，这些结果表明，应更多关注噬菌体对耐药性贡献的动态变化的监测，携带 ARG 的噬菌体管理应侧重于使用控制核心 ARG 的技术，而不仅仅是 ARG 在噬菌体中的整体分布。