College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China.
Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China.
Ecotoxicol Environ Saf. 2021 Oct 1;222:112552. doi: 10.1016/j.ecoenv.2021.112552. Epub 2021 Jul 26.
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.
大量的抗生素耐药基因（ARGs）已在人为环境或动物养殖场的噬菌体基因组中广泛检测到，然而，在饲料废水处理设施（WTF）压力下，噬菌体对抗生素耐药性的动态变化却知之甚少。在这里，采用宏基因组学方法来描述污水噬菌体组并鉴定抗生素耐药组。结果表明，Siphoviridae、Myoviridae 和 Podoviridae 噬菌体家族始终占主导地位。对细菌和噬菌体携带的 ARGs 进行分析表明，MLS 和四环素耐药基因的丰度始终最高，其他 ARG 类型也有固定的层次结构，这表明总体 ARGs 丰度分布没有明显变化。然而，在好氧环境中，特定地鉴定出了一个广泛核心的抗生素耐药组。编码核糖体保护蛋白的 ARGs 尤其倾向于被噬菌体选择，特别是 ARG 亚型 lsaE、tet44、tetM、tetP、macB、MdlB 和 rpoB2，这表明可能涉及更精细的机制，如专门转导和侧向转导。总之，这些结果表明，应该更加关注噬菌体对抗生素耐药性的动态贡献变化的监测，并且应该集中于使用控制核心 ARGs 的技术来管理携带 ARGs 的噬菌体，而不仅仅是噬菌体中 ARGs 的总体分布。
