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通过宏基因组组装和分类方法解析抗生素选择压力下抗生素抗性基因的迁移和细菌宿主。

Deciphering the mobility and bacterial hosts of antibiotic resistance genes under antibiotic selection pressure by metagenomic assembly and binning approaches.

机构信息

Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.

School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen 518055, China.

出版信息

Water Res. 2020 Nov 1;186:116318. doi: 10.1016/j.watres.2020.116318. Epub 2020 Aug 25.

Abstract

The presence of antibiotics can exert significant selection pressure on the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB). However, co-selection effects for ARGs, the mobility of ARGs and the identification of ARG hosts under high antibiotic selection pressures are poorly understood. Here, metagenomic assembly and binning approaches were used to comprehensively decipher the prevalence of ARGs and their potential mobility and hosts in activated sludge reactors treating antibiotic production wastewater. We found the abundance of different ARG types in antibiotic treatments varied greatly and certain antibiotic pressure promoted the co-selection for the non-corresponding types of ARGs. Antibiotic selection pressures significantly increased the abundance and proportions of ARGs mediated by plasmids (57.9%), which were more prevalent than those encoded in chromosomes (19.2%). The results indicated that plasmids and chromosomes had a tendency to carry different types of ARGs. Moreover, higher co-occurrence frequency of ARGs and MGEs revealed that antibiotics enhanced the mobility potential of ARGs mediated by both plasmids and integrative and conjugative elements. Among the 689 metagenome-assembled genomes (MAGs) with high estimated quality, 119 MAGs assigning to nine bacterial phyla were identified as the ARG hosts and 33 MAGs exhibited possible multi-resistance to antibiotics. Some ARG types tended to be carried by certain bacteria (e.g. bacitracin resistance genes carried by the family Burkholderiaceae) and thus showed a pronounced host-specific pattern. This study enhances the understanding of the mobility and hosts of ARGs and provides important insights into the risk assessment and management of antibiotic resistance.

摘要

抗生素的存在会对抗生素耐药基因 (ARGs) 和抗生素耐药菌 (ARB) 的出现和传播产生显著的选择压力。然而,在高抗生素选择压力下,ARGs 的共选择效应、ARGs 的可移动性以及 ARG 宿主的鉴定仍知之甚少。在这里,我们使用宏基因组组装和分箱方法来全面解析处理抗生素生产废水的活性污泥反应器中 ARGs 的流行情况及其潜在的可移动性和宿主。我们发现,抗生素处理中不同 ARG 类型的丰度差异很大,某些抗生素压力促进了非对应类型的 ARGs 的共选择。抗生素选择压力显著增加了质粒介导的 ARGs 的丰度和比例(57.9%),这比染色体编码的 ARGs 更为普遍。结果表明,质粒和染色体有携带不同类型 ARGs 的趋势。此外,ARGs 和 MGEs 的更高共现频率表明,抗生素增强了质粒和整合子转座子介导的 ARGs 的移动潜力。在具有高估计质量的 689 个宏基因组组装基因组 (MAG) 中,鉴定出 119 个 MAG 归属于 9 个细菌门,作为 ARG 宿主,33 个 MAG 表现出对多种抗生素的可能多抗性。一些 ARG 类型倾向于由某些细菌携带(例如,家族 Burkholderiaceae 携带的杆菌肽抗性基因),因此表现出明显的宿主特异性模式。本研究增强了对 ARGs 的移动性和宿主的理解,并为抗生素耐药性的风险评估和管理提供了重要的见解。

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