摘要

       污水处理厂（WWTPs）是各种抗生素耐药基因（ARGs）随后传播的源库。然而，对WWTPs中ARGs的活动和主机知之甚少。在本研究中，我们同时利用基因组学和转录组学的方法，全面揭示台湾三个传统污水处理厂活性污泥中精氨酸的多样性、丰度、表达及宿主。根据深度测序数据和定制的ARG数据库，从3个亚基因组中共鉴定出360个与24类抗生素相关的ARG，其丰度范围为7.06    10-1-1.20     10-4拷贝。差异覆盖binning分析表明，22个以上的细菌门是所鉴定ARGs的假定宿主。令人惊讶的是，分枝杆菌属和伯克霍尔德菌科被发现具有14和50个arg的多重耐药。亚转录组分析显示65.8%的ARGs被表达，表明ARGs不仅存在于AS中，而且在AS中具有转录活性。值得注意的是，110个已鉴定的精氨酸被注释为与质粒相关的，并且显示出与仅在细菌染色体中发现的精氨酸相比，转录表达的可能性增加了近两倍。进一步分析表明，氨基糖苷类、磺胺类和四环素类耐药基因的转录丰度主要由质粒携带的ARGs决定。我们的方法使我们能够将ARGs与它们的转录本和遗传背景特别地联系起来，从而全面了解ARGs在AS中的流行、表达和宿主。总的来说，本研究的结果增进了我们对污水处理厂ARGs分布和传播的了解，有利于ARB和ARGs的环境风险评估和管理。

        Wastewater treatment plants (WWTPs) are a source and reservoir for subsequent spread of various antibiotic resistance genes (ARGs). However, little is known about the activity and hosts of ARGs in WWTPs. Here, we utilized both metagenomic and metatranscriptomic approaches to comprehensively reveal the diversity, abundance, expression and hosts of ARGs in activated sludge (AS) from three conventional WWTPs in Taiwan. Based on deep sequencing data and a custom-made ARG database, a total of 360 ARGs associated with 24 classes of antibiotics were identified from the three AS metagenomes, with an abundance range of 7.06 × 10^-1-1.20 × 10^-4 copies of ARG/copy of 16S rRNA gene. Differential coverage binning analysis revealed that >22 bacterial phyla were the putative hosts of the identified ARGs. Surprisingly, genus Mycobacterium and family Burkholderiaceae were observed as multi-drug resistant harboring 14 and 50 ARGs. Metatranscriptome analysis showed 65.8% of the identified ARGs were being expressed, highlighting that ARGs were not only present, but also transcriptionally active in AS. Remarkably, 110 identified ARGs were annotated as plasmid-associated and displayed a close to two-fold increased likelihood of being transcriptionally expressed compared to those ARGs found exclusively within bacterial chromosomes. Further analysis showed the transcript abundance of aminoglycoside, sulfonamide, and tetracycline resistance genes was mainly contributed by plasmid-borne ARGs. Our approach allowed us to specifically link ARGs to their transcripts and genetic context, providing a comprehensive insight into the prevalence, expression and hosts of ARGs in AS. Overall, results of this study enhance our understanding of the distribution and dissemination of ARGs in WWTPs, which benefits environmental risk assessment and management of ARB and ARGs.

         https://linkinghub.elsevier.com/retrieve/pii/S0160-4120(19)30760-3