Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems
Congmin Zhu, Linwei Wu, Daliang Ning, Renmao Tian, Shu-Hong Gao, Bing Zhang, Jianshu Zhao, Ya Zhang, Naijia Xiao, Yajiao Wang, Mathew R. Brown, Qichao Tu, Qichao Tu, Dany Acevedo, Miriam Agullo-Barcelo, Juliana Calabria de Araujo, Érika Ferreira de Abreu Mac Conell, Kevin Boehnke, Philip Bond, Charles B. Bott, Patricia Bovio-Winkler, Rebecca K. Brewster, Faizal Bux, Angela Cabezas, Léa Cabrol, Si Chen, Claudia Etchebehere, Amanda Ford, Janeth Sanabria Gómez, Pedro J. J. Alvarez, April Z. Gu, Moshe Habagil, Lauren Hale, Marc Harmon, Harald Horn, Zhiqiang Hu, David R. Johnson, Deborah Garbani Marcantini, Alexander Keucken, Sheena Kumari, Cintia Dutra Leal, Zarraz MP Lee, Yong Li, Zhenxin Li, Mengyan Li, Yu Liu, Leda C. Mendonça-Hagler, Francisca Gleire Rodriguez de Menezes, Arthur J. Meyers, Andrew Palmer, Prathap Parameswaran, Valeria Reginatto, Francis L. de los Reyes, Simona Rossetti, Jatinder Sidhu, Kylie Smith, Oscarina Viana de Sousa, Kyle Stephens, Chenxiang Sun, Nicholas B. Tooker, Joy D. Van Nostrand, Steve Wakelin, Bei Wang, Joseph E. Weaver, Stephanie West, Sung-Geun Woo, Jer-Horng Wu, Liyou Wu, Liyou Wu, Chuanwu Xi, Tao Yan, Min Yang, Michelle Young, Chiqian Zhang, Qian Zhang, Wen Zhang, Wanlin Zheng, Hongde Zhou, Weiqin Zhuang, Feng Ju, George F. Wells, Jianhua Guo, Zhili He, Per H. Nielsen, Aijie Wang, Yu Zhang, Ting Chen, Qiang He, Craig S. Criddle, Michael Wagner, James M. Tiedje, Thomas P. Curtis, Xianghua Wen, Yunfeng Yang, Lisa Alvarez-Cohen, David A. Stahl, Pedro J. J. Alvarez, Bruce E. Rittmann, Jizhong Zhou
Abstract
Antibiotic resistance poses a significant threat to human health, and wastewater treatment plants (WWTPs) are important reservoirs of antibiotic resistance genes (ARGs). Here, we analyze the antibiotic resistomes of 226 activated sludge samples from 142 WWTPs across six continents, using a consistent pipeline for sample collection, DNA sequencing and analysis. We find that ARGs are diverse and similarly abundant, with a core set of 20 ARGs present in all WWTPs. ARG composition differs across continents and is distinct from that of the human gut and the oceans. ARG composition strongly correlates with bacterial taxonomic composition, with Chloroflexi, Acidobacteria and Deltaproteobacteria being the major carriers. ARG abundance positively correlates with the presence of mobile genetic elements, and 57% of the 1112 recovered high-quality genomes possess putatively mobile ARGs. Resistome variations appear to be driven by a complex combination of stochastic processes and deterministic abiotic factors. Wastewater treatment plants are important reservoirs of antibiotic resistance genes (ARGs). Here, the authors analyze ARGs in a global collection of samples from wastewater treatment plants across six continents, providing insights into biotic and abiotic mechanisms that appear to control ARG diversity and distribution.