Metagenomic insights into the abundance and composition of resistance genes in aquatic environments: Influence of stratification and geography

Baker-Austin, 2006, Co-selection of antibiotic and metal resistance, Trends Microbiol., 14, 176, 10.1016/j.tim.2006.02.006 Bao, 2016, Metagenomic profiles of antibiotic resistance genes in paddy soils from South China, FEMS Microbiol. Ecol., 92 Bastian, 2009, Gephi: an open source software for exploring and manipulating networks, ICWSM, 8, 361, 10.1609/icwsm.v3i1.13937 Bengtsson-Palme, 2014, Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India, Front. Microbiol., 5, e648, 10.3389/fmicb.2014.00648 Bhardwaj, 2018, Persistent organic pollutants in biotic and abiotic components of Antarctic pristine environment, Earth Syst. Environ., 2, 35, 10.1007/s41748-017-0032-8 Buchfink, 2014, Fast and sensitive protein alignment using DIAMOND, Nat. Methods, 12, 59, 10.1038/nmeth.3176 Chauhan, 2017, Identification of arsenic resistance genes from marine sediment metagenome, Indian J. Microbiol., 57, 299, 10.1007/s12088-017-0658-0 Chen, 2011, VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R, BMC bioinformatics, 12, 5 Chen, 2013, Metagenomic profiles of antibiotic resistance genes (ARGs) between human impacted estuary and deep ocean sediments, Environ. Sci. Technol., 47, 12753, 10.1021/es403818e Czekalski, 2014, Wastewater as a point source of antibiotic-resistance genes in the sediment of a freshwater lake, ISME J, 8, 1381, 10.1038/ismej.2014.8 Czekalski, 2015, Does human activity impact the natural antibiotic resistance background? Abundance of antibiotic resistance genes in 21 Swiss lakes, Environ. Int., 81, 45, 10.1016/j.envint.2015.04.005 Di Cesare, 2016, Co-selection of antibiotic and heavy metal resistance in freshwater bacteria, J. Limnol., 75, 59, 10.4081/jlimnol.2016.1198 Duan, 2009, Two-decade reconstruction of algal blooms in China's Lake Taihu, Environ. Sci. Technol., 43, 3522, 10.1021/es8031852 Edwardson, 2017, Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA, ISME J, 11, 2195, 10.1038/ismej.2017.80 Gillings, 2018, DNA as a pollutant: the clinical class 1 integron, Curr. Pollut. Rep., 4, 49, 10.1007/s40726-018-0076-x Guo, 2018, The antibiotic resistome of free-living and particle-attached bacteria under a reservoir cyanobacterial bloom, Environ. Int., 117, 107, 10.1016/j.envint.2018.04.045 Gupta, 2018, Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant, J. Microbiol., 56, 408, 10.1007/s12275-018-8195-z Hao, 2018, Data-mining of antibiotic resistance genes provides insight into the community structure of ocean microbiome, bioRxiv Harrell Hatosy, 2015, The ocean as a global reservoir of antibiotic resistance genes, Appl. Environ. Microbiol., 81, 7593, 10.1128/AEM.00736-15 Hobman, 2015, Bacterial antimicrobial metal ion resistance, J. Med. Microbiol., 64, 471, 10.1099/jmm.0.023036-0 Hu, 2013, Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota, Nat. Commun., 4, 10.1038/ncomms3151 Huang, 2019, How successful are the restoration efforts of China's lakes and reservoirs?, Environ. Int., 123, 96, 10.1016/j.envint.2018.11.048 Imran, 2019, Co-selection of multi-antibiotic resistance in bacterial pathogens in metal and microplastic contaminated environments: an emerging health threat, Chemosphere, 215, 846, 10.1016/j.chemosphere.2018.10.114 Jackson, 2003, Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase, BMC Evol. Biol., 3 Ju, 2015, Bacterial assembly and temporal dynamics in activated sludge of a full-scale municipal wastewater treatment plant, ISME J, 9, 683, 10.1038/ismej.2014.162 Ju, 2016, Antibiotic resistance genes and human bacterial pathogens: co-occurrence, removal, and enrichment in municipal sewage sludge digesters, Water Res., 91, 1, 10.1016/j.watres.2015.11.071 Kolpin, 2002, Pharmaceuticals, hormones, and other organic wastewater contaminants in US streams, 1999− 2000: A national reconnaissance, Environ. Sci. Technol., 36, 1202, 10.1021/es011055j Kristiansson, 2011, Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements, PLoS One, 6, 10.1371/journal.pone.0017038 Larsson, 2018, Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance, Environ. Int., 117, 132, 10.1016/j.envint.2018.04.041 Li, 2015, Exploring antibiotic resistance genes and metal resistance genes in plasmid metagenomes from wastewater treatment plants, Front. Microbiol., 6, 1025, 10.3389/fmicb.2015.01025 Li, 2015, Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes, ISME J, 9, 2490, 10.1038/ismej.2015.59 Li, 2017, Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection, ISME J, 11, 65, 10.1038/ismej.2016.155 Li, 2018, Tracking antibiotic resistance gene pollution from different sources using machine-learning classification, Microbiome, 6, 10.1186/s40168-018-0480-x Liu, 2018, Large-scale biogeographical patterns of bacterial antibiotic resistome in the waterbodies of China, Environ. Int., 117, 292, 10.1016/j.envint.2018.05.023 Luo, 2017, Antibiotic resistance genes and correlations with microbial community and metal resistance genes in full-scale biogas reactors as revealed by metagenomic analysis, Environ. Sci. Technol., 51, 4069, 10.1021/acs.est.6b05100 Marti, 2014, The role of aquatic ecosystems as reservoirs of antibiotic resistance, Trends Microbiol., 22, 36, 10.1016/j.tim.2013.11.001 Nesme, 2014, Large-scale metagenomic-based study of antibiotic resistance in the environment, Curr. Biol., 24, 1096, 10.1016/j.cub.2014.03.036 Oksanen, 2013 Pal, 2015, Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential, BMC Genomics, 16, 10.1186/s12864-015-2153-5 Pal, 2016, The structure and diversity of human, animal and environmental resistomes, Microbiome, 4, 54, 10.1186/s40168-016-0199-5 Peng, 2015, The nutrient, total petroleum hydrocarbon and heavy metal contents in the seawater of Bohai Bay, China: temporal–spatial variations, sources, pollution statuses, and ecological risks, Mar. Pollut. Bull., 95, 445, 10.1016/j.marpolbul.2015.03.032 Peura, 2012, Distinct and diverse anaerobic bacterial communities in boreal lakes dominated by candidate division OD1, ISME J, 6, 1640, 10.1038/ismej.2012.21 Qiao, 2018, Review of antibiotic resistance in China and its environment, Environ. Int., 110, 160, 10.1016/j.envint.2017.10.016 Roosa, 2014, Bacterial metal resistance genes and metal bioavailability in contaminated sediments, Environ. Pollut., 189, 143, 10.1016/j.envpol.2014.02.031 Saarenheimo, 2016, Bacterial community response to changes in a tri-trophic cascade during a whole-lake fish manipulation, Ecology, 97, 684 Seiler, 2012, Heavy metal driven co-selection of antibiotic resistance in soil and water bodies impacted by agriculture and aquaculture, Front. Microbiol., 3, 399, 10.3389/fmicb.2012.00399 Stepanauskas, 2006, Coselection for microbial resistance to metals and antibiotics in freshwater microcosms, Environ. Microbiol., 8, 1510, 10.1111/j.1462-2920.2006.01091.x Wright, 2012, Antibiotic resistance is ancient: implications for drug discovery, Trends Microbiol., 20, 157, 10.1016/j.tim.2012.01.002 Yang, 2017, Antibiotic resistance genes in lakes from middle and lower reaches of the Yangtze River, China: effect of land use and sediment characteristics, Chemosphere, 178, 19, 10.1016/j.chemosphere.2017.03.041 Yang, 2017, Antibiotic resistance genes in surface water of eutrophic urban lakes are related to heavy metals, antibiotics, lake morphology and anthropic impact, Ecotoxicology, 26, 831, 10.1007/s10646-017-1814-3 Yang, 2018, Antibiotics and antibiotic resistance genes in global lakes: a review and meta-analysis, Environ. Int., 116, 60, 10.1016/j.envint.2018.04.011 Yang, 2019, Plastics in the marine environment are reservoirs for antibiotic and metal resistance genes, Environ. Int., 123, 79, 10.1016/j.envint.2018.11.061 Yang, 2019, Bacterial community and climate change implication affected the diversity and abundance of antibiotic resistance genes in wetlands on the Qinghai-Tibetan Plateau, J. Hazard. Mater., 361, 283, 10.1016/j.jhazmat.2018.09.002 Yin, 2018, ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes, Bioinformatics, 34, 2263, 10.1093/bioinformatics/bty053 Zeng, 2019, Metagenomic insights into the distribution of antibiotic resistome between the gut-associated environments and the pristine environments, Environ. Int., 126, 346, 10.1016/j.envint.2019.02.052 Zhang, 2015, Vertical distribution of bacterial community diversity and water quality during the reservoir thermal stratification, Int. J. Environ. Res. Public Health, 12, 6933, 10.3390/ijerph120606933 Zhang, 2015, Spatial and seasonal characteristics of dissolved heavy metals in the east and west Guangdong coastal waters, South China, Mar. Pollut. Bull., 95, 419, 10.1016/j.marpolbul.2015.03.035 Zhang, 2018, Occurrence of intracellular and extracellular antibiotic resistance genes in coastal areas of Bohai Bay (China) and the factors affecting them, Environ. Pollut., 236, 126, 10.1016/j.envpol.2018.01.033 Zheng, 2017, High-throughput profiling and analysis of antibiotic resistance genes in East Tiaoxi River, China, Environ. Pollut., 230, 648, 10.1016/j.envpol.2017.07.025 Zhou, 2017, Antibiotic resistance genes in an urban river as impacted by bacterial community and physicochemical parameters, Environ. Sci. Pollut. Res., 24, 23753, 10.1007/s11356-017-0032-0 Zhu, 2017, Continental-scale pollution of estuaries with antibiotic resistance genes, Nat. Microbiol., 2, 10.1038/nmicrobiol.2016.270