Ilyas, M. et al. Environmental and health impacts of industrial wastewater effluents in Pakistan: A review. Rev. Environ. Health 34, 171–186 (2019).
Roy, M. A. et al. A Metagenomic approach to evaluating surface water quality in Haiti. Int. J. Environ. Res. Public Health 15, 2211 (2018).
Liu, M. & Lu, J. Support vector machine-an alternative to artificial neuron network for water quality forecasting in an agricultural nonpoint source polluted river?. Environ. Sci. Pollut. Res. 21, 11036–11053 (2014).
Yao, H., Qian, X., Yin, H., Gao, H. & Wang, Y. Regional risk assessment for point source pollution based on a water quality model of the Taipu River, China. Risk Anal. 35, 265–277 (2015).
Dey, S., Bano, F. & Malik, A. Pharmaceuticals and personal care product (PPCP) contamination—a global discharge inventory. in Pharmaceuticals and Personal Care Products: Waste Management and Treatment Technology 1–26 (Elsevier, 2019). doi:doi.org/10.1016/B978-0-12-816189-0.00001-9.
Richardson, S. D. & Ternes, T. A. Water analysis: Emerging contaminants and current issues. Anal. Chem. 86, 2813–2848 (2014).
Felis, E. et al. Antimicrobial pharmaceuticals in the aquatic environment—occurrence and environmental implications. Eur. J. Pharmacol. 866, 172813 (2020).
Nassiri Koopaei, N. & Abdollahi, M. Health risks associated with the pharmaceuticals in wastewater. Daru 25, 9 (2017).
Gillings, M. R. et al. Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. ISME J. 9, 1269–1279 (2015).
Baquero, F., Martínez, J.-L. & Cantón, R. Antibiotics and antibiotic resistance in water environments. Curr. Opin. Biotechnol. 19, 260–265 (2008).
Martínez, J. L. Antibiotics and antibiotic resistance genes in natural environments. Science 321, 365–367 (2008).
Grenni, P., Ancona, V. & Barra Caracciolo, A. Ecological effects of antibiotics on natural ecosystems: A review. Microchem. J. 136, 25–39 (2018).
Kraemer, S. A., Ramachandran, A. & Perron, G. G. Antibiotic pollution in the environment: From microbial ecology to public policy. Microorganisms 7, 180 (2019).
Subirats, J. et al. Emerging contaminants and nutrients synergistically affect the spread of class 1 integron-integrase (intI1) and sul1 genes within stable streambed bacterial communities. Water Res. 138, 77–85 (2018).
Partridge, S. R., Kwong, S. M., Firth, N. & Jensen, S. O. Mobile genetic elements associated with antimicrobial resistance. Clin. Microbiol. Rev. doi.org/10.1128/CMR.00088-17 (2018).
Wein, T., Hülter, N. F., Mizrahi, I. & Dagan, T. Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance. Nat. Commun. 10, 2595 (2019).
Walker, A. Welcome to the plasmidome. Nat. Rev. Microbiol. 10, 379 (2012).
Norman, A. et al. An improved method for including upper size range plasmids in metamobilomes. PLoS ONE 9, e104405 (2014).
Aminov, R. I. & Mackie, R. I. Evolution and ecology of antibiotic resistance genes. FEMS Microbiol. Lett. 271, 147–161 (2007).
Rahman, M. H., Nonaka, L., Tago, R. & Suzuki, S. Occurrence of two genotypes of tetracycline (TC) resistance gene tet(M) in the TC-resistant bacteria in marine sediments of Japan. Environ. Sci. Technol. 42, 5055–5061 (2008).
Unc, A. & Goss, M. J. Transport of bacteria from manure and protection of water resources. Appl. Soil Ecol. 25, 1–18 (2004).
Alawi, M., Torrijos, T. V. & Walsh, F. Plasmid-mediated antimicrobial resistance in drinking water. Environ. Adv. doi.org/10.1016/j.envadv.2022.100191 (2022).
Kümmerer, K. Antibiotics in the aquatic environment–a review–part I. Chemosphere 75, 417–434 (2009).
Kümmerer, K. Antibiotics in the aquatic environment—A review—Part II. Chemosphere doi.org/10.1016/j.chemosphere.2008.12.006 (2009).
Cardoso, O., Porcher, J.-M. & Sanchez, W. Factory-discharged pharmaceuticals could be a relevant source of aquatic environment contamination: Review of evidence and need for knowledge. Chemosphere 115, 20–30 (2014).
He, Y. et al. Antibiotic resistance genes from livestock waste: occurrence, dissemination, and treatment. npj Clean Water 3, 4 (2020).
Topp, E., Renaud, J., Sumarah, M. & Sabourin, L. Reduced persistence of the macrolide antibiotics erythromycin, clarithromycin and azithromycin in agricultural soil following several years of exposure in the field. Sci. Total Environ. doi.org/10.1016/j.scitotenv.2016.03.210 (2016).
Segura, P. A., François, M., Gagnon, C. & Sauvé, S. Review of the occurrence of anti-infectives in contaminated wastewaters and natural and drinking waters. Environ. Health Perspect. 117, 675–684 (2009).
Benotti, M. J. et al. Pharmaceuticals and endocrine disrupting compounds in U.S. drinking water. Environ. Sci. Technol. 43, 597–603 (2009).
Ben, Y. et al. Human health risk assessment of antibiotic resistance associated with antibiotic residues in the environment: A review. Environ. Res. 169, 483–493 (2018).
Vaz-Moreira, I., Nunes, O. C. & Manaia, C. M. Bacterial diversity and antibiotic resistance in water habitats: Searching the links with the human microbiome. FEMS Microbiol. Rev. 38, 761–778 (2014).
Feng, B.-W. et al. Bacterial diversity of water and sediment in the Changjiang estuary and coastal area of the East China Sea. FEMS Microbiol. Ecol. 70, 80–92 (2009).
Qin, Y. et al. Bacterial abundance and diversity in pond water supplied with different feeds. Sci. Rep. doi.org/10.1038/srep35232 (2016).
Forsberg, K. J. et al. Bacterial phylogeny structures soil resistomes across habitats. Nature doi.org/10.1038/nature13377 (2014).
Stanish, L. F. et al. Factors influencing bacterial diversity and community composition in municipal drinking waters in the Ohio River Basin, USA. PLoS ONE 11, e0157966 (2016).
Medeiros, J. D. et al. Comparative metagenome of a stream impacted by the urbanization phenomenon. Braz. J. Microbiol. doi.org/10.1016/j.bjm.2016.06.011 (2016).
Paul, Michael J. & Meyer, Judy L. Streams in the urban landscape. In Urban Ecology (eds Marzluff, John M. et al.) (Springer, 2008).
Nogueira, I. S., Nabout, J. C., Oliveira, J. E. & Silva, K. D. Diversidade (alfa, beta e gama) da comunidade fitoplanctônica de quatro lagos artificiais urbanos do município de Goiânia, GO. Hoehnea 35, 219–233 (2008).
Tuomisto, H. A consistent terminology for quantifying species diversity? Yes, it does exist. Oecologia 164, 853–860 (2010).
Cabral, L. et al. Anthropogenic impact on mangrove sediments triggers differential responses in the heavy metals and antibiotic resistomes of microbial communities. Environ. Pollut. doi.org/10.1016/j.envpol.2016.05.078 (2016).
Conejo, M. C., García, I., Martínez-Martínez, L., Picabea, L. & Pascual, A. Zinc eluted from siliconized latex urinary catheters decreases OprD expression, causing carbapenem resistance in Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 47, 2313–2315 (2003).
Perron, K. et al. CzcR-CzcS, a two-component system involved in heavy metal and carbapenem resistance in Pseudomonas aeruginosa. J. Biol. Chem. 279, 8761–8768 (2004).
Guo, X., Li, J., Yang, F., Yang, J. & Yin, D. Prevalence of sulfonamide and tetracycline resistance genes in drinking water treatment plants in the Yangtze River Delta, China. Sci. Total Environ. doi.org/10.1016/j.scitotenv.2014.06.035 (2014).
Furukawa, T., Jikumaru, A., Ueno, T. & Sei, K. Inactivation effect of antibiotic-resistant gene using chlorine disinfection. Water (Switzerland) doi.org/10.3390/w9070547 (2017).
Khan, H., Miao, X., Liu, M., Ahmad, S. & Bai, X. Behavior of last resort antibiotic resistance genes (mcr-1 and blaNDM-1) in a drinking water supply system and their possible acquisition by the mouse gut flora. Environ. Pollut. doi.org/10.1016/j.envpol.2019.113818 (2020).
Li, A.-D., Li, L.-G. & Zhang, T. Exploring antibiotic resistance genes and metal resistance genes in plasmid metagenomes from wastewater treatment plants. Front. Microbiol. 6, 1025 (2015).
Nesme, J. et al. Large-scale metagenomic-based study of antibiotic resistance in the environment. Curr. Biol. doi.org/10.1016/j.cub.2014.03.036 (2014).
Taggar, G., Attiq Rehman, M., Boerlin, P. & Diarra, M. Molecular epidemiology of carbapenemases in enterobacteriales from humans, animals, food and the environment. Antibiotics 9, 693 (2020).
Liu, Y.-Y. et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: A microbiological and molecular biological study. Lancet. Infect. Dis. 16, 161–168 (2016).
Fernandes, M. R. et al. Silent dissemination of colistin-resistant Escherichia coli in South America could contribute to the global spread of the mcr-1 gene. Eurosurveillance doi.org/10.2807/1560-7917.ES.2016.21.17.30214 (2016).
Kempf, I., Jouy, E. & Chauvin, C. Colistin use and colistin resistance in bacteria from animals. Int. J. Antimicrob. Agents doi.org/10.1016/j.ijantimicag.2016.09.016 (2016).
Catry, B. et al. Use of colistin-containing products within the European Union and European Economic Area (EU/EEA): Development of resistance in animals and possible impact on human and animal health. Int. J. Antimicrob. Agents 46, 297–306 (2015).
Rossolini, G. M. et al. Metallo-β-lactamase producers in environmental microbiota: New molecular class B enzyme in Janthinobacterium lividum. Antimicrob. Agents Chemother. doi.org/10.1128/AAC.45.3.837-844.2001 (2001).
Marathe, N. P. et al. Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics. Water Res. doi.org/10.1016/j.watres.2017.07.060 (2017).
Piedra-Carrasco, N. et al. Carbapenemase-producing enterobacteriaceae recovered from a Spanish river ecosystem. PLoS ONE doi.org/10.1371/journal.pone.0175246 (2017).
Islam, M. A. et al. Environmental spread of New Delhi metallo-β- lactamase-1-producing multidrug-resistant bacteria in Dhaka, Bangladesh. Appl. Environ. Microbiol. doi.org/10.1128/AEM.00793-17 (2014).
Mombini, S., Rezatofighi, S. E., Kiyani, L. & Motamedi, H. Diversity and metallo-β-lactamase-producing genes in Pseudomonas aeruginosa strains isolated from filters of household water treatment systems. J. Environ. Manage. doi.org/10.1016/j.jenvman.2018.10.068 (2019).
Ashbolt, N. J. et al. Human health risk assessment (HHRA) for environmental development and transfer of antibiotic resistance. Environ. Health Perspect. doi.org/10.1289/ehp.1206316 (2013).
Seiler, C. & Berendonk, T. U. Heavy metal driven co-selection of antibiotic resistance in soil and water bodies impacted by agriculture and aquaculture. Front. Microbiol. 3, 399 (2012).
Zhang, Y., Gu, A. Z., He, M., Li, D. & Chen, J. Subinhibitory concentrations of disinfectants promote the horizontal transfer of multidrug resistance genes within and across genera. Environ. Sci. Technol. 51, 570–580 (2017).
Li, D., Zeng, S., He, M. & Gu, A. Z. Water disinfection byproducts induce antibiotic resistance-role of environmental pollutants in resistance phenomena. Environ. Sci. Technol. 50, 3193–3201 (2016).
Ding, C. et al. Enhanced uptake of antibiotic resistance genes in the presence of nanoalumina. Nanotoxicology 10, 1051–1060 (2016).
Fish, K. E., Reeves-McLaren, N., Husband, S. & Boxall, J. Author Correction: Uncharted waters: The unintended impacts of residual chlorine on water quality and biofilms. NPJ Biofilms Microbiomes 8, 55 (2022).
Bergeron, S., Boopathy, R., Nathaniel, R., Corbin, A. & LaFleur, G. Presence of antibiotic resistant bacteria and antibiotic resistance genes in raw source water and treated drinking water. Int. Biodeterior. Biodegrad. 102, 370–374 (2015).
Xi, C. et al. Prevalence of antibiotic resistance in drinking water treatment and distribution systems. Appl. Environ. Microbiol. 75, 5714–5718 (2009).
Colomer-Lluch, M., Jofre, J. & Muniesa, M. Antibiotic resistance genes in the bacteriophage DNA fraction of environmental samples. PLoS ONE 6, e17549 (2011).
Britto, A. L., Maiello, A. & Quintslr, S. Water supply system in the Rio de Janeiro Metropolitan Region: Open issues, contradictions, and challenges for water access in an emerging megacity. J. Hydrol. 573, 1007–1020 (2019).
Bacha, L. et al. Risk of Collapse in water quality in the Guandu River (Rio de Janeiro, Brazil). Microb. Ecol. 84, 314–324 (2022).
U. S. Environmental Protection Agency. Method 1694 : Pharmaceuticals and Personal Care Products in Water, Soil, Sediment, and Biosolids by HPLC/MS/MS. EPA Method (2007) doi:doi.org/10.1002/etc.3451.
Monteiro, M. et al. Development and validation of liquid chromatography-tandem mass spectrometry methods for determination of beta-lactams, macrolides, fluoroquinolones, sulfonamides and tetracyclines in surface and drinking water from Rio de Janeiro, Brazil. J. Braz. Chem. Soc. doi.org/10.21577/0103-5053.20170203 (2017).
Communities European. Commission Decision of 12 August 2002 implementing Council Directive 96/23/EC concerning the performance of analytical methods and the interpretation of results. 8–36 (2002).
Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K. & Schloss, P. D. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl. Environ. Microbiol. 79, 5112–5120 (2013).
Andrews, S. FastQC: A quality control tool for high throughput sequence data. Babraham Bioinformatics www.bioinformatics.babraham.ac.uk/projects/ (2010) doi:citeulike-article-id:11583827.
Schmieder, R. & Edwards, R. Insights into antibiotic resistance through metagenomic approaches. Future Microbiol. 7, 73–89 (2012).
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336 (2010).
Dhariwal, A. et al. MicrobiomeAnalyst: A web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Res. 45, W180–W188 (2017).
Chong, J., Liu, P., Zhou, G. & Xia, J. Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data. Nat. Protoc. doi.org/10.1038/s41596-019-0264-1 (2020).
Schmieder, R. & Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863–864 (2011).
Bankevich, A. et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).
Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: A new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017).
Keegan, K. P., Glass, E. M. & Meyer, F. MG-RAST, a metagenomics service for analysis of microbial community structure and function. Methods Mol. Biol. 1399, 207–233 (2016).
Overbeek, R. et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. doi.org/10.1093/nar/gki866 (2005).
Dinsdale, E. A. et al. Functional metagenomic profiling of nine biomes. Nature doi.org/10.1038/nature06810 (2008).
Jia, B. et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 45, D566–D573 (2017).
Alcock, B. P. et al. CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. doi.org/10.1093/nar/gkz935 (2020).
Buchfink, B., Reuter, K. & Drost, H.-G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368 (2021).
Dias, M. F. et al. Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings. Water Res. 174, 115630 (2020).
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