{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,26]],"date-time":"2026-10-26T20:00:48Z","timestamp":1793044848826,"version":"4.5.0"},"reference-count":104,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,2,26]],"date-time":"2025-02-26T00:00:00Z","timestamp":1740528000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004543","name":"China Scholarship Council","doi-asserted-by":"publisher","award":["202006050016"],"award-info":[{"award-number":["202006050016"]}],"id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005156","name":"Alexander von Humboldt Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005156","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","award":["NNF22OC0071609"],"award-info":[{"award-number":["NNF22OC0071609"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>The introduction of antibiotic-resistant bacteria into riverine systems through the discharge of wastewater treatment plant (WWTP) effluent and agricultural waste poses significant health risks. Even when not pathogenic, these bacteria can act as reservoirs for antibiotic resistance genes (ARGs), transferring them to pathogens that infect humans and animals. In this study, we used fluorescence <jats:italic>in situ<\/jats:italic> hybridization, qPCR, and metagenomics to investigate how anthropogenic activities affect microbial abundance and the resistome along the Holtemme River, a small river in Germany, from near-pristine to human-impacted sites. Our results showed higher bacterial abundance, a greater absolute and relative abundance of ARGs, and a more diverse ARG profile at the impacted sites. Overall, the ARG profiles at these sites reflected antibiotic usage in Germany, with genes conferring resistance to drug classes such as beta-lactams, aminoglycosides, folate biosynthesis inhibitors, and tetracyclines. There were also variations in the ARG profiles of the impacted sites. Notably, there was a high abundance of the oxacillin resistance gene <jats:italic>OXA-4<\/jats:italic> at the downstream site in the river. In the metagenome assembly, this gene was associated with a contig homologous to small plasmids previously identified in members of the <jats:italic>Thiotrichaceae<\/jats:italic>. The likely in-situ host of the putative plasmid was a close relative of <jats:italic>Thiolinea<\/jats:italic> (also known as <jats:italic>Thiothrix<\/jats:italic>) <jats:italic>eikelboomii<\/jats:italic>, a prominent member of WWTP microbiomes worldwide. Our results show that the effluent from WWTPs can introduce bacteria into the environment that act as shuttle systems for clinically relevant ARG.<\/jats:p>","DOI":"10.3389\/fmicb.2025.1516033","type":"journal-article","created":{"date-parts":[[2025,2,26]],"date-time":"2025-02-26T07:22:14Z","timestamp":1740554534000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Riverine antibiotic resistome along an anthropogenic gradient"],"prefix":"10.3389","volume":"16","author":[{"given":"Gangan","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Haenelt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felipe Borim","family":"Corr\u00eaa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ulisses Nunes","family":"da Rocha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florin","family":"Musat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junya","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jochen A.","family":"M\u00fcller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niculina","family":"Musat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,2,26]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1016\/j.scitotenv.2017.10.322","article-title":"Metagenomic analysis of the bacterial communities and their functional profiles in water and sediments of the Apies River, South Africa, as a function of land use","author":"Abia","year":"2018","journal-title":"Sci. Total Environ."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"D517","DOI":"10.1093\/nar\/gkz935","article-title":"CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database","volume":"48","author":"Alcock","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref3","first-page":"1","article-title":"CONCOCT: Clustering contigs on coverage and composition","author":"Alneberg","year":"2013","journal-title":"arXiv Prepr"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"2016","DOI":"10.1080\/10643389.2019.1692611","article-title":"Understanding human health risks caused by antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG) in water environments: current knowledge and questions to be answered","volume":"50","author":"Amarasiri","year":"2020","journal-title":"Crit. Rev. Environ. Sci. Technol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"e0291742","DOI":"10.1371\/journal.pone.0291742","article-title":"Quantitative detection and reduction of potentially pathogenic bacterial groups of Aeromonas, Arcobacter, Klebsiella pneumoniae species complex, and Mycobacterium in wastewater treatment facilities","volume":"18","author":"Aoki","year":"2023","journal-title":"PLoS One"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"129","DOI":"10.4103\/ijmr.IJMR","article-title":"Efflux pump inhibitors for bacterial pathogens: from bench to bedside","volume":"149","author":"Atin","year":"2019","journal-title":"Indian J. Med. Res."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1080\/20477724.2022.2088496","article-title":"A review on the mechanistic details of OXA enzymes of ESKAPE pathogens","volume":"117","author":"Avci","year":"2023","journal-title":"Pathog. Glob. Health"},{"key":"ref8","volume-title":"Bacterial pangenomics","author":"Bacci","year":"2021"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"138388","DOI":"10.1016\/j.scitotenv.2020.138388","article-title":"Unraveling longitudinal pollution patterns of organic micropollutants in a river by non-target screening and cluster analysis","volume":"727","author":"Beckers","year":"2020","journal-title":"Sci. Total Environ."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1038\/nrmicro3439","article-title":"Tackling antibiotic resistance: the environmental framework","volume":"13","author":"Berendonk","year":"2015","journal-title":"Nat. Rev. Microbiol."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"D621","DOI":"10.1093\/nar\/gkr846","article-title":"ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria","volume":"40","author":"Bi","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"2490","DOI":"10.1038\/ismej.2015.59","article-title":"Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes","volume":"9","author":"Bing","year":"2015","journal-title":"ISME J."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"2226","DOI":"10.1099\/ijsem.0.002816","article-title":"Evaluation of the genus Thiothrix Winogradsky 1888 (Approved lists 1980) emend. Aruga et al. 2002: reclassification of Thiothrix disciformis to Thiolinea disciformis gen. Nov., comb. nov., and of Thiothrix flexilis to Thiofilum flexile gen. Nov., comb nov., with emended description of Thiothrix","volume":"68","author":"Boden","year":"2018","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"1666","DOI":"10.1038\/emboj.2009.125","article-title":"Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains","volume":"28","author":"Boer","year":"2009","journal-title":"EMBO J."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1128\/CMR.14.4.933-951.2001","article-title":"Extended-spectrum \u03b2-lactamases in the 21st century: characterization, epidemiology, and detection of this important resistance threat","volume":"14","author":"Bradford","year":"2001","journal-title":"Clin. Microbiol. Rev."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/femsec\/fiw060","article-title":"Seasonality of antibiotic prescriptions for outpatients and resistance genes in sewers and wastewater treatment plant outflow","volume":"92","author":"Caucci","year":"2016","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","article-title":"GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database","volume":"36","author":"Chaumeil","year":"2020","journal-title":"Bioinformatics"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"398","DOI":"10.1016\/j.envpol.2018.11.024","article-title":"A metagenomic analysis framework for characterization of antibiotic resistomes in river environment: application to an urban river in Beijing","volume":"245","author":"Chen","year":"2019","journal-title":"Environ. Pollut."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"2586","DOI":"10.3390\/w11122586","article-title":"Seasonal variability in the microbial community and pathogens in wastewater final effluents","volume":"11","author":"Chen","year":"2019","journal-title":"Water"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.envint.2013.01.019","article-title":"Occurrence and removal of antibiotic resistance genes in municipal wastewater and rural domestic sewage treatment systems in eastern China","volume":"55","author":"Chen","year":"2013","journal-title":"Environ. Int."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"e0225323","DOI":"10.1128\/aem.02253-23","article-title":"Accounting for the microbial assembly of each process in wastewater treatment plants (WWTPs): study of four WWTPs receiving similar influent streams","volume":"90","author":"Cheng","year":"2024","journal-title":"Appl. Environ. Microbiol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"e398","DOI":"10.1016\/S2542-5196(18)30186-4","article-title":"Anthropological and socioeconomic factors contributing to global antimicrobial resistance: a univariate and multivariable analysis","volume":"2","author":"Collignon","year":"2018","journal-title":"Lancet Planet. Health"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fmicb.2012.00106","article-title":"Increased levels of multiresistant bacteria and resistance genes after wastewater treatment and their dissemination into Lake Geneva, Switzerland","volume":"3","author":"Czekalski","year":"2012","journal-title":"Front. Microbiol."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1126\/science.1120800","article-title":"Sampling the antibiotic Resistome","volume":"311","author":"D\u2019Costa","year":"2006","journal-title":"Science"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"434","DOI":"10.1016\/S0723-2020(99)80053-8","article-title":"The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set","volume":"22","author":"Daims","year":"1999","journal-title":"Syst. Appl. Microbiol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"e11147","DOI":"10.1371\/journal.pone.0011147","article-title":"Progressivemauve: multiple genome alignment with gene gain, loss and rearrangement","volume":"5","author":"Darling","year":"2010","journal-title":"PLoS One"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/nature10388","article-title":"Antibiotic resistance is ancient","volume":"477","author":"D'Costa","year":"2011","journal-title":"Nature"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"138800","DOI":"10.1016\/j.chemosphere.2023.138800","article-title":"Anthropogenic pollution drives the bacterial resistome in a complex freshwater ecosystem","volume":"331","author":"Di Cesare","year":"2023","journal-title":"Chemosphere"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"1","DOI":"10.7554\/eLife.66834","article-title":"Linking plasmid-based beta-lactamases to their bacterial hosts using single-cell fusion pcr","volume":"10","author":"Diebold","year":"2021","journal-title":"eLife"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"817","DOI":"10.1093\/bioinformatics\/btu745","article-title":"Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods","volume":"31","author":"Dr\u00f6ge","year":"2015","journal-title":"Bioinformatics"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"30106","DOI":"10.1074\/jbc.M401701200","article-title":"The bacA gene of Escherichia coli encodes an undecaprenyl pyrophosphate phosphatase activity","volume":"279","author":"El Ghachi","year":"2004","journal-title":"J. Biol. Chem."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1128\/CMR.00117-13","article-title":"OXA \u03b2-lactamases","volume":"27","author":"Evans","year":"2014","journal-title":"Clin. Microbiol. Rev."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"1107","DOI":"10.1126\/science.1220761","article-title":"The shared antibiotic Resistome of soil Bacteria and human pathogens","volume":"337","author":"Forsberg","year":"2012","journal-title":"Science"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1038\/s42003-021-02489-0","article-title":"Predicting the taxonomic and environmental sources of integron gene cassettes using structural and sequence homology of attC sites","volume":"4","author":"Ghaly","year":"2021","journal-title":"Commun. Biol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"1269","DOI":"10.1038\/ismej.2014.226","article-title":"Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution","volume":"9","author":"Gillings","year":"2015","journal-title":"ISME J."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"652","DOI":"10.1002\/jeq2.20453","article-title":"Elevated levels of anthropogenic antibiotic resistance gene marker, sul1, linked with extreme fecal contamination and poor water quality in wastewater-receiving ponds","volume":"52","author":"Gunjyal","year":"2023","journal-title":"J. Environ. Qual."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"2772","DOI":"10.1016\/j.watres.2012.02.039","article-title":"Profiling bulking and foaming bacteria in activated sludge by high throughput sequencing","volume":"46","author":"Guo","year":"2012","journal-title":"Water Res."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"9093","DOI":"10.3390\/ijms25169093","article-title":"Wastewater treatment with bacterial representatives of the Thiothrix Morphotype","volume":"25","author":"Gureeva","year":"2024","journal-title":"Int. J. Mol. Sci."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fmicb.2023.1252870","article-title":"Antibiotic resistance indicator genes in biofilm and planktonic microbial communities after wastewater discharge","volume":"14","author":"Haenelt","year":"","journal-title":"Front. Microbiol."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fmicb.2023.1058350","article-title":"The fate of sulfonamide resistance genes and anthropogenic pollution marker intI1 after discharge of wastewater into a pristine river stream","volume":"14","author":"Haenelt","year":"","journal-title":"Front. Microbiol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"1817","DOI":"10.1099\/00207713-49-4-1817","article-title":"Phylogenetic relationships of filamentous sulfur bacteria (Thiothrix spp. and Eikelboom type 021N bacteria) isolated from wastewater-treatment plants and description of Thiothrix eikelboomii sp. nov., Thiothrix unzii sp. nov., Thiothrix fructosivorans sp","author":"Howarth","year":"1999","journal-title":"Int. J. Syst. Bacteriol."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"114919","DOI":"10.1016\/j.watres.2019.114919","article-title":"Molecular change of dissolved organic matter and patterns of bacterial activity in a stream along a land-use gradient","volume":"164","author":"Kamjunke","year":"2019","journal-title":"Water Res."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"e7359","DOI":"10.7717\/peerj.7359","article-title":"MetaBAT 2: An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies","volume":"7","author":"Kang","year":"2019","journal-title":"PeerJ"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"4395","DOI":"10.1080\/10643389.2021.2024739","article-title":"A framework for standardized qPCR-targets and protocols for quantifying antibiotic resistance in surface water, recycled water and wastewater","volume":"52","author":"Keenum","year":"2022","journal-title":"Crit. Rev. Environ. Sci. Technol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"2432","DOI":"10.3390\/w15132432","article-title":"Identification of antibiotic resistance gene hosts in treatment wetlands using a single-cell based high-throughput approach","volume":"15","author":"Knecht","year":"2023","journal-title":"Water"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"909","DOI":"10.1007\/s00248-016-0843-4","article-title":"Abundance of class 1 Integron-integrase and sulfonamide resistance genes in river water and sediment is affected by anthropogenic pressure and environmental factors","volume":"72","author":"Koczura","year":"2016","journal-title":"Microb. Ecol."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12302-019-0231-z","article-title":"Prioritising site-specific micropollutants in surface water from LC-HRMS non-target screening data using a rarity score","volume":"31","author":"Krauss","year":"2019","journal-title":"Environ. Sci. Eur."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"e35","DOI":"10.1093\/nar\/gkx1321","article-title":"PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures","volume":"46","author":"Krawczyk","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"e1197","DOI":"10.1002\/mbo3.1197","article-title":"Environmental hotspots for antibiotic resistance genes","volume":"10","author":"Kunhikannan","year":"2021","journal-title":"Microbiology"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"9543","DOI":"10.1021\/es202775r","article-title":"Tertiary-treated municipal wastewater is a significant point source of antibiotic resistance genes into Duluth-Superior Harbor","volume":"45","author":"Lapara","year":"2011","journal-title":"Environ. Sci. Technol."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"117050","DOI":"10.1016\/j.watres.2021.117050","article-title":"Unraveling the riverine antibiotic resistome: the downstream fate of anthropogenic inputs","volume":"197","author":"Lee","year":"2021","journal-title":"Water Res."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1016\/j.envpol.2017.12.001","article-title":"Metagenomic exploration reveals a marked change in the river resistome and mobilome after treated wastewater discharges","volume":"234","author":"Lekunberri","year":"2018","journal-title":"Environ. Pollut."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"D458","DOI":"10.1093\/nar\/gkaa937","article-title":"SMART: recent updates, new developments and status in 2020","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.ymeth.2016.02.020","article-title":"MEGAHIT v1.0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices","volume":"102","author":"Li","year":"2016","journal-title":"Methods"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"420","DOI":"10.1021\/acs.est.5b03522","article-title":"Metagenomic assembly reveals hosts of antibiotic resistance genes and the shared Resistome in pig, chicken, and human feces","volume":"50","author":"Ma","year":"2016","journal-title":"Environ. Sci. Technol."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"e78906","DOI":"10.1371\/journal.pone.0078906","article-title":"Prevalence of antibiotic resistance genes and bacterial community composition in a river influenced by a wastewater treatment plant","volume":"8","author":"Marti","year":"2013","journal-title":"PLoS One"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1126\/science.1159483","article-title":"Antibiotics and antibiotic resistance genes in natural environments","volume":"321","author":"Mart\u00ednez","year":"2008","journal-title":"Semin. Perinatol."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1128\/9781555819743.ch8","article-title":"Ecology and evolution of chromosomal gene transfer between environmental microorganisms and pathogens","author":"Mart\u00ednez","year":"2019","journal-title":"Microb. Transm."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"3057","DOI":"10.1111\/j.1462-2920.2010.02281.x","article-title":"GeneFISH \u2013 an in situ technique for linking gene presence and cell identity in environmental microorganisms","volume":"12","author":"Moraru","year":"2010","journal-title":"Environ. Microbiol."},{"key":"ref62","doi-asserted-by":"publisher","first-page":"1199","DOI":"10.1016\/S0140-6736(24)01867-1","article-title":"Articles global burden of bacterial antimicrobial resistance 1990\u20132021: a systematic analysis with forecasts to 2050","volume":"404","author":"Naghavi","year":"2024","journal-title":"Lancet"},{"key":"ref63","doi-asserted-by":"publisher","first-page":"e39223","DOI":"10.1371\/journal.pone.0039223","article-title":"Class 1 integrons in environments with different degrees of urbanization","volume":"7","author":"Nardelli","year":"2012","journal-title":"PLoS One"},{"key":"ref64","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1111\/1462-2920.13480","article-title":"Direct-geneFISH: tuning up microscopic and molecular methodologies for targeted cell visualization","volume":"19","author":"Neufeld","year":"2017","journal-title":"Environ. Microbiol."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"1356","DOI":"10.1016\/j.scitotenv.2017.10.180","article-title":"Human exposure assessment to antibiotic-resistant Escherichia coli through drinking water","author":"O\u2019Flaherty","year":"2018","journal-title":"Sci. Total Environ."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"786","DOI":"10.1016\/j.scitotenv.2018.09.018","article-title":"The potential human exposure to antibiotic resistant-Escherichia coli through recreational water","volume":"650","author":"O\u2019Flaherty","year":"2019","journal-title":"Sci. Total Environ."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"2864","DOI":"10.1038\/ismej.2017.126","article-title":"DRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication","volume":"11","author":"Olm","year":"2017","journal-title":"ISME J."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"1539","DOI":"10.3390\/antibiotics10121539","article-title":"Investigating the OXA variants of ESKAPE pathogens","volume":"10","author":"Pandey","year":"2021","journal-title":"Antibiotics"},{"key":"ref69","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1093\/bioinformatics\/btx644","article-title":"MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes","volume":"34","author":"Pericard","year":"2018","journal-title":"Bioinformatics"},{"key":"ref70","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1128\/AEM.68.6.3094-3101.2002","article-title":"Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria","volume":"68","author":"Pernthaler","year":"2002","journal-title":"Appl. Environ. Microbiol."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"14982","DOI":"10.1021\/acs.est.1c08673","article-title":"Demonstrating a comprehensive wastewater-based surveillance approach that differentiates globally sourced Resistomes","volume":"56","author":"Prieto Riquelme","year":"2022","journal-title":"Environ. Sci. Technol."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"11541","DOI":"10.1021\/es302657r","article-title":"Correlation between upstream human activities and riverine antibiotic resistance genes","volume":"46","author":"Pruden","year":"2012","journal-title":"Environ. Sci. Technol."},{"key":"ref73","doi-asserted-by":"publisher","first-page":"9531","DOI":"10.3390\/ijms23179531","article-title":"History of the study of the genus Thiothrix: from the first enrichment cultures to Pangenomic analysis","volume":"23","author":"Ravin","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"142755","DOI":"10.1016\/j.scitotenv.2020.142755","article-title":"Metagenomic exploration of antibiotic resistome in treated wastewater effluents and their receiving water","volume":"765","author":"Raza","year":"2021","journal-title":"Sci. Total Environ."},{"key":"ref75","doi-asserted-by":"publisher","first-page":"e2584","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: a versatile open source tool for metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"ref76","doi-asserted-by":"publisher","first-page":"1541","DOI":"10.2166\/wst.2015.634","article-title":"Comparative metagenomics reveals a diverse range of antimicrobial resistance genes in effluents entering a river catchment","volume":"73","author":"Rowe","year":"2016","journal-title":"Water Sci. Technol."},{"key":"ref77","doi-asserted-by":"publisher","first-page":"140199","DOI":"10.1016\/j.scitotenv.2020.140199","article-title":"Fate of antibiotics and antibiotic resistance genes during conventional and additional treatment technologies in wastewater treatment plants","volume":"741","author":"Sabri","year":"2020","journal-title":"Sci. Total Environ."},{"key":"ref78","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1016\/S0924-8579(01)00422-8","article-title":"Antibiotic resistance in Escherichia coli isolates obtained from animals, foods and humans in Spain","volume":"18","author":"S\u00e1enz","year":"2001","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref79","doi-asserted-by":"publisher","first-page":"150020","DOI":"10.1016\/j.scitotenv.2021.150020","article-title":"Demonstration of an aggregated biomarker response approach to assess the impact of point and diffuse contaminant sources in feral fish in a small river case study","volume":"804","author":"Schmitz","year":"2022","journal-title":"Sci. Total Environ."},{"key":"ref80","doi-asserted-by":"publisher","first-page":"000685","DOI":"10.1099\/MGEN.0.000685","article-title":"Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification","volume":"7","author":"Schwengers","year":"2021","journal-title":"Microb. Genom."},{"key":"ref81","doi-asserted-by":"publisher","first-page":"165199","DOI":"10.1016\/j.scitotenv.2023.165199","article-title":"Identification of significant live bacterial community shifts in different reclaimed waters during ozone and chlorine disinfection","volume":"896","author":"Shi","year":"2023","journal-title":"Sci. Total Environ."},{"key":"ref82","doi-asserted-by":"publisher","first-page":"134885","DOI":"10.1016\/j.jhazmat.2024.134885","article-title":"Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes","volume":"475","author":"Sivalingam","year":"2024","journal-title":"J. Hazard. Mater."},{"key":"ref83","doi-asserted-by":"publisher","first-page":"2437","DOI":"10.1038\/s41396-019-0446-4","article-title":"Linking the resistome and plasmidome to the microbiome","volume":"13","author":"Stalder","year":"2019","journal-title":"ISME J."},{"key":"ref84","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fmicb.2017.00014","article-title":"Editorial: antibiotic resistance in aquatic systems","volume":"8","author":"Suzuki","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref85","doi-asserted-by":"publisher","first-page":"6087","DOI":"10.1021\/acs.est.0c07839","article-title":"Chemical pollution levels in a river explain site-specific sensitivities to micropollutants within a genetically homogeneous population of freshwater amphipods","volume":"55","author":"\u0160vara","year":"2021","journal-title":"Environ. Sci. Technol."},{"key":"ref86","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1016\/j.ecoenv.2016.06.016","article-title":"Metagenomic analysis of bacterial community composition and antibiotic resistance genes in a wastewater treatment plant and its receiving surface water","volume":"132","author":"Tang","year":"2016","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"ref87","doi-asserted-by":"publisher","first-page":"158698","DOI":"10.1016\/j.scitotenv.2022.158698","article-title":"A proposed framework for the identification of indicator genes for monitoring antibiotic resistance in wastewater: insights from metagenomic sequencing","volume":"854","author":"Tarek","year":"2023","journal-title":"Sci. Total Environ."},{"key":"ref88","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-018-0541-1","article-title":"MetaWRAP\u2014a flexible pipeline for genome-resolved metagenomic data analysis","volume":"6","author":"Uritskiy","year":"2018","journal-title":"Microbiome"},{"key":"ref89","doi-asserted-by":"publisher","first-page":"743","DOI":"10.14202\/vetworld.2022.743-749","article-title":"Antimicrobial resistance: one health approach","volume":"15","author":"Velazquez-Meza","year":"2022","journal-title":"Vet. World"},{"key":"ref90","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1186\/s13059-019-1817-x","article-title":"Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT","volume":"20","author":"Von Meijenfeldt","year":"2019","journal-title":"Genome Biol."},{"key":"ref91","doi-asserted-by":"publisher","first-page":"600","DOI":"10.1016\/j.scitotenv.2018.01.203","article-title":"Shift in the microbial community composition of surface water and sediment along an urban river","volume":"627","author":"Wang","year":"2018","journal-title":"Sci. Total Environ."},{"key":"ref92","doi-asserted-by":"publisher","first-page":"122110","DOI":"10.1016\/J.JHAZMAT.2020.122110","article-title":"Occurrence, distribution, and source track of antibiotics and antibiotic resistance genes in the main rivers of Chongqing city, Southwest China","volume":"389","author":"Wang","year":"2020","journal-title":"J. Hazard. Mater."},{"key":"ref93","doi-asserted-by":"publisher","first-page":"144324","DOI":"10.1016\/j.scitotenv.2020.144324","article-title":"Disentangling multiple chemical and non-chemical stressors in a lotic ecosystem using a longitudinal approach","volume":"769","author":"Weitere","year":"2021","journal-title":"Sci. Total Environ."},{"key":"ref94","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1128\/aem.49.4.887-898.1985","article-title":"Filamentous sulfur bacteria of activated sludge: characterization of Thiothrix, Beggiatoa, and Eikelboom type 021N strains","volume":"49","author":"Williams","year":"1985","journal-title":"Appl. Environ. Microbiol."},{"key":"ref95","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1007\/s12665-016-6327-5","article-title":"The bode hydrological observatory: a platform for integrated, interdisciplinary hydro-ecological research within the TERENO Harz\/central German lowland observatory","volume":"76","author":"Wollschl\u00e4ger","year":"2017","journal-title":"Environ. Earth Sci."},{"key":"ref96","doi-asserted-by":"publisher","first-page":"20140083","DOI":"10.1098\/rstb.2014.0083","article-title":"Antimicrobial resistance in humans, livestock and the wider environment","volume":"370","author":"Woolhouse","year":"2015","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"ref97","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1038\/nrmicro1614","article-title":"The antibiotic resistome: the nexus of chemical and genetic diversity","volume":"5","author":"Wright","year":"2007","journal-title":"Nat. Rev. Microbiol."},{"key":"ref7001","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1093\/bioinformatics\/btv638","article-title":"MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets","volume":"32","author":"Wu","year":"2016","journal-title":"Bioinformatics"},{"key":"ref98","doi-asserted-by":"publisher","first-page":"52346","DOI":"10.1074\/jbc.M409573200","article-title":"TetX is a flavin-dependent monooxygenase conferring resistance to tetracycline antibiotics","volume":"279","author":"Yang","year":"2004","journal-title":"J. Biol. Chem."},{"key":"ref99","doi-asserted-by":"publisher","first-page":"2681","DOI":"10.1007\/s00253-012-4082-4","article-title":"Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing","volume":"97","author":"Ye","year":"2013","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref100","doi-asserted-by":"publisher","first-page":"10862","DOI":"10.1021\/acs.est.1c02483","article-title":"Pathogenic and indigenous denitrifying Bacteria are transcriptionally active and key multi-antibiotic-resistant players in wastewater treatment plants","volume":"55","author":"Yuan","year":"2021","journal-title":"Environ. Sci. Technol."},{"key":"ref101","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1038\/s43705-021-00082-4","article-title":"In situ visualization of glycoside hydrolase family 92 genes in marine flavobacteria","volume":"1","author":"Zeugner","year":"2021","journal-title":"ISME Commun."},{"key":"ref102","doi-asserted-by":"publisher","first-page":"4765","DOI":"10.1038\/s41467-021-25096-3","article-title":"An omics-based framework for assessing the health risk of antimicrobial resistance genes","volume":"12","author":"Zhang","year":"2021","journal-title":"Nat. Commun."},{"key":"ref103","doi-asserted-by":"publisher","first-page":"157054","DOI":"10.1016\/J.SCITOTENV.2022.157054","article-title":"Ferric chloride further simplified the horizontal gene transfer network of antibiotic resistance genes in anaerobic digestion","volume":"844","author":"Zhang","year":"2022","journal-title":"Sci. Total Environ."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1516033\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,26]],"date-time":"2025-02-26T07:22:21Z","timestamp":1740554541000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1516033\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,26]]},"references-count":104,"alternative-id":["10.3389\/fmicb.2025.1516033"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2025.1516033","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,26]]},"article-number":"1516033"}}