{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T18:22:39Z","timestamp":1792174959132,"version":"4.4.0"},"reference-count":49,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2024,9,1]],"date-time":"2024-09-01T00:00:00Z","timestamp":1725148800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,9,1]],"date-time":"2024-09-01T00:00:00Z","timestamp":1725148800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,9,1]],"date-time":"2024-09-01T00:00:00Z","timestamp":1725148800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2024,9,1]],"date-time":"2024-09-01T00:00:00Z","timestamp":1725148800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2024,9,1]],"date-time":"2024-09-01T00:00:00Z","timestamp":1725148800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2024,9,1]],"date-time":"2024-09-01T00:00:00Z","timestamp":1725148800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2024,9,1]],"date-time":"2024-09-01T00:00:00Z","timestamp":1725148800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100003453","name":"Natural Science Foundation of Guangdong Province","doi-asserted-by":"publisher","award":["2023A1515011526"],"award-info":[{"award-number":["2023A1515011526"]}],"id":[{"id":"10.13039\/501100003453","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2020YFC1806901"],"award-info":[{"award-number":["2020YFC1806901"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["42277382"],"award-info":[{"award-number":["42277382"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Environmental Pollution"],"published-print":{"date-parts":[[2024,9]]},"DOI":"10.1016\/j.envpol.2024.124482","type":"journal-article","created":{"date-parts":[[2024,7,1]],"date-time":"2024-07-01T02:13:35Z","timestamp":1719800015000},"page":"124482","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":17,"special_numbering":"C","title":["Metagenomic investigation of antibiotic resistance genes and resistant bacteria contamination in pharmaceutical plant sites in China"],"prefix":"10.1016","volume":"357","author":[{"given":"Run-Dong","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fang-Zhou","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4952-7535","authenticated-orcid":false,"given":"Yi-Jing","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian-Liang","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"You-Sheng","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang-Ying","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guang-Guo","family":"Ying","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.envpol.2024.124482_bib1","doi-asserted-by":"crossref","first-page":"780","DOI":"10.4315\/0362-028X-70.3.780","article-title":"Antimicrobial resistance in nontyphoidal Salmonella","volume":"70","author":"Alcaine","year":"2007","journal-title":"J. Food Protect."},{"key":"10.1016\/j.envpol.2024.124482_bib2","doi-asserted-by":"crossref","first-page":"6751","DOI":"10.1128\/AEM.01156-06","article-title":"Natural genetic transformation: a novel tool for efficient genetic engineering of the dairy bacterium Streptococcus thermophilus","volume":"72","author":"Blomqvist","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.envpol.2024.124482_bib3","doi-asserted-by":"crossref","DOI":"10.1128\/aem.00991-22","article-title":"mobileOG-db: a manually curated database of protein families mediating the life cycle of bacterial mobile genetic elements","volume":"88","author":"Brown","year":"2022","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.envpol.2024.124482_bib4","series-title":"GTDB-tk: a Toolkit to Classify Genomes with the Genome Taxonomy Database","author":"Chaumeil","year":"2020"},{"key":"10.1016\/j.envpol.2024.124482_bib5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40168-019-0663-0","article-title":"Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing","volume":"7","author":"Che","year":"2019","journal-title":"Microbiome"},{"key":"10.1016\/j.envpol.2024.124482_bib6","doi-asserted-by":"crossref","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":"10.1016\/j.envpol.2024.124482_bib7","doi-asserted-by":"crossref","DOI":"10.1016\/j.chemosphere.2021.129563","article-title":"Metagenomic insights into dissemination of antibiotic resistance across bacterial genera in wastewater treatment","volume":"271","author":"Cheng","year":"2021","journal-title":"Chemosphere"},{"key":"10.1016\/j.envpol.2024.124482_bib8","doi-asserted-by":"crossref","first-page":"1685","DOI":"10.1128\/AAC.34.9.1685","article-title":"Identification of chromosomal antibiotic resistance genes in Streptococcus anginosus (\"S. milleri\")","volume":"34","author":"Clermont","year":"1990","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.envpol.2024.124482_bib9","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/s40168-021-01216-5","article-title":"Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge","volume":"10","author":"Dai","year":"2022","journal-title":"Microbiome"},{"key":"10.1016\/j.envpol.2024.124482_bib10","doi-asserted-by":"crossref","first-page":"15108","DOI":"10.1021\/acs.est.0c05567","article-title":"Demonstrating an integrated antibiotic resistance gene surveillance approach in Puerto Rican watersheds Post-Hurricane Maria","volume":"54","author":"Davis","year":"2020","journal-title":"Environ. Sci. Technol."},{"key":"10.1016\/j.envpol.2024.124482_bib11","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.plasmid.2018.09.009","article-title":"Impact of plasmid interactions with the chromosome and other plasmids on the spread of antibiotic resistance","volume":"99","author":"Gama","year":"2018","journal-title":"Plasmid"},{"key":"10.1016\/j.envpol.2024.124482_bib12","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.scitotenv.2017.08.229","article-title":"Behavior of antibiotic resistance genes under extremely high-level antibiotic selection pressures in pharmaceutical wastewater treatment plants","volume":"612","author":"Guo","year":"2018","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.envpol.2024.124482_bib13","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2022.976657","article-title":"The source, fate and prospect of antibiotic resistance genes in soil: a review","volume":"13","author":"Han","year":"2022","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.envpol.2024.124482_bib14","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1016\/j.envint.2016.03.023","article-title":"Discharge of swine wastes risks water quality and food safety: antibiotics and antibiotic resistance genes from swine sources to the receiving environments","volume":"92\u201393","author":"He","year":"2016","journal-title":"Environ. Int."},{"key":"10.1016\/j.envpol.2024.124482_bib15","series-title":"Soil Survey Field Handbook: Describing and Sampling Soil Profiles","author":"Hodgson","year":"1974"},{"key":"10.1016\/j.envpol.2024.124482_bib16","doi-asserted-by":"crossref","DOI":"10.1016\/j.envint.2023.108304","article-title":"Comprehensive discovery and migration evaluation of antimicrobial drugs and their transformation products in a swine farm by target, suspect, and nontarget screening","volume":"181","author":"Huang","year":"2023","journal-title":"Environ. Int."},{"key":"10.1016\/j.envpol.2024.124482_bib17","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.envpol.2024.124482_bib18","doi-asserted-by":"crossref","DOI":"10.1002\/mbo3.1035","article-title":"The incidence of antibiotic resistance within and beyond the agricultural ecosystem: a concern for public health","volume":"9","author":"Iwu","year":"2020","journal-title":"Microbiol. Open"},{"key":"10.1016\/j.envpol.2024.124482_bib19","doi-asserted-by":"crossref","first-page":"3556","DOI":"10.1111\/mec.14138","article-title":"Deciphering conjugative plasmid permissiveness in wastewater microbiomes","volume":"26","author":"Jacquiod","year":"2017","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.envpol.2024.124482_bib20","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1038\/s41396-018-0277-8","article-title":"Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes","volume":"13","author":"Ju","year":"2019","journal-title":"ISME J."},{"key":"10.1016\/j.envpol.2024.124482_bib21","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1093\/cid\/ciw283","article-title":"Fecal colonization with extended-spectrum beta-lactamase\u2013producing Enterobacteriaceae and risk factors among healthy individuals: a systematic review and metaanalysis","volume":"63","author":"Karanika","year":"2016","journal-title":"Rev. Infect. Dis."},{"key":"10.1016\/j.envpol.2024.124482_bib22","doi-asserted-by":"crossref","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":"10.1016\/j.envpol.2024.124482_bib23","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1038\/s41579-021-00649-x","article-title":"Antibiotic resistance in the environment","volume":"20","author":"Larsson","year":"2022","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.envpol.2024.124482_bib24","doi-asserted-by":"crossref","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":"Li","year":"2015","journal-title":"ISME J."},{"key":"10.1016\/j.envpol.2024.124482_bib25","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.envpol.2024.124482_bib26","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/j.biortech.2018.04.008","article-title":"Dynamics of bacterial composition and the fate of antibiotic resistance genes and mobile genetic elements during the co-composting with gentamicin fermentation residue and lovastatin fermentation residue","volume":"261","author":"Liu","year":"2018","journal-title":"Bioresour. Technol."},{"key":"10.1016\/j.envpol.2024.124482_bib27","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.jes.2021.04.029","article-title":"Levels, distributions, and sources of legacy and novel per- and perfluoroalkyl substances (PFAS) in the topsoil of Tianjin, China","volume":"112","author":"Ma","year":"2022","journal-title":"J. Environ. Sci. (China)"},{"key":"10.1016\/j.envpol.2024.124482_bib28","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2021.657954","article-title":"Evaluation of metagenomic-enabled antibiotic resistance surveillance at a conventional wastewater treatment plant","volume":"12","author":"Majeed","year":"2021","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.envpol.2024.124482_bib29","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.envint.2018.05.040","article-title":"Bacterial lineages putatively associated with the dissemination of antibiotic resistance genes in a full-scale urban wastewater treatment plant","volume":"118","author":"Narciso-da-Rocha","year":"2018","journal-title":"Environ. Int."},{"key":"10.1016\/j.envpol.2024.124482_bib30","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.aau9124","article-title":"Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence","volume":"5","author":"P\u00e4rn\u00e4nen","year":"2019","journal-title":"Sci. Adv."},{"key":"10.1016\/j.envpol.2024.124482_bib31","doi-asserted-by":"crossref","DOI":"10.1128\/CMR.00088-17","article-title":"Mobile genetic elements associated with antimicrobial resistance","volume":"31","author":"Partridge","year":"2018","journal-title":"Clin. Microbiol. Rev."},{"key":"10.1016\/j.envpol.2024.124482_bib32","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1186\/s40168-021-01047-4","article-title":"Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems","volume":"9","author":"Qian","year":"2021","journal-title":"Microbiome"},{"key":"10.1016\/j.envpol.2024.124482_bib33","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2024464118","article-title":"Long-read sequencing revealed cooccurrence, host range, and potential mobility of antibiotic resistome in cow feces","volume":"118","author":"Qian","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.envpol.2024.124482_bib34","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1021\/acs.estlett.0c00202","article-title":"Determining hosts of antibiotic resistance genes: a review of methodological advances","volume":"7","author":"Rice","year":"2020","journal-title":"Environ. Sci. Technol. Lett."},{"key":"10.1016\/j.envpol.2024.124482_bib35","doi-asserted-by":"crossref","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":"Riquelme","year":"2022","journal-title":"Environ. Sci. Technol."},{"key":"10.1016\/j.envpol.2024.124482_bib36","article-title":"MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies","volume":"4","author":"Robertson","year":"2018","journal-title":"Microb. Genom."},{"key":"10.1016\/j.envpol.2024.124482_bib37","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1016\/j.lwt.2017.12.022","article-title":"Mutually stimulating interactions between lactic acid bacteria and Saccharomyces cerevisiae in sourdough fermentation","volume":"90","author":"Sieuwerts","year":"2018","journal-title":"Lwt"},{"key":"10.1016\/j.envpol.2024.124482_bib38","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1128\/MMBR.00020-10","article-title":"Mobility of plasmids","volume":"74","author":"Smillie","year":"2010","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"10.1016\/j.envpol.2024.124482_bib39","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13073-021-00874-2","article-title":"Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer","volume":"13","author":"Tzeng","year":"2021","journal-title":"Genome Med."},{"key":"10.1016\/j.envpol.2024.124482_bib40","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40168-018-0541-1","article-title":"MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis","volume":"6","author":"Uritskiy","year":"2018","journal-title":"Microbiome"},{"key":"10.1016\/j.envpol.2024.124482_bib41","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1016\/j.scitotenv.2015.05.046","article-title":"Fate and proliferation of typical antibiotic resistance genes in five full-scale pharmaceutical wastewater treatment plants","volume":"526","author":"Wang","year":"2015","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.envpol.2024.124482_bib42","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1086\/649223","article-title":"Acute emergence of Elizabethkingia meningoseptica infection among mechanically ventilated patients in a long-term acute care facility","volume":"31","author":"Weaver","year":"2010","journal-title":"Infect. Control Hosp. Epidemiol."},{"key":"10.1016\/j.envpol.2024.124482_bib43","doi-asserted-by":"crossref","first-page":"W587","DOI":"10.1093\/nar\/gkad359","article-title":"Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees","volume":"51","author":"Xie","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.envpol.2024.124482_bib44","doi-asserted-by":"crossref","first-page":"2263","DOI":"10.1093\/bioinformatics\/bty053","article-title":"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","volume":"34","author":"Yin","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.envpol.2024.124482_bib45","doi-asserted-by":"crossref","DOI":"10.1016\/j.jhazmat.2022.128277","article-title":"Metagenomics insights into the profiles of antibiotic resistome in combined sewage overflows from reads to metagenome assembly genomes","volume":"429","author":"Zhang","year":"2022","journal-title":"J. Hazard Mater."},{"key":"10.1016\/j.envpol.2024.124482_bib46","doi-asserted-by":"crossref","first-page":"6772","DOI":"10.1021\/acs.est.5b00729","article-title":"Comprehensive evaluation of antibiotics emission and fate in the river basins of China: source analysis, multimedia modeling, and linkage to bacterial resistance","volume":"49","author":"Zhang","year":"2015","journal-title":"Environ. Sci. Technol."},{"key":"10.1016\/j.envpol.2024.124482_bib47","doi-asserted-by":"crossref","first-page":"11429","DOI":"10.1021\/acs.est.2c03627","article-title":"Using culture-enriched phenotypic metagenomics for targeted high-throughput monitoring of the clinically important fraction of the \u03b2-lactam resistome","volume":"56","author":"Zhang","year":"2022","journal-title":"Environ. Sci. Technol."},{"key":"10.1016\/j.envpol.2024.124482_bib48","doi-asserted-by":"crossref","DOI":"10.1016\/j.watres.2020.116318","article-title":"Deciphering the mobility and bacterial hosts of antibiotic resistance genes under antibiotic selection pressure by metagenomic assembly and binning approaches","volume":"186","author":"Zhao","year":"2020","journal-title":"Water Res."},{"key":"10.1016\/j.envpol.2024.124482_bib49","doi-asserted-by":"crossref","first-page":"586","DOI":"10.1016\/j.csbj.2020.12.027","article-title":"The ecology of plasmid-coded antibiotic resistance: a basic framework for experimental research and modeling","volume":"19","author":"Zwanzig","year":"2021","journal-title":"Comput. Struct. Biotechnol. J."}],"container-title":["Environmental Pollution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0269749124011965?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0269749124011965?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,8,17]],"date-time":"2024-08-17T18:15:42Z","timestamp":1723918542000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0269749124011965"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9]]},"references-count":49,"alternative-id":["S0269749124011965"],"URL":"https:\/\/doi.org\/10.1016\/j.envpol.2024.124482","relation":{},"ISSN":["0269-7491"],"issn-type":[{"value":"0269-7491","type":"print"}],"subject":[],"published":{"date-parts":[[2024,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Metagenomic investigation of antibiotic resistance genes and resistant bacteria contamination in pharmaceutical plant sites in China","name":"articletitle","label":"Article Title"},{"value":"Environmental Pollution","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.envpol.2024.124482","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 Elsevier Ltd. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"124482"}}