{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T03:55:01Z","timestamp":1792641301746,"version":"4.5.0"},"reference-count":178,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,9,16]],"date-time":"2022-09-16T00:00:00Z","timestamp":1663286400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>The intensive use of antibiotics in the veterinary sector, linked to the application of manure-derived amendments in agriculture, translates into increased environmental levels of chemical residues, AR bacteria (ARB) and antibiotic resistance genes (ARG). The aim of this review was to evaluate the current evidence regarding the impact of animal farming and manure application on the antibiotic resistance pool in the environment. Several studies reported correlations between the prevalence of clinically relevant ARB and the amount and classes of antibiotics used in animal farming (high resistance rates being reported for medically important antibiotics such as penicillins, tetracyclines, sulfonamides and fluoroquinolones). However, the results are difficult to compare, due to the diversity of the used antimicrobials quantification techniques and to the different amounts and types of antibiotics, exhibiting various degradation times, given in animal feed in different countries. The soils fertilized with manure-derived products harbor a higher and chronic abundance of ARB, multiple ARG and an enriched associated mobilome, which is also sometimes seen in the crops grown on the amended soils. Different manure processing techniques have various efficiencies in the removal of antibiotic residues, ARB and ARGs, but there is only a small amount of data from commercial farms. The efficiency of sludge anaerobic digestion appears to be dependent on the microbial communities composition, the ARB\/ARG and operating temperature (mesophilic vs. thermophilic conditions). Composting seems to reduce or eliminate most of antibiotics residues, enteric bacteria, ARB and different representative ARG in manure more rapidly and effectively than lagoon storage. Our review highlights that despite the body of research accumulated in the last years, there are still important knowledge gaps regarding the contribution of manure to the AMR emergence, accumulation, spread and risk of human exposure in countries with high clinical resistance rates. Land microbiome before and after manure application, efficiency of different manure treatment techniques in decreasing the AMR levels in the natural environments and along the food chain must be investigated in depth, covering different geographical regions and countries and using harmonized methodologies. The support of stakeholders is required for the development of specific best practices for prudent \u2013 cautious use of antibiotics on farm animals. The use of human reserve antibiotics in veterinary medicine and of unprescribed animal antimicrobials should be stopped and the use of antibiotics on farms must be limited. This integrated approach is needed to determine the optimal conditions for the removal of antibiotic residues, ARB and ARG, to formulate specific recommendations for livestock manure treatment, storage and handling procedures and to translate them into practical on-farm management decisions, to ultimately prevent exposure of human population.<\/jats:p>","DOI":"10.3389\/fmicb.2022.965132","type":"journal-article","created":{"date-parts":[[2022,9,16]],"date-time":"2022-09-16T00:40:18Z","timestamp":1663288818000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":94,"title":["Insights into the impact of manure on the environmental antibiotic residues and resistance pool"],"prefix":"10.3389","volume":"13","author":[{"given":"Luminita Gabriela","family":"Marutescu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mihaela","family":"Jaga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carmen","family":"Postolache","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florica","family":"Barbuceanu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicoleta Manuela","family":"Milita","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luminita Maria","family":"Romascu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heike","family":"Schmitt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Maria","family":"de Roda Husman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paria","family":"Sefeedpari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefanie","family":"Glaeser","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"K\u00e4mpfer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick","family":"Boerlin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward","family":"Topp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gratiela","family":"Gradisteanu Pircalabioru","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariana Carmen","family":"Chifiriuc","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcela","family":"Popa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2022,9,16]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"20140085","DOI":"10.1098\/rstb.2014.0085","article-title":"The livestock reservoir for antimicrobial resistance: a personal view on changing patterns of risks, effects of interventions and the way forward","volume":"370","author":"Aarestrup","year":"2015","journal-title":"Phil. Trans. R. Soc."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"2677","DOI":"10.1021\/jf063709j","article-title":"Environmental fate of two sulfonamide antimicrobial agents in soil","volume":"55","author":"Accinelli","year":"2007","journal-title":"J. Agric. Food Chem."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"391","DOI":"10.3390\/antibiotics11030391","article-title":"Lagoon, anaerobic digestion, and composting of animal manure treatments impact on tetracycline resistance genes","volume":"11","author":"Agga","year":"2022","journal-title":"Antibiotics"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"614424","DOI":"10.3389\/fmicb.2020.614424","article-title":"Anaerobic digestion of tetracycline spiked livestock manure and poultry litter increased the abundances of antibiotic and heavy metal resistance genes","volume":"11","author":"Agga","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1016\/j.chemosphere.2004.06.024","article-title":"Assessment of degradation of 18 antibiotics in the closed bottle test","volume":"57","author":"Alexy","year":"2004","journal-title":"Chemosphere"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"8581","DOI":"10.1016\/j.biortech.2010.06.075","article-title":"The effect and fate of antibiotics during the anaerobic digestion of pig manure","volume":"101","author":"Alvarez","year":"2010","journal-title":"Bioresour. Technol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"23","DOI":"10.3390\/antibiotics8010023","article-title":"Prevalence of antibiotic resistance genes in multidrug-resistant Enterobacteriaceae on Portuguese livestock manure","volume":"8","author":"Amador","year":"2019","journal-title":"Antibiotics"},{"key":"ref8","article-title":"Committee for medicinal products for veterinary use (CVMP)","volume-title":"European Medicines Agency Veterinary Medicines and Inspections","year":"2015"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1016\/j.jhazmat.2008.08.019","article-title":"Management of antibiotic residues from agricultural sources: use of composting to reduce chlortetracycline residues in beef manure from treated animals","volume":"164","author":"Arikan","year":"2009","journal-title":"J. Hazard. Mater."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1016\/j.copbio.2008.05.006","article-title":"Antibiotics and antibiotic resistance in water environments","volume":"19","author":"Baquero","year":"2008","journal-title":"Curr. Opin. Biotechnol."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"fux053","DOI":"10.1093\/femsre\/fux053","article-title":"Environmental factors influencing the development and spread of antibiotic resistance","volume":"42","author":"Bengtsson-Palme","year":"2018","journal-title":"FEMS Microbiol. Rev."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1016\/j.talanta.2014.09.022","article-title":"The analysis of animal faeces as a tool to monitor antibiotic usage","volume":"132","author":"Berendsen","year":"2015","journal-title":"Talanta"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"1350","DOI":"10.1126\/science.aao1495","article-title":"Reducing antimicrobial use in food animals","volume":"357","author":"Boeckel","year":"2017","journal-title":"Science"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"152144","DOI":"10.1016\/j.scitotenv.2021.152144","article-title":"Structure of the manure resistome and the associated mobilome for assessing the risk of antimicrobial resistance transmission to crops","volume":"808","author":"Buta-Hubeny","year":"2022","journal-title":"Sci. Total Environ."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1016\/S0048-9697(02)00233-4","article-title":"Antimicrobial residues in animal waste and water resources proximal to large-scale swine and poultry feeding operations","volume":"299","author":"Campagnolo","year":"2002","journal-title":"Sci. Total Environ."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"138367","DOI":"10.1016\/j.scitotenv.2020.138367","article-title":"Co-selection of antibiotic-resistant bacteria in a paddy soil exposed to As(III) contamination with an emphasis on potential pathogens","volume":"725","author":"Cao","year":"2020","journal-title":"Sci. Total Environ."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"82","DOI":"10.4236\/jep.2016.71008","article-title":"Environmental assessment of Tetracycline\u2019s residues detected in pig slurry and poultry manure","volume":"7","author":"Carballo","year":"2016","journal-title":"J. Environ. Prot."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"295","DOI":"10.4236\/abb.2013.42A040","article-title":"Occurrence of tetracycline residues and antimicrobial resistance in gram negative bacteria isolates from cattle farms in Spain","volume":"4","author":"Carballo","year":"2013","journal-title":"Adv. Biosci. Biotechnol."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1897\/04-657R.1","article-title":"Dissipation kinetics and mobility of chlortetracycline, tylosin, and monensin in an agricultural soil in Northumberland County, Ontario, Canada","volume":"25","author":"Carlson","year":"2006","journal-title":"Environ. Toxicol. Chem."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1099\/jmm.0.001176","article-title":"Antimicrobial resistance prevalence in commensal Escherichia coli from broilers, fattening turkeys, fattening pigs and veal calves in European countries and association with antimicrobial usage at country level","volume":"69","author":"Ceccarelli","year":"2020","journal-title":"J. Med. Microbiol."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1093\/jac\/dkt443","article-title":"Correlation between veterinary antimicrobial use and antimicrobial resistance in food-producing animals: a report on seven countries","volume":"69","author":"Chantziaras","year":"2013","journal-title":"J. Antimicrob. Chemother."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1007\/s00248-010-9634-5","article-title":"Occurrence and persistence of erythromycin resistance genes (erm) and tetracycline resistance genes (tet) in waste treatment systems on swine","volume":"60","author":"Chen","year":"2010","journal-title":"Farms. Microb. Ecol."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"947","DOI":"10.1016\/j.envpol.2019.02.093","article-title":"Antibiotic resistance genes and bacterial communities in cornfield and pasture soils receiving swine and dairy manures","volume":"248","author":"Chen","year":"2019","journal-title":"Environ. Pollut."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.envint.2013.08.023","article-title":"Abundance and persistence of antibiotic resistance genes in livestock farms: a comprehensive investigation in eastern China","volume":"61","author":"Cheng","year":"2013","journal-title":"Environ. Int."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1016\/j.jenvman.2018.09.074","article-title":"Dynamics of oxytetracycline, sulfamerazine, and ciprofloxacin and related antibiotic resistance genes during swine manure composting","volume":"230","author":"Cheng","year":"2019","journal-title":"J. Environ. Manag."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"22","DOI":"10.3390\/tropicalmed4010022","article-title":"One health-its importance in helping to better control antimicrobial resistance","volume":"4","author":"Collignon","year":"2019","journal-title":"Trop. Med. Infect. Dis."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1111\/j.1574-6976.2009.00165.x","article-title":"Side effects of antibiotics on genetic variability","volume":"33","author":"Couce","year":"2009","journal-title":"FEMS Microbiol. Rev."},{"key":"ref01","doi-asserted-by":"publisher","first-page":"550","DOI":"10.3389\/fmicb.2018.00550","article-title":"Prevalence and characterization of multi-drug-resistant gram-negative bacilli isolated from Lebanese poultry: A nationwide study","volume":"9","author":"Dandachi","year":"2018","journal-title":"Front Microbiol."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1016\/S0045-6535(03)00284-4","article-title":"Use of oxytetracycline and tylosin in intensive calf farming: evaluation of transfer to manure and soil","volume":"52","author":"De Liguoro","year":"2003","journal-title":"Chemosphere"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"S565","DOI":"10.1093\/cid\/ciz830","article-title":"Treatment options for carbapenem-resistant gram-negative bacterial infections","volume":"69","author":"Doi","year":"2019","journal-title":"Clin. Infect. Dis."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"1245","DOI":"10.2134\/jeq2007.0399","article-title":"Antibiotic degradation during manure composting","volume":"37","author":"Dolliver","year":"2008","journal-title":"J. Environ. Qual."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"1477","DOI":"10.1016\/j.scitotenv.2018.04.020","article-title":"Tracking antibiotic resistance genes in soil irrigated with dairy wastewater","volume":"635","author":"Dungan","year":"2018","journal-title":"Sci. Total Environ."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"414","DOI":"10.1007\/s10393-018-1324-7","article-title":"One health and antibiotic resistance in Agroecosystems","volume":"16","author":"Durso","year":"2019","journal-title":"EcoHealth"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"737247","DOI":"10.3389\/fenvs.2021.737247","article-title":"Assessing antibiotics biodegradation and effects at sub-inhibitory concentrations by quantitative microbial community Deconvolution","volume":"9","author":"Duygan","year":"2021","journal-title":"Front. Environ. Sci."},{"key":"ref34","article-title":"A global treaty to reduce antimicrobial use in livestock","volume-title":"CGD Policy Paper","author":"Elliott","year":"2017"},{"key":"ref35","year":"2018"},{"key":"ref36","year":"2019"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"2643","DOI":"10.1021\/es404988k","article-title":"Effect of manure application on abundance of antibiotic resistance genes and their attenuation rates in soil: field-scale mass balance approach","volume":"48","author":"Fahrenfeld","year":"2014","journal-title":"Environ. Sci. Technol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"1095","DOI":"10.1021\/es504157v","article-title":"Prevalence of antibiotic resistance genes and bacterial pathogens in long-term manured greenhouse soils as revealed by metagenomic survey","volume":"49","author":"Fang","year":"2015","journal-title":"Environ. Sci. Technol."},{"key":"ref39","year":"2019"},{"key":"ref40","year":"2019"},{"key":"ref41","year":"2020"},{"key":"ref42","doi-asserted-by":"publisher","DOI":"10.1128\/microbiolspec.ARBA-0021-2017","article-title":"Antimicrobial resistance in Corynebacterium spp., Arcanobacterium spp., and Trueperella pyogenes","volume":"5","author":"Fe\u00dfler","year":"2017","journal-title":"Microbiol. Spectr."},{"key":"ref43","first-page":"175","article-title":"Faecal occurrence and emissions of livestock-associated methicillin-resistant Staphylococcus aureus (laMRSA) and ESBL\/AmpC-producing E. coli from animal farms in Germany","volume":"126","author":"Friese","year":"2013","journal-title":"Berl. Munch. Tierarztl. Wochenschr."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"180","DOI":"10.3382\/ps.2009-00198","article-title":"Veterinary pharmaceuticals and antibiotic resistance of Escherichia coli isolates in poultry litter from commercial farms and controlled feeding trials","volume":"89","author":"Furtula","year":"2010","journal-title":"Poult. Sci."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/j.envint.2019.02.015","article-title":"Elimination of the risks of colistin resistance gene (mcr-1) in livestock manure during composting","volume":"126","author":"Gao","year":"2019","journal-title":"Environ. Int."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"1300","DOI":"10.1016\/j.scitotenv.2017.09.028","article-title":"Aerobic composting reduces antibiotic resistance genes in cattle manure and the resistome dissemination in agricultural soils","volume":"612","author":"Gou","year":"2018","journal-title":"Sci. Total Environ."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"682","DOI":"10.1016\/j.envres.2009.05.005","article-title":"Fate of antimicrobial-resistant enterococci and staphylococci and resistance determinants in stored poultry litter","volume":"109","author":"Graham","year":"2009","journal-title":"Environ. Res."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"21550","DOI":"10.1038\/srep21550","article-title":"Appearance of \u03b2-lactam resistance genes in agricultural soils and clinical isolates over the 20th century","volume":"6","author":"Graham","year":"2016","journal-title":"Sci. Rep."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"2037","DOI":"10.1093\/jac\/dkq247","article-title":"Comparison of the sales of veterinary antimicrobial agents between 10 European countries","volume":"65","author":"Grave","year":"2010","journal-title":"J. Antimicrob. Chemother."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"120716","DOI":"10.1016\/j.jhazmat.2019.05.109","article-title":"Fate of pharmaceuticals and antibiotic resistance genes in a full-scale on-farm livestock waste treatment plant","volume":"378","author":"Gros","year":"2019","journal-title":"J. Hazard. Mater."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/S0021-9673(02)00083-3","article-title":"Quantification of veterinary antibiotics (sulfonamides and trimethoprim) in animal manure by liquid chromatography\u2013mass spectrometry","volume":"952","author":"Haller","year":"2002","journal-title":"J. Chromat. A"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"802","DOI":"10.1897\/03-576.1","article-title":"Dissipation and effects of chlortetracycline and tylosin in two agricultural soils: A field-scale study in southern Denmark","volume":"24","author":"Halling-S\u00f8rensen","year":"2005","journal-title":"Environ. Toxicol. Chem."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"861","DOI":"10.1897\/04-182R.1","article-title":"Different behavior of Tetracyclines and sulfonamides in Sandy soils after repeated fertilization with liquid manure","volume":"24","author":"Hamscher","year":"2005","journal-title":"Environ. Toxicol. Chem.\/SETAC"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/j.soilbio.2018.08.018","article-title":"Antibiotic resistance genes and associated bacterial communities in agricultural soils amended with different sources of animal manures","volume":"126","author":"Han","year":"2018","journal-title":"Soil Biol. Biochem."},{"key":"ref55","first-page":"293","article-title":"Detection and occurrence of antibiotics and their metabolites in pig manure in Bavaria (Germany)","volume-title":"Antimicrobial Resistance in the Environment","author":"Harms","year":"2012"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"83","DOI":"10.3389\/fmicb.2012.00083","article-title":"Occurrence of CTX-M producing Escherichia coli in soils, cattle, and farm environment in France (Burgundy region)","volume":"3","author":"Hartmann","year":"2012","journal-title":"Front. Microbiol."},{"key":"ref57","first-page":"e259","volume-title":"Lancet Planet Health","author":"Hassell","year":"2019"},{"key":"ref58","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1016\/j.tim.2004.07.003","article-title":"Antibiotic-induced lateral transfer of antibiotic resistance","volume":"12","author":"Hastings","year":"2004","journal-title":"Trends Microbiol."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"13120","DOI":"10.1021\/es5041267","article-title":"Dissemination of antibiotic resistance genes in representative broiler feedlots environments: identification of indicator ARGs and correlations with environmental variables","volume":"48","author":"He","year":"2014","journal-title":"Environ. Sci. Technol."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"2527","DOI":"10.1128\/AEM.02577-10","article-title":"Accumulation of sulfonamide resistance genes in arable soils due to repeated application of manure containing sulfadiazine","volume":"77","author":"Heuer","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref61","first-page":"blz. 29","article-title":"Wageningen Livestock Research, Rapport.","author":"Hoeksma","year":"2015"},{"key":"ref02","first-page":"46","author":"Hoeksma","year":"2020","journal-title":"Milieurisico van Antibiotica in Mest voor Bodem en Grondwater Mogelijk Beperkt"},{"key":"ref62","author":"Hoeksma","year":"2021"},{"key":"ref63","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1016\/j.envres.2010.02.009","article-title":"Sewage sludge and liquid pig manure as possible sources of antibiotic resistant bacteria","volume":"110","author":"H\u00f6lzel","year":"2010","journal-title":"Environ. Res."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1021\/acs.est.6b04524","article-title":"Nutrient recovery and emissions of ammonia, nitrous oxide, and methane from animal manure in Europe: effects of manure treatment technologies","volume":"51","author":"Hou","year":"2017","journal-title":"Environ. Sci. Technol."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"fiv169","DOI":"10.1093\/femsec\/fiv169","article-title":"Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils treated with cattle manure","volume":"92","author":"Hu","year":"2016","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"7329","DOI":"10.1016\/j.biortech.2011.05.003","article-title":"Characterization of organic matter degradation during composting of manure-straw mixtures spiked with tetracyclines","volume":"102","author":"Hu","year":"2011","journal-title":"Bioresour. Technol."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"6672","DOI":"10.1128\/AEM.01802-16","article-title":"The bacterial mobile resistome transfer network connecting the animal and human microbiomes","volume":"82","author":"Hu","year":"2016","journal-title":"Appl. Environ. Microbiol."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"e02878\u201318","DOI":"10.1128\/AEM.02878-18","article-title":"Higher temperatures do not always achieve better antibiotic resistance gene removal in anaerobic digestion of swine manure","volume":"85","author":"Huang","year":"2019","journal-title":"Appl. Environ. Microbiol."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"11993","DOI":"10.1021\/acs.est.5b02566","article-title":"Role of the environment in the transmission of antimicrobial resistance to humans: a review","volume":"49","author":"Huijbers","year":"2015","journal-title":"Environ. Sci. Technol."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"104880","DOI":"10.1016\/j.envint.2019.05.074","article-title":"A conceptual framework for the environmental surveillance of antibiotics and antibiotic resistance","volume":"130","author":"Huijbers","year":"2019","journal-title":"Environ. Int."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"410","DOI":"10.3390\/antibiotics10040410","article-title":"Presence of antibiotic residues and antibiotic resistant bacteria in cattle manure intended for fertilization of agricultural fields: a one health perspective","volume":"10","author":"Huygens","year":"2021","journal-title":"Antibiotics"},{"key":"ref72","doi-asserted-by":"publisher","first-page":"633858","DOI":"10.3389\/fvets.2021.633858","article-title":"Antibiotic resistance in agricultural soil and crops associated to the application of cow manure-derived amendments From conventional and organic livestock farms","volume":"8","author":"Jauregi","year":"2021","journal-title":"Front. Vet."},{"key":"ref73","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1016\/j.scitotenv.2017.10.312","article-title":"Antibiotics and common antibacterial biocides stimulate horizontal transfer of resistance at low concentrations","author":"Jutkina","year":"2018","journal-title":"Sci. Total Environ."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/j.scitotenv.2016.01.044","article-title":"An assay for determining minimal concentrations of antibiotics that drive horizontal transfer of resistance","author":"Jutkina","year":"2016","journal-title":"Sci. Total Environ."},{"key":"ref75","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1080\/03601234.2019.1667190","article-title":"Anaerobic digestion of livestock and poultry manures spiked with tetracycline antibiotics","volume":"55","author":"Kasumba","year":"2020","journal-title":"J. Environ. Sci. Health B"},{"key":"ref76","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ecolind.2007.06.002","article-title":"Veterinary antibiotics in the aquatic and terrestrial environment","volume":"8","author":"Kemper","year":"2008","journal-title":"Ecol. Indic."},{"key":"ref77","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1016\/j.wasman.2011.07.026","article-title":"Decline in extractable antibiotics in manure-based composts during composting","volume":"32","author":"Kim","year":"2012","journal-title":"Waste Manag."},{"key":"ref78","doi-asserted-by":"publisher","first-page":"2413","DOI":"10.1016\/j.chemosphere.2013.08.058","article-title":"Cow excrements enhance the occurrence of tetracycline resistance genes in soil regardless of their oxytetracycline content","volume":"93","author":"Kyselkov\u00e1","year":"2013","journal-title":"Chemosphere"},{"key":"ref79","doi-asserted-by":"publisher","first-page":"536","DOI":"10.3389\/fmicb.2015.00536","article-title":"Spread of tetracycline resistance genes at a conventional dairy farm","volume":"6","author":"Kyselkov\u00e1","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref80","doi-asserted-by":"publisher","first-page":"143404","DOI":"10.1016\/j.scitotenv.2020.143404","article-title":"Microbial community composition and antimicrobial resistance in agricultural soils fertilized with livestock manure from conventional farming in northern Italy","volume":"760","author":"Laconi","year":"2021","journal-title":"Sci. Total Environ."},{"key":"ref81","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1177\/003335491212700103","article-title":"A review of antibiotic use in food animals: perspective, policy, and potential","volume":"127","author":"Landers","year":"2012","journal-title":"Public Health Rep."},{"key":"ref05","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1016\/j.envint.2018.04.041","article-title":"Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance","volume":"117","author":"Larsson","year":"2018","journal-title":"Environ. Int."},{"key":"ref82","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1016\/j.vetmic.2015.11.012","article-title":"Impact of colistin sulfate treatment of broilers on the presence of resistant bacteria and resistance genes in stored or composted manure","volume":"194","author":"Le Devendec","year":"2016","journal-title":"Vet. Microbiol."},{"key":"ref83","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1016\/j.scitotenv.2012.06.002","article-title":"Occurrence and sorption of fluoroquinolones in poultry litters and soils from S\u00e3o Paulo State, Brazil","volume":"432","author":"Leal","year":"2012","journal-title":"Sci Total Environ."},{"key":"ref84","doi-asserted-by":"publisher","first-page":"121894","DOI":"10.1016\/j.jhazmat.2019.121894","article-title":"Fate of chlortetracycline antibiotics during anaerobic degradation of cattle manure","volume":"386","author":"Lee","year":"2020","journal-title":"J. Hazard. Mater."},{"key":"ref85","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":"Li","year":"2015","journal-title":"ISME J."},{"key":"ref86","doi-asserted-by":"publisher","first-page":"2211","DOI":"10.1007\/s10661-012-2702-1","article-title":"The residues and environmental risks of multiple veterinary antibiotics in animal faeces","volume":"185","author":"Li","year":"2013","journal-title":"Environ. Monit. Assess."},{"key":"ref87","year":"2015"},{"key":"ref88","doi-asserted-by":"publisher","first-page":"110","DOI":"10.3390\/vetsci7030110","article-title":"Manure as a potential hotspot for antibiotic resistance dissemination by horizontal gene transfer events","volume":"7","author":"Lima","year":"2020","journal-title":"Vet Sci."},{"key":"ref89","doi-asserted-by":"publisher","first-page":"2119","DOI":"10.3389\/fmicb.2019.02119","article-title":"Antibiotic-induced, increased conjugative transfer is common to diverse naturally occurring ESBL plasmids in Escherichia coli","volume":"10","author":"Liu","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref90","doi-asserted-by":"publisher","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":"ref91","doi-asserted-by":"publisher","first-page":"692298","DOI":"10.3389\/fenvs.2021.692298","article-title":"A review of the distribution of antibiotics in water in different regions of China and current antibiotic degradation pathways","volume":"9","author":"Liu","year":"2021","journal-title":"Front. Environ. Sci."},{"key":"ref92","doi-asserted-by":"crossref","first-page":"1691","DOI":"10.1073\/pnas.1120238109","article-title":"In-feed antibiotic effects on the swine intestinal microbiome","volume":"109","author":"Looft","year":"2011","journal-title":"PNAS"},{"key":"ref93","doi-asserted-by":"publisher","first-page":"1283","DOI":"10.1002\/bies.201600133","article-title":"Dissecting the effects of antibiotics on horizontal gene transfer: analysis suggests a critical role of selection dynamics","volume":"38","author":"Lopatkin","year":"2016","journal-title":"BioEssays"},{"key":"ref94","doi-asserted-by":"publisher","first-page":"e0220770","DOI":"10.1371\/journal.pone.0220770","article-title":"Characterizing the soil microbiome and quantifying antibiotic resistance gene dynamics in agricultural soil following swine CAFO manure application","volume":"14","author":"Lopatto","year":"2019","journal-title":"PLoS One"},{"key":"ref95","author":"Lyngs\u00f8","year":"2011"},{"key":"ref96","year":"2018"},{"key":"ref97","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":"ref98","doi-asserted-by":"publisher","first-page":"3258","DOI":"10.1128\/AEM.00231-14","article-title":"Safely coupling livestock and crop production systems: how rapidly do antibiotic resistance genes dissipate in soil following a commercial application of swine or dairy manure?","volume":"80","author":"Marti","year":"2014","journal-title":"Appl. Environ. Microb."},{"key":"ref99","doi-asserted-by":"publisher","first-page":"570","DOI":"10.1016\/j.envpol.2006.11.035","article-title":"Environmental monitoring study of selected veterinary antibiotics in animal manure and soils in Austria","volume":"148","author":"Mart\u00ednez-Carballo","year":"2007","journal-title":"Environ. Pollut."},{"key":"ref100","doi-asserted-by":"publisher","first-page":"146","DOI":"10.3390\/ani4020146","article-title":"Potential of biological processes to eliminate antibiotics in livestock manure: an overview","volume":"4","author":"Mass\u00e9","year":"2014","journal-title":"Animals (Basel)."},{"key":"ref101","volume-title":"Manure Treatment and Utilization Options.","author":"Melse","year":"2020"},{"key":"ref102","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/s40813-022-00255-0","article-title":"Longitudinal study of the mcr-1 gene prevalence in Spanish food-producing pigs from 1998 to 2021 and its relationship with the use of polymyxins","volume":"8","author":"Miguela-Villoldo","year":"2022","journal-title":"Porc. Health Manag."},{"key":"ref103","doi-asserted-by":"publisher","first-page":"248","DOI":"10.2134\/jeq2010.0209","article-title":"Levels of antibiotic resistance genes in manure, biosolids, and fertilized soil","volume":"40","author":"Munir","year":"2011","journal-title":"J. Environ. Qual."},{"key":"ref104","doi-asserted-by":"publisher","first-page":"135882","DOI":"10.1016\/j.scitotenv.2019.135882","article-title":"Microbial regulation of natural antibiotic resistance: understanding the protist-bacteria interactions for evolution of soil resistome","volume":"705","author":"Nguyen","year":"2020","journal-title":"Sci. Total Environ."},{"key":"ref105","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1016\/j.scitotenv.2016.04.035","article-title":"Inorganic and organic fertilizers impact the abundance and proportion of antibiotic resistance and integron-integrase genes in agricultural grassland soil","volume":"562","author":"N\u00f5lvak","year":"2016","journal-title":"Sci. Total Environ."},{"key":"ref106","year":"2018"},{"key":"ref107","doi-asserted-by":"publisher","first-page":"1051","DOI":"10.3168\/jds.2019-16778","article-title":"Invited review: fate of antibiotic residues, antibiotic-resistant bacteria, and antibiotic resistance genes in US dairy manure management systems","volume":"103","author":"Oliver","year":"2020","journal-title":"J. Dairy Sci."},{"key":"ref03","doi-asserted-by":"publisher","first-page":"1637","DOI":"10.1016\/j.procbio.2006.03.010","article-title":"The fate and effect of oxytetracycline during the anaerobic digestion of manure from therapeutically treated calves","volume":"41","author":"Osman","year":"2006","journal-title":"J. Dairy Sci."},{"key":"ref108","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1186\/s40168-016-0199-5","article-title":"The structure and diversity of human, animal and environmental resistomes","volume":"4","author":"Pal","year":"2016","journal-title":"Microbiome"},{"key":"ref109","doi-asserted-by":"publisher","first-page":"6760","DOI":"10.1038\/s41598-019-42734-5","article-title":"Native soil microorganisms hinder the soil enrichment with antibiotic resistance genes following manure applications","volume":"9","author":"P\u00e9rez-Valera","year":"2019","journal-title":"Sci. Rep."},{"key":"ref110","author":"Pikkemaat","year":"2016"},{"key":"ref111","first-page":"263","article-title":"Mobile genetic elements involved in the horizontal transfer of antibiotic resistance genes","volume":"77","author":"Popa","year":"2018","journal-title":"ROAMI"},{"key":"ref112","doi-asserted-by":"publisher","first-page":"e0164621","DOI":"10.1371\/journal.pone.0164621","article-title":"Assessing the impact of manure application in commercial swine farms on the transmission of antimicrobial resistant salmonella in the environment","volume":"11","author":"Pornsukarom","year":"2016","journal-title":"PLoS One"},{"key":"ref113","doi-asserted-by":"publisher","first-page":"878","DOI":"10.1289\/ehp.1206446","article-title":"Management options for reducing the release of antibiotics and antibiotic resistance genes to the environment","volume":"121","author":"Pruden","year":"2013","journal-title":"Environ. Health Perspect."},{"key":"ref114","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1016\/j.jhazmat.2017.10.031","article-title":"Impact of direct application of biogas slurry and residue in fields: in situ analysis of antibiotic resistance genes from pig manure to fields","volume":"344","author":"Pu","year":"2018","journal-title":"J. Hazard. Mater."},{"key":"ref115","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1016\/j.scitotenv.2019.06.081","article-title":"Exploring the persistence and spreading of antibiotic resistance from manure to biocompost, soils and vegetables","volume":"688","author":"Pu","year":"2019","journal-title":"Sci. Total Environ."},{"key":"ref116","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1016\/j.biortech.2016.08.101","article-title":"Reducing antibiotic resistance genes, integrons, and pathogens in dairy manure by continuous thermophilic composting","volume":"220","author":"Qian","year":"2016","journal-title":"Bioresour. Technol."},{"key":"ref117","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1016\/j.envpol.2018.04.135","article-title":"Effects of long-term pig manure application on antibiotics, abundance of antibiotic resistance genes (ARGs), anammox and denitrification rates in paddy soils","volume":"240","author":"Rahman","year":"2018","journal-title":"Environ. Pollut."},{"key":"ref118","doi-asserted-by":"publisher","first-page":"34","DOI":"10.3390\/antibiotics9010034","article-title":"Antibiotic residues and antibiotic-resistant bacteria in pig slurry used to fertilize agricultural fields","volume":"9","author":"Rasschaert","year":"2020","journal-title":"Antibiotics"},{"key":"ref119","doi-asserted-by":"publisher","first-page":"45","DOI":"10.2134\/jeq2016.07.0269","article-title":"Fate and effect of antibiotics in beef and dairy manure during static and turned composting","volume":"46","author":"Ray","year":"2017","journal-title":"J. Environ. Qual."},{"key":"ref120","doi-asserted-by":"publisher","first-page":"7905","DOI":"10.1128\/AEM.02363-15","article-title":"Abundance of antibiotic resistance genes in bacteriophage following soil fertilization with dairy manure or municipal biosolids, and evidence for potential transduction","volume":"81","author":"Ross","year":"2015","journal-title":"Appl. Environ. Microbiol."},{"key":"ref121","doi-asserted-by":"publisher","first-page":"488","DOI":"10.2134\/jeq2015.05.0250","article-title":"Fertilizing with animal manure disseminates antibiotic resistance genes to the farm environment","volume":"45","author":"Ruuskanen","year":"2016","journal-title":"J. Environ. Qual."},{"key":"ref122","doi-asserted-by":"publisher","first-page":"fiw001","DOI":"10.1093\/femsec\/fiw001","article-title":"The fate of antibiotic resistance genes and class 1 integrons following the application of swine and dairy manure to soils","volume":"10","author":"Sandberg","year":"2016","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref123","doi-asserted-by":"publisher","first-page":"e0119791","DOI":"10.1371\/journal.pone.0119791","article-title":"Improved detection of extended spectrum beta-lactamase (ESBL)-producing Escherichia coli in input and output samples of German biogas plants by a selective pre-enrichment procedure","volume":"10","author":"Schauss","year":"2015","journal-title":"PLoS One"},{"key":"ref124","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1007\/s00248-006-9035-y","article-title":"Tetracyclines and tetracycline resistance in agricultural soils: microcosm and field studies","volume":"51","author":"Schmitt","year":"2006","journal-title":"Microb. Ecol."},{"key":"ref125","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1111\/nyas.14058","article-title":"Critically important antibiotics: criteria and approaches for measuring and reducing their use in food animal agriculture","volume":"1441","author":"Scott","year":"2019","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref126","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1016\/j.biortech.2012.03.045","article-title":"Fate of tetracycline, sulfonamide and fluoroquinolone resistance genes and the changes in bacterial diversity during composting of swine manure","volume":"126","author":"Selvam","year":"2012","journal-title":"Bioresour. Technol."},{"key":"ref128","author":"Shober","year":"2018"},{"key":"ref129","doi-asserted-by":"publisher","first-page":"1373","DOI":"10.1111\/jam.13553","article-title":"Prudent use and regulatory guidelines for veterinary antibiotics-politics or science?","volume":"123","author":"Silley","year":"2017","journal-title":"J. Appl. Microbiol."},{"key":"ref130","doi-asserted-by":"publisher","first-page":"2513","DOI":"10.1007\/s00216-014-7649-3","article-title":"Simultaneous determination of 14 sulfonamides and tetracyclines in biogas plants by liquid-liquid-extraction and liquid chromatography tandem mass spectrometry","volume":"406","author":"Spielmeyer","year":"2014","journal-title":"Anal. Bioanal. Chem."},{"key":"ref131","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1016\/j.biortech.2015.06.081","article-title":"Elimination patterns of worldwide used sulfonamides and tetracyclines during anaerobic fermentation","volume":"193","author":"Spielmeyer","year":"2015","journal-title":"Bioresour. Technol."},{"key":"ref132","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1016\/j.chemosphere.2017.03.020","article-title":"Long-term monitoring of sulfonamide leaching from manure amended soil into groundwater","volume":"177","author":"Spielmeyer","year":"2017","journal-title":"Chemosphere"},{"key":"ref133","doi-asserted-by":"publisher","first-page":"7397","DOI":"10.1021\/es101657s","article-title":"Tracking antibiotic resistance genes in the South Platte river basin using molecular signatures of urban, agricultural, and pristine sources","volume":"44","author":"Storteboom","year":"2010","journal-title":"Environ. Sci. Technol."},{"key":"ref134","doi-asserted-by":"publisher","first-page":"1695","DOI":"10.2134\/jeq2007.0006","article-title":"Response of antibiotics and resistance genes to high-intensity and low-intensity manure management","volume":"36","author":"Storteboom","year":"2007","journal-title":"J. Environ. Qual."},{"key":"ref135","doi-asserted-by":"publisher","first-page":"141113","DOI":"10.1016\/j.scitotenv.2020.141113","article-title":"Composting of chicken litter from commercial broiler farms reduces the abundance of viable enteric bacteria, Firmicutes, and selected antibiotic resistance genes","volume":"746","author":"Subirats","year":"2020","journal-title":"Sci. Total Environ."},{"key":"ref136","doi-asserted-by":"publisher","first-page":"30237","DOI":"10.1038\/srep30237","article-title":"Mechanism and effect of temperature on variations in antibiotic resistance genes during anaerobic digestion of dairy manure","volume":"6","author":"Sun","year":"2016","journal-title":"Sci. Rep."},{"key":"ref137","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1016\/j.envpol.2015.07.022","article-title":"Positive relationship detected between soil bioaccessible organic pollutants and antibiotic resistance genes at dairy farms in Nanjing","volume":"206","author":"Sun","year":"2015","journal-title":"Eastern China. Environ Pollut."},{"key":"ref138","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.2134\/jeq2013.11.0455","article-title":"Dissipation of three veterinary antimicrobials in beef cattle feedlot manure stockpiled over winter","volume":"43","author":"Sura","year":"2014","journal-title":"J. Environ. Qual."},{"key":"ref139","doi-asserted-by":"publisher","first-page":"918","DOI":"10.3390\/antibiotics9120918","article-title":"Global trends in antimicrobial use in food animals from 2017 to 2030","volume":"9","author":"Tiseo","year":"2020","journal-title":"Antibiotics (Basel)"},{"key":"ref140","doi-asserted-by":"publisher","first-page":"173","DOI":"10.2134\/jeq2012.0162","article-title":"Accelerated biodegradation of veterinary antibiotics in agricultural soil following long-term exposure, and isolation of a Sulfamethazine-degrading sp","volume":"42","author":"Topp","year":"2013","journal-title":"J. Environ. Qual."},{"key":"ref141","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1093\/femsec\/fix185","article-title":"Antimicrobial resistance and the environment: assessment, advances, gaps and recommendations for agriculture, aquaculture and pharmaceutical manufacturing","volume":"94","author":"Topp","year":"2018","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref142","doi-asserted-by":"publisher","first-page":"e0298020","DOI":"10.1128\/AEM.02980-20","article-title":"On-farm anaerobic digestion of dairy manure reduces the abundance of antibiotic resistance-associated gene targets, and the potential for plasmid transfer","volume":"87","author":"Tran","year":"2021","journal-title":"Appl. Environ. Microbiol."},{"key":"ref143","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1042\/BST20180552","article-title":"Antibiotic resistance in grass and soil","volume":"47","author":"Tyrrell","year":"2019","journal-title":"Biochem. Soc. Trans."},{"key":"ref144","doi-asserted-by":"publisher","first-page":"1811","DOI":"10.1093\/jac\/dks166","article-title":"Diversity of vanA-type vancomycin-resistant enterococcus faecium isolated from broilers, poultry slaughterers and hospitalized humans in Greece","volume":"67","author":"Tzavaras","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref145","doi-asserted-by":"publisher","first-page":"15202","DOI":"10.1073\/pnas.1409836111","article-title":"Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization","volume":"111","author":"Udikovic-Kolic","year":"2014","journal-title":"PNAS"},{"key":"ref147","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1016\/j.ecoenv.2019.01.127","article-title":"Presence and fate of antibiotic residues, antibiotic resistance genes and zoonotic bacteria during biological swine manure treatment","volume":"175","author":"Van den Meersche","year":"2019","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"ref148","doi-asserted-by":"publisher","first-page":"28016","DOI":"10.1007\/s11356-020-09119-y","article-title":"Longitudinal screening of antibiotic residues, antibiotic resistance genes and zoonotic bacteria in soils fertilized with pig manure","volume":"27","author":"Van den Meersche","year":"2020","journal-title":"Environ. Sci. Pollut. Res. Int."},{"key":"ref149","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1016\/j.chroma.2015.12.046","article-title":"Development, validation and application of an ultra-high performance liquid chromatographic-tandem mass spectrometric method for the simultaneous detection and quantification of five different classes of veterinary antibiotics in swine manure","volume":"1429","author":"van den Meersche","year":"2016","journal-title":"J. Chromatogr. A"},{"key":"ref150","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1007\/s40726-016-0037-1","article-title":"Antibiotic residues in animal waste: occurrence and degradation in conventional agricultural waste management practices","volume":"2","author":"Van Epps","year":"2016","journal-title":"Curr. Pollution Rep."},{"key":"ref151","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1093\/jac\/dky518","article-title":"The antimicrobial resistome in relation to antimicrobial use and biosecurity in pig farming, a metagenome-wide association study in nine European countries","volume":"74","author":"Van Gompel","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"ref152","doi-asserted-by":"publisher","first-page":"203","DOI":"10.3389\/fmicb.2011.00203","article-title":"Acquired antibiotic resistance genes: an overview","volume":"2","author":"van Hoek","year":"2011","journal-title":"Front. Microbiol."},{"key":"ref153","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1016\/j.jgar.2019.07.031","article-title":"Antibiotic use in food animals worldwide, with a focus on Africa: pluses and minuses","volume":"20","author":"Van","year":"2020","journal-title":"J. Global Antimicrob. Resist."},{"key":"ref154","doi-asserted-by":"publisher","first-page":"13061","DOI":"10.1021\/acs.est.7b03623","article-title":"Toward a comprehensive strategy to mitigate dissemination of environmental sources of antibiotic resistance","volume":"51","author":"Vikesland","year":"2017","journal-title":"Environ. Sci. Technol."},{"key":"ref155","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1007\/s11270-010-0729-x","article-title":"Manure as a source of antibiotic-resistant Escherichia coli and enterococci: a case study of a Wisconsin, USA family dairy farm","volume":"219","author":"Walczak","year":"2011","journal-title":"Water Air Soil Pollut."},{"key":"ref04","doi-asserted-by":"publisher","first-page":"471","DOI":"10.2134\/jeq2015.05.0246","article-title":"Enhancing extraction and detection of veterinary antibiotics in solid and liquid fractions of manure","volume":"45","author":"Wallace","year":"2016","journal-title":"J. Environ. Qual."},{"key":"ref156","doi-asserted-by":"publisher","first-page":"764","DOI":"10.1016\/j.envpol.2018.02.024","article-title":"Occurrence and transformation of veterinary antibiotics and antibiotic resistance genes in dairy manure treated by advanced anaerobic digestion and conventional treatment methods","volume":"236","author":"Wallace","year":"2018","journal-title":"Environ. Pollut."},{"key":"ref157","doi-asserted-by":"publisher","first-page":"255","DOI":"10.3389\/fmicb.2013.00255","article-title":"The multiple roles of antibiotics and antibiotic resistance in nature","volume":"4","author":"Walsh","year":"2013","journal-title":"Front. Microbiol."},{"key":"ref158","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1016\/j.biortech.2017.03.134","article-title":"Effects of chlortetracycline and copper on tetracyclines and copper resistance genes and microbial community during swine manure anaerobic digestion","volume":"238","author":"Wang","year":"2017","journal-title":"Bioresour. Technol."},{"key":"ref160","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1111\/lam.12450","article-title":"Changes in diversity of cultured bacteria resistant to erythromycin and tetracycline in swine manure during simulated composting and lagoon storage","volume":"61","author":"Wang","year":"2015","journal-title":"Lett. Appl. Microbiol."},{"key":"ref161","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1007\/s00248-011-9921-9","article-title":"Persistence of resistance to erythromycin and tetracycline in swine manure during simulated composting and lagoon treatments","volume":"63","author":"Wang","year":"2012","journal-title":"Microb. Ecol."},{"key":"ref162","doi-asserted-by":"publisher","first-page":"6591","DOI":"10.1021\/es100834s","article-title":"Use and environmental occurrence of antibiotics in freestall dairy farms with manured forage fields","volume":"44","author":"Watanabe","year":"2010","journal-title":"Environ. Sci. Technol."},{"key":"ref164","first-page":"20162233","article-title":"Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities","volume":"284","author":"Wepking","year":"2017","journal-title":"PNAS"},{"key":"ref166","doi-asserted-by":"publisher","first-page":"e01017","DOI":"10.1128\/mBio.01017-13","article-title":"Diverse antibiotic resistance genes in dairy cow manure","volume":"5","author":"Wichmann","year":"2014","journal-title":"mBio"},{"key":"ref167","doi-asserted-by":"publisher","first-page":"671","DOI":"10.3389\/fmicb.2020.00671","article-title":"Cell-free DNA: an underestimated source of antibiotic resistance gene dissemination at the interface between human activities and downstream environments in the context of wastewater reuse","volume":"11","author":"Woegerbauer","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref169","year":"2015"},{"key":"ref168","volume-title":"Critically Important Antimicrobials for Human Medicine","year":"2019"},{"key":"ref165","year":"2021"},{"key":"ref170","doi-asserted-by":"publisher","first-page":"5924","DOI":"10.1016\/j.biortech.2011.03.007","article-title":"The behavior of tetracyclines and their degradation products during swine manure composting","volume":"102","author":"Wu","year":"2011","journal-title":"Bioresour. Technol."},{"key":"ref171","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1016\/j.envpol.2017.05.073","article-title":"Molecular characterization of antibiotic resistance in cultivable multidrug-resistant bacteria from livestock manure","volume":"229","author":"Yang","year":"2017","journal-title":"Environ. Pollut."},{"key":"ref172","doi-asserted-by":"publisher","first-page":"537","DOI":"10.2134\/jeq2015.05.0256","article-title":"Fate of antibiotics and antibiotic resistance during digestion and composting: a review","volume":"45","author":"Youngquist","year":"2016","journal-title":"J. Environ. Qual."},{"key":"ref173","doi-asserted-by":"publisher","first-page":"125736","DOI":"10.1016\/j.chemosphere.2019.125736","article-title":"Transfer potentials of antibiotic resistance genes in Escherichia spp. strains from different sources","volume":"246","author":"Yuan","year":"2020","journal-title":"Chemosphere"},{"key":"ref174","doi-asserted-by":"publisher","first-page":"610656","DOI":"10.3389\/fmicb.2021.610656","article-title":"Antibiotics and antibiotic resistance genes in animal manure \u2013 consequences of its application in agriculture","volume":"12","author":"Zalewska","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref175","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1016\/j.envpol.2018.01.032","article-title":"Sub-inhibitory concentrations of heavy metals facilitate the horizontal transfer of plasmid-mediated antibiotic resistance genes in water environment","volume":"237","author":"Zhang","year":"2018","journal-title":"Environ. Pollut."},{"key":"ref176","doi-asserted-by":"publisher","first-page":"1069","DOI":"10.1016\/j.scitotenv.2009.11.014","article-title":"Residues of veterinary antibiotics in manures from feedlot livestock in eight provinces of China","volume":"408","author":"Zhao","year":"2010","journal-title":"Sci. Total Environ."},{"key":"ref177","doi-asserted-by":"publisher","first-page":"121433","DOI":"10.1016\/j.jhazmat.2019.121433","article-title":"New insight into fates of sulfonamide and tetracycline resistance genes and resistant bacteria during anaerobic digestion of manure at thermophilic and mesophilic temperatures","volume":"384","author":"Zou","year":"2020","journal-title":"J. Hazard. Mater."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.965132\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,16]],"date-time":"2022-09-16T00:40:39Z","timestamp":1663288839000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.965132\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,9,16]]},"references-count":178,"alternative-id":["10.3389\/fmicb.2022.965132"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2022.965132","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,9,16]]},"article-number":"965132"}}