{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T03:34:23Z","timestamp":1790220863274,"version":"4.1.0"},"reference-count":165,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T00:00:00Z","timestamp":1766534400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>The extensive and often inappropriate use of antibiotics has led to the rapid emergence and spread of antibiotic resistance, reducing their effectiveness against pathogenic microorganisms. Fosfomycin has become an increasingly important therapeutic option in both human and veterinary medicine, particularly when other antibiotics fail. This review summarises current knowledge on the occurrence of fosfomycin resistance and evaluates the role of agricultural practices in its dissemination. Multiple microbial resistance mechanisms have been identified, including genes from the fosA, fosB, and fosC families, and new determinants continue to be reported. Agriculture contributes to the environmental spread of resistance through the use of antibiotics in food-producing animals, the exchange of resistant microorganisms between humans and animals, and the application of manure as fertiliser. Fosfomycin resistance genes have been detected in livestock such as pigs, chickens, pigeons, and cows, as well as in vegetables. Their presence in soil is influenced by fertilisation, nitrogen levels, microplastics, heavy metals, and pesticide application. Additionally, climate warming may facilitate the broader dissemination of fosfomycin resistance. Despite increasing evidence, current understanding remains limited. Further research is needed to elucidate the mechanisms driving the spread of fosfomycin resistance in agricultural environments and to develop effective monitoring strategies.<\/jats:p>","DOI":"10.3390\/pathogens15010029","type":"journal-article","created":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T14:27:51Z","timestamp":1766586471000},"page":"29","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Fosfomycin Resistance: An Update on the Anthropogenic Impact Through Agriculture"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2234-5133","authenticated-orcid":false,"given":"Weronika","family":"Goraj","sequence":"first","affiliation":[{"name":"Department of Microbiology and Translational Medicine, The John Paul II Catholic University of Lublin, Konstantyn\u00f3w 1I, 20-708 Lublin, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4025-3750","authenticated-orcid":false,"given":"Pawe\u0142","family":"Kowalczyk","sequence":"additional","affiliation":[{"name":"Department of Animal Nutrition, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Instytucka 3, 05-110 Jab\u0142onna, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2237-1454","authenticated-orcid":false,"given":"Grzegorz","family":"Be\u0142\u017cecki","sequence":"additional","affiliation":[{"name":"Department of Animal Nutrition, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Instytucka 3, 05-110 Jab\u0142onna, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9424-3147","authenticated-orcid":false,"given":"Adam","family":"Furtak","sequence":"additional","affiliation":[{"name":"Department of Natural Environment Biogeochemistry, Institute of Agrophysics, Polish Academy of Sciences, Do\u015bwiadczalna 4, 20-290 Lublin, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7941-1766","authenticated-orcid":false,"given":"Anna","family":"Pytlak","sequence":"additional","affiliation":[{"name":"Department of Natural Environment Biogeochemistry, Institute of Agrophysics, Polish Academy of Sciences, Do\u015bwiadczalna 4, 20-290 Lublin, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3257-0158","authenticated-orcid":false,"given":"Anna","family":"Szafranek-Nakonieczna","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Translational Medicine, The John Paul II Catholic University of Lublin, Konstantyn\u00f3w 1I, 20-708 Lublin, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,24]]},"reference":[{"key":"ref_1","unstructured":"WHO (2024). WHO Bacterial Priority Pathogens List, 2024: Bacterial Pathogens of Public Health Importance to Guide Research, Development and Strategies to Prevent and Control Antimicrobial Resistance, WHO."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1016\/S0140-6736(24)01867-1","article-title":"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":"ref_3","unstructured":"WHO (2025). Analysis of Antibacterial Agents in Clinical and Preclinical Development: Overview and Analysis 2025, WHO."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"525","DOI":"10.2147\/TCRM.S199119","article-title":"Fosfomycin: The Characteristics, Activity, and Use in Critical Care","volume":"15","author":"Hashemian","year":"2019","journal-title":"Ther. Clin. Risk Manag."},{"key":"ref_5","unstructured":"WHO (2024). WHO List of Medically Important Antimicrobials A Risk Management Tool for Mitigating Antimicrobial Resistance Due to Non-Human Use, WHO."},{"key":"ref_6","first-page":"2226","article-title":"Fosfomycin: Uses and Potentialities in Veterinary Medicine","volume":"4","author":"Tapia","year":"2014","journal-title":"Open Vet. J."},{"key":"ref_7","unstructured":"(2025, November 30). WOAH List of Antimicrobial Agents of Veterinary Importance. Available online: https:\/\/www.woah.org\/app\/uploads\/2021\/06\/amended-91gs-tech-03-amr-working-group-report-en.pdf."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1016\/j.jgar.2020.08.025","article-title":"Gold Standard Susceptibility Testing of Fosfomycin in Staphylococcus Aureus and Enterobacterales Using a New Agar Dilution Panel\u00ae","volume":"23","author":"Campanile","year":"2020","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Nollkaemper, A. (2025). Building Alliances between the WHO, the FAO, WOAH and UNEP in: Unity in Diversity: Perspectives on the Law of International Organizations. Unity in Diversity: Perspectives on the Law of International Organizations, Brill|Nijhoff.","DOI":"10.1163\/9789004699939_013"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1111\/1758-5899.70046","article-title":"Cooperation Across International Organizations: Effects of Regime Complexity on the Quadripartite of One Health","volume":"16","author":"Lobermeyer","year":"2025","journal-title":"Glob. Policy"},{"key":"ref_11","unstructured":"WHO (2025, December 16). One Health Initiative. Available online: https:\/\/www.who.int\/teams\/one-health-initiative\/quadripartite-secretariat-for-one-health."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"106473","DOI":"10.1016\/j.ejps.2023.106473","article-title":"European Regulations on the Use of Antibiotics in Veterinary Medicine","volume":"189","author":"Schmerold","year":"2023","journal-title":"Eur. J. Pharm. Sci."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Mattioni Marchetti, V., Hrabak, J., and Bitar, I. (2023). Fosfomycin Resistance Mechanisms in Enterobacterales: An Increasing Threat. Front. Cell Infect. Microbiol., 13.","DOI":"10.3389\/fcimb.2023.1178547"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1126\/science.166.3901.122","article-title":"Phosphonomycin, a New Antibiotic Produced by Strains of Streptomyces","volume":"166","author":"Hendlin","year":"1969","journal-title":"Science"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"238","DOI":"10.7164\/antibiotics.43.238","article-title":"Fosfadecin and Fosfocytocin, New Nucleotide Antibiotics Produced by Bacteria","volume":"43","author":"Katayama","year":"1990","journal-title":"J. Antibiot."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.7164\/antibiotics.39.1011","article-title":"Production of Fosfomycin (Phosphonomycin) by Pseudomonas Syringae","volume":"39","author":"Shoji","year":"1986","journal-title":"J. Antibiot."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"3510","DOI":"10.1021\/jo00835a070","article-title":"New Synthesis of the Antibiotic Phosphonomycin","volume":"35","author":"Glamkowski","year":"2002","journal-title":"J. Org. Chem."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1128\/CMR.00068-15","article-title":"Fosfomycin","volume":"29","author":"Falagas","year":"2016","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1111\/j.1469-0691.2011.03636.x","article-title":"Fosfomycin: An Old-New Antibiotic","volume":"18","author":"Raz","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"42204","DOI":"10.1039\/C9RA08299A","article-title":"The Intriguing Biology and Chemistry of Fosfomycin: The Only Marketed Phosphonate Antibiotic","volume":"9","author":"Cao","year":"2019","journal-title":"RSC Adv."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Dijkmans, A.C., Zacar\u00edas, N.V.O., Burggraaf, J., Mouton, J.W., Wilms, E.B., van Nieuwkoop, C., Touw, D.J., Stevens, J., and Kamerling, I.M.C. (2017). Fosfomycin: Pharmacological, Clinical and Future Perspectives. Antibiotics, 6.","DOI":"10.3390\/antibiotics6040024"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"5744","DOI":"10.1128\/AAC.00402-12","article-title":"Experience with Fosfomycin for Treatment of Urinary Tract Infections Due to Multidrug-Resistant Organisms","volume":"56","author":"Neuner","year":"2012","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"120453","DOI":"10.1016\/j.jenvman.2024.120453","article-title":"A Review of Organophosphonates, Their Natural and An-thropogenic Sources, Environmental Fate and Impact on Microbial Greenhouse Gases Emissions\u2014Identifying Knowledge Gaps","volume":"355","author":"Furtak","year":"2024","journal-title":"J. Environ. Manag."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Li, S., Liu, Z., S\u00fcring, C., Chen, L., M\u00fcller, S., and Zeng, P. (2022). The Impact of the Antibiotic Fosfomycin on Wastewater Communities Measured by Flow Cytometry. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.737831"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1176","DOI":"10.1016\/j.scitotenv.2017.09.223","article-title":"Organophosphonates: A Review on Environmental Relevance, Biodegradability and Removal in Wastewater Treatment Plants","volume":"615","author":"Rott","year":"2018","journal-title":"Sci. Total Environ."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1128\/AAC.44.3.647-650.2000","article-title":"Characterization of the FomA and FomB Gene Products from Streptomyces Wed-morensis, Which Confer Fosfomycin Resistance on Escherichia coli","volume":"44","author":"Kobayashi","year":"2000","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1128\/AAC.18.2.215","article-title":"Plasmid-Determined Resistance to Fosfomycin in Serratia Marcescens","volume":"18","author":"Mendoza","year":"1980","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.2147\/IDR.S251360","article-title":"Identification of FosA10, a Novel Plasmid-Mediated Fosfomycin Resistance Gene of Klebsiella Pneumoniae Origin, in Escherichia coli","volume":"13","author":"Huang","year":"2020","journal-title":"Infect. Drug Resist."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"106068","DOI":"10.1016\/j.idairyj.2024.106068","article-title":"The Prevalence, Antimicrobial Resistance and Molecular Genetic Characteristics of Fosfomycin-Resistant Klebsiella Pneumoniae Isolated from Raw Milk","volume":"159","author":"Ye","year":"2024","journal-title":"Int. Dairy. J."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1016\/j.jgar.2023.08.001","article-title":"Occurrence of Plasmid-Mediated Fosfomycin Resistance (Fos Genes) among Escherichia coli Isolates, Portugal","volume":"35","author":"Grilo","year":"2023","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.jgar.2025.02.011","article-title":"Spread of the Fosfomycin Resistance FosA3 Gene via the IS26 Mobile Element between Plasmids and the Chromosome of Carbapenem-Resistant Escherichia coli in China","volume":"42","author":"Zhang","year":"2025","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1564","DOI":"10.3201\/eid2309.170560","article-title":"Emergence of Plasmid-Mediated Fosfomycin-Resistance Genes among Escherichia coli Isolates, France","volume":"23","author":"Benzerara","year":"2017","journal-title":"Emerg. Infect. Dis."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Abdelraheem, W.M., Mahdi, W.K.M., Abuelela, I.S., and Hassuna, N.A. (2023). High Incidence of Fosfomycin-Resistant Uropathogenic E. Coli among Children. BMC Infect. Dis., 23.","DOI":"10.1186\/s12879-023-08449-9"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1007\/s00430-022-00749-2","article-title":"Resistance to Fosfomycin Is Increasing and Is Significantly Associated with Extended-Spectrum \u03b2-Lactamase-Production in Urinary Isolates of Escherichia coli","volume":"211","author":"Culebras","year":"2022","journal-title":"Med. Microbiol. Immunol."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Tartor, Y.H., Abd El-Aziz, N.K., Gharieb, R.M.A., El Damaty, H.M., Enany, S., Soliman, E.A., Abdellatif, S.S., Attia, A.S.A., Bahnass, M.M., and El-Shazly, Y.A. (2021). Whole-Genome Sequencing of Gram-Negative Bacteria Isolated From Bovine Mastitis and Raw Milk: The First Emergence of Colistin Mcr-10 and Fosfomycin FosA5 Resistance Genes in Klebsiella Pneumoniae in Middle East. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.770813"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Xin, L., Xu, X., Shi, Q., Han, R., Wang, J., Guo, Y., and Hu, F. (2022). High Prevalence and Overexpression of Fosfomycin-Resistant Gene FosX in Enterococcus Faecium From China. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.900185"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1002\/pro.4253","article-title":"Structural and Functional Characterization of Fosfomycin Resistance Conferred by FosB from Enterococcus faecium","volume":"31","author":"Wiltsie","year":"2022","journal-title":"Protein Sci."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"a025262","DOI":"10.1101\/cshperspect.a025262","article-title":"Fosfomycin: Mechanism and Resistance","volume":"7","author":"Silver","year":"2017","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Lu, J., Zhang, R., Yu, Y., Lou, H., Li, D., Bao, Q., and Feng, C. (2025). Identification of a Novel Chromosome-Encoded Fosfomycin Resistance Gene FosC3 in Aeromonas Caviae. Front. Microbiol., 16.","DOI":"10.3389\/fmicb.2025.1577167"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/j.jgar.2025.07.026","article-title":"Transmission of FosD-Carrying Methicillin-Resistant Staphylococcus Aureus ST764 in East Asia: Evidence of Human and Livestock Transmission","volume":"44","author":"Sun","year":"2025","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"4978","DOI":"10.1128\/AAC.03131-14","article-title":"Novel Integron-Mediated Fosfomycin Resistance Gene FosK","volume":"58","author":"Kitanaka","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"e01712-20","DOI":"10.1128\/AAC.01712-20","article-title":"FosM, a New Family of Fosfomycin Resistance Genes Identified in Bacterial Species Isolated from Human Microbiota","volume":"65","author":"Khabthani","year":"2021","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Zhang, R., Yu, Y., Huang, L., Chen, S., Hu, R., Wang, X., Huang, D., Song, C., Lu, J., and Bao, Q. (2025). Characterization of FosA13, a Novel Fosfomycin Glutathione Transferase Identified in a Morganella Morganii Isolate from Poultry. Front. Cell Infect. Microbiol., 15.","DOI":"10.3389\/fcimb.2025.1534084"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.ijantimicag.2014.08.010","article-title":"Dissemination of a Clone Carrying a FosA3-Harbouring Plasmid Mediates High Fosfomycin Resistance Rate of KPC-Producing Klebsiella Pneumoniae in China","volume":"45","author":"Jiang","year":"2015","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"e00410-17","DOI":"10.1128\/AAC.00410-17","article-title":"First Detection of a Fosfomycin Resistance Gene, FosA7, in Salmonella Enterica Serovar Heidelberg Isolated from Broiler Chickens","volume":"61","author":"Rehman","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1111\/lam.12366","article-title":"Characterization of FosA5, a New Plasmid-mediated Fosfomycin Resistance Gene in Escherichia coli","volume":"60","author":"Ma","year":"2015","journal-title":"Lett. Appl. Microbiol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e01403-19","DOI":"10.1128\/AAC.01403-19","article-title":"Identification of FosA8, a Plas-mid-Encoded Fosfomycin Resistance Determinant from Escherichia coli, and Its Origin in Leclercia adecarboxylata","volume":"63","author":"Poirel","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1126","DOI":"10.48047\/s7xym825","article-title":"Role of MurA and FosB Genes in Fosfomycin Resistance in Staphylococcus Aureus Isolated from Urinary Tract Infection Patients","volume":"54","author":"Shehab","year":"2025","journal-title":"Cuest. Fisioter."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1016\/S2666-5247(24)00026-0","article-title":"Mining Staphylococcus Aureus Genomic Data for Identifying Fosfomycin Resistance Genes","volume":"5","author":"Chen","year":"2024","journal-title":"Lancet Microbe"},{"key":"ref_50","first-page":"1","article-title":"Molecular Characterisation of Fosfomycin Resistance Genes in Escherichia coli Isolates","volume":"2025","author":"Yag","year":"2025","journal-title":"Folia Microbiol."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Xu, W., Chen, T., Wang, H., Zeng, W., Wu, Q., Yu, K., Xu, Y., Zhang, X., and Zhou, T. (2020). Molecular Mechanisms and Epidemiology of Fosfomycin Resistance in Staphylococcus Aureus Isolated From Patients at a Teaching Hospital in China. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.01290"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"e02042-19","DOI":"10.1128\/AAC.02042-19","article-title":"Characterization of FosL1, a Plasmid-Encoded Fosfomycin Re-sistance Protein Identified in Escherichia coli","volume":"64","author":"Kieffer","year":"2020","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1080\/22221751.2022.2058421","article-title":"The Novel Fosfomycin Resistance Gene FosY Is Present on a Genomic Island in CC1 Methicillin-Resistant Staphylococcus Aureus","volume":"11","author":"Chen","year":"2022","journal-title":"Emerg. Microbes Infect."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"107162","DOI":"10.1016\/j.ijantimicag.2024.107162","article-title":"Identification of the Novel Fosfomycin Resistance Gene FosSC in Staphylococcus Capitis","volume":"63","author":"Hong","year":"2024","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1016\/j.jgar.2022.05.026","article-title":"Asp50Glu Mutation in MurA Results in Fosfomycin Resistance in Enterococcus Faecium","volume":"30","author":"Xin","year":"2022","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"3611","DOI":"10.1007\/s00253-021-11272-4","article-title":"Screening of Compound Library Identifies Novel Inhibitors against the MurA Enzyme of Escherichia coli","volume":"105","author":"Raina","year":"2021","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1016\/j.ijantimicag.2009.11.011","article-title":"Molecular Mechanisms of Fosfomycin Resistance in Clinical Isolates of Escherichia coli","volume":"35","author":"Takahata","year":"2010","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Xu, S., Fu, Z., Zhou, Y., Liu, Y., Xu, X., and Wang, M. (2017). Mutations of the Transporter Proteins Glpt and Uhpt Confer Fosfomycin Resistance in Staphylococcus Aureus. Front. Microbiol., 8.","DOI":"10.3389\/fmicb.2017.00914"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"e01417-24","DOI":"10.1128\/aac.01417-24","article-title":"Chromosomal Genes Modulating Fosfomycin Susceptibility in Uropathogenic Escherichia coli: A Genome-Wide Analysis","volume":"69","author":"Ma","year":"2025","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"107027","DOI":"10.1016\/j.ijantimicag.2023.107027","article-title":"Role of the Phosphotransferase System in the Transport of Fosfomycin in Escherichia coli","volume":"63","year":"2024","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1128\/JB.01151-13","article-title":"Role of the CpxAR Two-Component Signal Transduction System in Control of Fosfomycin Resistance and Carbon Substrate Uptake","volume":"196","author":"Kurabayashi","year":"2014","journal-title":"J. Bacteriol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"e00927-18","DOI":"10.1128\/AAC.00927-18","article-title":"Tet38 Efflux Pump Contributes to Fosfomycin Resistance in Staphylococcus Aureus","volume":"62","author":"Wang","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Food Safety Commission of Japan (2019). Fosfomycin (Veterinary Medicinal Products): Summary. Food Saf., 7, 96.","DOI":"10.14252\/foodsafetyfscj.D-19-00020"},{"key":"ref_64","unstructured":"(2025, November 30). Decree 39\/2017\/ND-CP. Available online: https:\/\/english.luatvietnam.vn\/decree-no-39-2017-nd-cp-dated-april-4-2017-of-the-government-on-providing-the-regulatory-framework-for-animal-feeds-and-aqua-feeds-113523-doc1.html."},{"key":"ref_65","unstructured":"(2025, November 30). Servicio Nacional De Sanidad y Calidad Agroalimentaria Resolution 445\/2024. Available online: https:\/\/www.boletinoficial.gob.ar\/detalleAviso\/primera\/306555\/20240429."},{"key":"ref_66","unstructured":"(2025, November 30). Resolution 80\/2025. Available online: https:\/\/www.boletinoficial.gob.ar\/detalleAviso\/primera\/321082\/20250213."},{"key":"ref_67","unstructured":"(2025, November 30). Portaria SDA Nr 798 DE 10\/05\/2023. Available online: https:\/\/www.legisweb.com.br\/legislacao\/?id=445358."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"2004","DOI":"10.1093\/jac\/dkab119","article-title":"Characteristics of FosA-Carrying Plasmids in E. coli and Klebsiella Spp. Isolates Originating from Food and Environmental Samples","volume":"76","author":"Biggel","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Menck-Costa, M.F., Baptista, A.A.S., Gazal, L.E.S., Justino, L., Sanches, M.S., de Souza, M., Nishio, E.K., Queiroz Dos Santos, B., Cruz, V.D., and Berbert, J.V.M. (2022). High-Frequency Detection of FosA3 and BlaCTX\u2013M\u201355 Genes in Escherichia coli From Longitudinal Monitoring in Broiler Chicken Farms. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.846116"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"e00545-22","DOI":"10.1128\/spectrum.00545-22","article-title":"Spread and Molecular Char-acteristics of Enterobacteriaceae Carrying FosA-Like Genes from Farms in China","volume":"10","author":"Zhang","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"e00859-17","DOI":"10.1128\/AAC.00859-17","article-title":"Plasmids of Diverse Inc Groups Dis-seminate the Fosfomycin Resistance Gene FosA3 among Escherichia coli Isolates from Pigs, Chickens, and Dairy Cows in Northeast China","volume":"61","author":"Wang","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"e00507-20","DOI":"10.1128\/msphere.00507-20","article-title":"Multiple Plasmid Vectors Mediate the Spread of FosA3 in Extended-Spectrum-\u03b2-Lactamase-Producing Enterobacterales Isolates from Retail Vege-tables in China","volume":"5","author":"Lv","year":"2020","journal-title":"mSphere"},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Ramadan, H., Soliman, A.M., Hiott, L.M., Elbediwi, M., Woodley, T.A., Chattaway, M.A., Jenkins, C., Frye, J.G., and Jackson, C.R. (2021). Emergence of Multidrug-Resistant Escherichia coli Producing CTX-M, MCR-1, and FosA in Retail Food From Egypt. Front. Cell Infect. Microbiol., 11.","DOI":"10.3389\/fcimb.2021.681588"},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Juscele, F., Saidenberg, A.B.S., Christoffersen, L.E.B., Edslev, S.M., Hallstr\u00f8m, S., Nacarato, J.R., Barbosa, F.B., Cunha, M.P., Esposito, F., and Lincopan, N.H. (2025). Escherichia coli in Brazilian Poultry Fecal Samples: Co-Carriage of Fosfomycin and ESBL Resistance. Antibiotics, 14.","DOI":"10.3390\/antibiotics14030269"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"e0167324","DOI":"10.1128\/msystems.01673-24","article-title":"Emergence of Plas-mid-Mediated Fosfomycin Resistance among Escherichia coli Harboring FosA4, Tet (X4), and Mcr-1 Genes in Wild Birds","volume":"10","author":"Munir","year":"2025","journal-title":"mSystems"},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Wang, J., Wang, Y., Wang, Z.Y., Wu, H., Mei, C.Y., Shen, P.C., Pan, Z.M., and Jiao, X. (2021). Chromosomally Located FosA7 in Sal-monella Isolates From China. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.781306"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1089\/fpd.2023.0132","article-title":"Escherichia coli Isolated from Bovine Sources Encoding the Fosfomycin Resistance Gene FosA7.5","volume":"22","author":"Haley","year":"2025","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"802","DOI":"10.1093\/jac\/dkad014","article-title":"Prevalence and Genetic Characteristics of FosB-Positive Staphylococcus Aureus in Duck Farms in Guangdong, China in 2020","volume":"78","author":"Hu","year":"2023","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Karki, A.B., Neyaz, L., and Fakhr, M.K. (2020). Comparative Genomics of Plasmid-Bearing Staphylococcus Aureus Strains Isolated From Various Retail Meats. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.574923"},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Bello Gonzalez, T.D.J., Van Gelderen, B., Harders, F., Bossers, A., Brouwer, M.S.M., and Haenen, O.L.M. (2025). An Insight into the Presence of Antimicrobial Resistance Genes in Opportunistic Pathogenic Bacteria Isolated from Farm-Reared Crickets. Microorganisms, 13.","DOI":"10.3390\/microorganisms13020391"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"e01388-17","DOI":"10.1128\/AAC.01388-17","article-title":"Colocation of the Multiresistance Gene Cfr and the Fosfomycin Resistance Gene FosD on a Novel Plasmid in Staphylococcus Arlettae from a Chicken Farm","volume":"61","author":"Liu","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1186\/s44280-025-00095-x","article-title":"Characterization of fosS, a Novel Fosfomycin-Modifying Enzyme Gene Identified in Staphylococcus haemolyticus","volume":"3","author":"Huang","year":"2025","journal-title":"One Health Adv."},{"key":"ref_83","doi-asserted-by":"crossref","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":"Schwaiger","year":"2010","journal-title":"Environ. Res."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1038\/s43247-023-00790-w","article-title":"Intensified Livestock Farming Increases Antibiotic Resistance Genotypes and Phenotypes in Animal Feces","volume":"4","author":"Wang","year":"2023","journal-title":"Commun. Earth Environ."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.envint.2019.04.043","article-title":"Effect of Antibiotic Use and Composting on Antibiotic Resistance Gene Abundance and Resistome Risks of Soils Receiving Manure-Derived Amendments","volume":"128","author":"Chen","year":"2019","journal-title":"Environ. Int."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"001384","DOI":"10.1099\/mic.0.001384","article-title":"Cultivating Antimicrobial Resistance: How Intensive Agriculture Ploughs the Way for Antibiotic Resistance","volume":"169","author":"Kelbrick","year":"2023","journal-title":"Microbiology"},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Tang, B., Wang, J., Zheng, X., Chang, J., Ma, J., Wang, J., Ji, X., Yang, H., and Ding, B. (2022). Antimicrobial Resistance Surveillance of Escherichia coli from Chickens in the Qinghai Plateau of China. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.885132"},{"key":"ref_88","doi-asserted-by":"crossref","unstructured":"Marutescu, L.G., Jaga, M., Postolache, C., Barbuceanu, F., Milita, N.M., Romascu, L.M., Schmitt, H., de Roda Husman, A.M., Sefeedpari, P., and Glaeser, S. (2022). Insights into the Impact of Manure on the Environmental Antibiotic Residues and Resistance Pool. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.965132"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"5701","DOI":"10.1128\/AEM.01682-13","article-title":"Impact of Manure Fertilization on the Abundance of Antibiotic-Resistant Bacteria and Frequency of Detection of Antibiotic Resistance Genes in Soil and on Vegetables at Harvest","volume":"79","author":"Marti","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"107965","DOI":"10.1016\/j.soilbio.2020.107965","article-title":"Antibiotic Resistance Gene Abundance and Bacterial Community Structure in Soils Altered by Ammonium and Nitrate Concentrations","volume":"149","author":"Sun","year":"2020","journal-title":"Soil. Biol. Biochem."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"117880","DOI":"10.1016\/j.envres.2023.117880","article-title":"The Connection between the Antibiotic Resistome and Nitro-gen-Cycling Microorganisms in Paddy Soil Is Enhanced by Application of Chemical and Plant-Derived Organic Fertilizers","volume":"243","author":"Wang","year":"2024","journal-title":"Environ. Res."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"139580","DOI":"10.1016\/j.jhazmat.2025.139580","article-title":"Nitrate Input Enriched the Antibiotic Resistance Genes in Lake Sediments by Shaping Co-Host Community and Promoting Horizontal Gene Transfer","volume":"497","author":"Zhang","year":"2025","journal-title":"J. Hazard. Mater."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"127578","DOI":"10.1016\/j.chemosphere.2020.127578","article-title":"Unraveling Consequences of Soil Micro- and Nano-Plastic Pollution on Soil-Plant System: Implications for Nitrogen (N) Cycling and Soil Microbial Activity","volume":"260","author":"Iqbal","year":"2020","journal-title":"Chemosphere"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s12302-023-00720-9","article-title":"Plastic Contamination in Agricultural Soils: A Review","volume":"35","author":"Farsang","year":"2023","journal-title":"Environ. Sci. Eur."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"144277","DOI":"10.1016\/j.chemosphere.2025.144277","article-title":"Mi-croplastics in Agricultural Soils Following Sewage Sludge Applications: Evidence from a 25-Year Study","volume":"376","author":"Ramage","year":"2025","journal-title":"Chemosphere"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1038\/s41579-023-00967-2","article-title":"The Soil Plastisphere","volume":"22","author":"Rillig","year":"2023","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"118899","DOI":"10.1016\/j.watres.2022.118899","article-title":"Persistent versus Transient, and Conventional Plastic versus Biodegradable Plastic?\u2014Two Key Questions about Microplastic-Water Exchange of Antibiotic Resistance Genes","volume":"222","author":"Zhou","year":"2022","journal-title":"Water Res."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"173881","DOI":"10.1016\/j.scitotenv.2024.173881","article-title":"How Micro-\/Nano-Plastics Influence the Horizontal Transfer of Antibiotic Resistance Genes\u2014A Review","volume":"944","author":"Wang","year":"2024","journal-title":"Sci. Total Environ."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1016\/j.cofs.2021.04.016","article-title":"Plastic Waste as the Potential Carriers of Pathogens","volume":"41","author":"Meng","year":"2021","journal-title":"Curr. Opin. Food Sci."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"136157","DOI":"10.1016\/j.jhazmat.2024.136157","article-title":"How Nanoscale Plastics Facilitate the Evolution of Antibiotic Resistance?","volume":"480","author":"Xu","year":"2024","journal-title":"J. Hazard. Mater."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.eehl.2023.09.005","article-title":"Nanoplastics Promote the Dissemination of Antibiotic Resistance Genes and Diversify Their Bacterial Hosts in Soil","volume":"3","author":"Liu","year":"2024","journal-title":"Eco-Environ. Health"},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"106294","DOI":"10.1016\/j.apsoil.2025.106294","article-title":"Selective Enrichment of Potential Pathogens and Antibiotic Resistance Genes Derived from Farmland Residual Microplastic Films","volume":"213","author":"Huang","year":"2025","journal-title":"Appl. Soil. Ecol."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"138208","DOI":"10.1016\/j.jhazmat.2025.138208","article-title":"Synergistic Effect of Horizontal Transfer of Antibiotic Resistance Genes between Bacteria Exposed to Microplastics and per\/Polyfluoroalkyl Substances: An Explanation from Theoretical Methods","volume":"492","author":"Xiao","year":"2025","journal-title":"J. Hazard. Mater."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"123190","DOI":"10.1016\/j.envpol.2023.123190","article-title":"Micro-plastics as Carriers of Toxic Pollutants: Source, Transport, and Toxicological Effects","volume":"343","author":"Rafa","year":"2024","journal-title":"Environ. Pollut."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"158057","DOI":"10.1016\/j.scitotenv.2022.158057","article-title":"Response of Microbial Antibiotic Resistance to Pesticides: An Emerging Health Threat","volume":"850","author":"Qiu","year":"2022","journal-title":"Sci. Total Environ."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"2337","DOI":"10.1093\/molbev\/msab029","article-title":"Herbicide Selection Promotes Antibiotic Resistance in Soil Microbiomes","volume":"38","author":"Liao","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_107","doi-asserted-by":"crossref","unstructured":"Lloyd, A.W., Percival, D., and Yurgel, S.N. (2021). Effect of Fungicide Application on Lowbush Blueberries Soil Microbiome. Microorganisms, 9.","DOI":"10.3390\/microorganisms9071366"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"137167","DOI":"10.1016\/j.scitotenv.2020.137167","article-title":"The Global Environmental Hazard of Glyphosate Use","volume":"717","author":"Maggi","year":"2020","journal-title":"Sci. Total Environ."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s12302-016-0070-0","article-title":"Trends in Glyphosate Herbicide Use in the United States and Globally","volume":"28","author":"Benbrook","year":"2016","journal-title":"Environ. Sci. Eur."},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1007\/s00128-018-2438-x","article-title":"Effects of Glyphosate-, Glufosinate- and Flazasul-furon-Based Herbicides on Soil Microorganisms in a Vineyard","volume":"101","author":"Mandl","year":"2018","journal-title":"Bull. Environ. Contam. Toxicol."},{"key":"ref_111","first-page":"25862","article-title":"Zinc and Copper in Animal Feed\u2014Development of Resistance and Co-Resistance to Antimicrobial Agents in Bacteria of Animal Origin","volume":"25","author":"Yazdankhah","year":"2014","journal-title":"Microb. Ecol. Health Dis."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1039\/D3VA00369H","article-title":"Environmental Risk Assessment of the Use of Zinc Oxide Medicated Feeds for Weaning Piglets in the UK","volume":"3","author":"Peters","year":"2024","journal-title":"Environ. Sci. Adv."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"121740","DOI":"10.1016\/j.envpol.2023.121740","article-title":"Effects of Atmospheric Deposition on Heavy Metals Accumulation in Agricultural Soils: Evidence from Field Monitoring and Pb Isotope Analysis","volume":"330","author":"Liu","year":"2023","journal-title":"Environ. Pollut."},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"fuae017","DOI":"10.1093\/femsre\/fuae017","article-title":"Unravelling the Mechanisms of Antibiotic and Heavy Metal Resistance Co-Selection in Environmental Bacteria","volume":"48","author":"Gillieatt","year":"2024","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"122285","DOI":"10.1016\/j.envres.2025.122285","article-title":"Metagenomic Insights into the Characteristics and Co-Migration of Antibiotic Resistome and Metal(Loid) Resistance Genes in Urban Landfill Soil and Groundwater","volume":"285","author":"Wang","year":"2025","journal-title":"Environ. Res."},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1111\/1751-7915.13578","article-title":"Co-occurrence of Antibiotic, Biocide, and Heavy Metal Resistance Genes in Bacteria from Metal and Radionuclide Contaminated Soils at the Savannah River Site","volume":"13","author":"Thomas","year":"2020","journal-title":"Microb. Biotechnol."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"108394","DOI":"10.1016\/j.envint.2023.108394","article-title":"Prevalence of Antibiotic and Metal Resistance Genes in Phytoremediated Cadmium and Zinc Contaminated Soil Assisted by Chitosan and Trichoderma Harzianum","volume":"183","author":"Song","year":"2024","journal-title":"Environ. Int."},{"key":"ref_118","first-page":"57","article-title":"Antibiotic- and Metal-Resistant Endophytes Inhabit Armeria Maritima Hyperaccumulator","volume":"495","author":"Myczka","year":"2023","journal-title":"Plant Soil."},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"113655","DOI":"10.1016\/j.ecoenv.2022.113655","article-title":"Profiles of Antibiotic- and Heavy Metal-Related Resistance Genes in Animal Manure Revealed Using a Metagenomic Analysis","volume":"239","author":"Liu","year":"2022","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"ref_120","unstructured":"Nabuurs, G.-J., Mrabet, R., Abu Hatab, A., Bustamante, M., Clark, H., Havl\u00edk, P., House, J., Mbow, C., Ninan, K., and Popp, A. (2022). Chapter 7: Agriculture, Forestry and Other Land Uses. IPCC Sixth Assessment Report. Mitigation of Climate Change, Cambridge University Press."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"101024","DOI":"10.1016\/j.isci.2020.101024","article-title":"Compounding Effects of Climate Warming and Antibiotic Resistance","volume":"23","author":"Savage","year":"2020","journal-title":"iScience"},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"e70097","DOI":"10.1111\/1462-2920.70097","article-title":"Warming Is Associated With More Encoded Antimicrobial Resistance Genes and Transcriptions Within Five Drug Classes in Soil Bacteria: A Case Study and Synthesis","volume":"27","author":"Hacopian","year":"2025","journal-title":"Environ. Microbiol."},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"1979","DOI":"10.2147\/IDR.S369023","article-title":"The Phenomenon of Antibiotic Resistance in the Polar Regions: An Overview of the Global Problem","volume":"16","author":"Depta","year":"2023","journal-title":"Infect. Drug Resist."},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"100130","DOI":"10.1016\/j.seh.2025.100130","article-title":"Unravelling the Effects of Climate Change on the Soil-Plant-Atmosphere Interactions: A Critical Review","volume":"3","author":"Oishy","year":"2025","journal-title":"Soil. Environ. Health"},{"key":"ref_125","doi-asserted-by":"crossref","unstructured":"Szadziul, M., Goryluk-Salmonowicz, A., and Popowska, M. (2025). The Link between Antibiotic Resistance Level and Soil Physi-co-Chemical Properties. Front. Microbiol., 16.","DOI":"10.3389\/fmicb.2025.1584660"},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"e02063-21","DOI":"10.1128\/JCM.02063-21","article-title":"Selective Culture Medium for Screening of Fosfomycin Resistance in Enterobacterales","volume":"60","author":"Nordmann","year":"2022","journal-title":"J. Clin. Microbiol."},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"6666","DOI":"10.1038\/s41598-019-43182-x","article-title":"Development of a Novel Cultivation Technique for Uncultured Soil Bacteria","volume":"9","author":"Chaudhary","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1007\/s00248-024-02385-0","article-title":"Design and Validation of Primer Sets for the Detection and Quantification of Antibiotic Resistance Genes in Environmental Samples by Quantitative PCR","volume":"87","author":"Cabrera","year":"2024","journal-title":"Microb. Ecol."},{"key":"ref_129","doi-asserted-by":"crossref","unstructured":"Waseem, H., Jameel, S., Ali, J., Ur Rehman, H.S., Tauseef, I., Farooq, U., Jamal, A., and Ali, M.I. (2019). Contributions and Challenges of High Throughput QPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review. Molecules, 24.","DOI":"10.3390\/molecules24010163"},{"key":"ref_130","doi-asserted-by":"crossref","unstructured":"Taylor, W., Bohm, K., Dyet, K., Weaver, L., and Pattis, I. (2025). Comparative Analysis of QPCR and Metagenomics for Detecting Antimicrobial Resistance in Wastewater: A Case Study. BMC Res. Notes, 18.","DOI":"10.1186\/s13104-024-07027-9"},{"key":"ref_131","doi-asserted-by":"crossref","first-page":"121989","DOI":"10.1016\/j.watres.2024.121989","article-title":"National-Scale Antimicrobial Resistance Surveillance in Wastewater: A Comparative Analysis of HT QPCR and Met-agenomic Approaches","volume":"262","author":"Knight","year":"2024","journal-title":"Water Res."},{"key":"ref_132","doi-asserted-by":"crossref","unstructured":"Elbait, G.D., Daou, M., Abuoudah, M., Elmekawy, A., Hasan, S.W., Everett, D.B., Alsafar, H., Henschel, A., and Yousef, A.F. (2024). Comparison of QPCR and Metagenomic Sequencing Methods for Quantifying Antibiotic Resistance Genes in Wastewater. PLoS ONE, 19.","DOI":"10.1371\/journal.pone.0298325"},{"key":"ref_133","doi-asserted-by":"crossref","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":"ref_134","doi-asserted-by":"crossref","first-page":"230217","DOI":"10.1007\/s42832-023-0217-z","article-title":"Soil Microbial Ecology through the Lens of Metatranscriptomics","volume":"6","author":"Peng","year":"2023","journal-title":"Soil. Ecol. Lett."},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"128418","DOI":"10.1016\/j.jhazmat.2022.128418","article-title":"Integrated Metagenomic and Metatranscriptomic Analysis Reveals Actively Expressed Antibiotic Resistomes in the Plastisphere","volume":"430","author":"Wu","year":"2022","journal-title":"J. Hazard. Mater."},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"11981","DOI":"10.1038\/srep11981","article-title":"Mining Microbial Metatranscriptomes for Expression of Antibiotic Resistance Genes under Natural Conditions","volume":"5","author":"Versluis","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"6192","DOI":"10.1021\/acs.est.4c08284","article-title":"Evaluating Quantitative Metagenomics for Environmental Monitoring of Antibiotic Resistance and Establishing Detection Limits","volume":"59","author":"Davis","year":"2025","journal-title":"Environ. Sci. Technol."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"3753","DOI":"10.1038\/s41598-021-83081-8","article-title":"Critical Evaluation of Short, Long, and Hybrid Assembly for Contextual Analysis of Antibiotic Resistance Genes in Complex Environmental Metagenomes","volume":"11","author":"Brown","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_139","first-page":"479","article-title":"Functional Metagenomics as a Tool for Identification of New Antibiotic Resistance Genes from Natural Environments","volume":"73","author":"Istvan","year":"2016","journal-title":"Microb. Ecol."},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"W493","DOI":"10.1093\/nar\/gkad384","article-title":"ResFinderFG v2.0: A Database of Antibiotic Resistance Genes Obtained by Functional Metagenomics","volume":"51","author":"Gschwind","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.jgar.2024.12.018","article-title":"Identification of Novel FosX Family Determinants from Diverse Environmental Samples","volume":"41","author":"Kieffer","year":"2025","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"443","DOI":"10.4161\/viru.28196","article-title":"Functional Metagenomics for the Investigation of Antibiotic Resistance","volume":"5","author":"Mullany","year":"2014","journal-title":"Virulence"},{"key":"ref_143","first-page":"410","article-title":"Characterization of Antibiotic Resistomes by Reprogrammed Bacteriophage-Enabled Functional Metagenomics in Clinical Strains","volume":"8","author":"Apjok","year":"2023","journal-title":"Nat. Microbiol."},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"126096","DOI":"10.1016\/j.envpol.2025.126096","article-title":"High-Throughput QPCR Profiling of Antimicrobial Resistance Genes and Bacterial Loads in Wastewater and Receiving Environments","volume":"373","author":"Silvester","year":"2025","journal-title":"Environ. Pollut."},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"112582","DOI":"10.1016\/j.ecoenv.2021.112582","article-title":"Effect of Heavy Metals Pollution on the Composition and Diversity of the Intestinal Microbial Community of a Pygmy Grasshopper (Eucriotettix oculatus)","volume":"223","author":"Li","year":"2021","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"17838","DOI":"10.1021\/acs.est.4c02906","article-title":"High-Throughput Single-Cell Metabolic Labeling, Sorting, and Sequencing of Active Antibiotic-Resistant Bacteria in the Environment","volume":"58","author":"Lin","year":"2024","journal-title":"Environ. Sci. Technol."},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"14629","DOI":"10.1021\/acs.analchem.5c02141","article-title":"SPARC: An Orthogonal Cas12a\/Cas13a Dual-Channel CRISPR Platform for Reliable SNV Identification and Mutation Confirmation","volume":"97","author":"Zhong","year":"2025","journal-title":"Anal. Chem."},{"key":"ref_148","doi-asserted-by":"crossref","unstructured":"Walflor, H.S.M., Lucena, A.R.C., Tuon, F.F., Medeiros, L.C.S., and Faoro, H. (2022). Resensitization of Fosfomycin-Resistant Escherichia coli Using the CRISPR System. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23169175"},{"key":"ref_149","unstructured":"WHO (2025, November 30). Global Action Plan on Antimicrobial Resistance. Available online: https:\/\/www.who.int\/publications\/i\/item\/9789241509763."},{"key":"ref_150","unstructured":"WHO (2025, November 30). Global Antimicrobial Resistance and Use Surveillance System (GLASS). Available online: https:\/\/dataindonesia.id\/sektor-riil\/detail\/angka-konsumsi-ikan-ri-naik-jadi-5648-kgkapita-pada-2022."},{"key":"ref_151","unstructured":"WHO (2025, November 30). Antimicrobial Resistance Diagnostic Initiative. Available online: https:\/\/www.who.int\/publications\/i\/item\/9789240072015."},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1111\/tmi.13839","article-title":"Examining 7 Years of Implementing Quality Management Systems in Medical Laboratories in Sub-Saharan Africa","volume":"28","author":"Odhiambo","year":"2023","journal-title":"Trop. Med. Int. Health"},{"key":"ref_153","doi-asserted-by":"crossref","unstructured":"Mao, S., Soputhy, C., Lay, S., Jacobs, J., Ku, G.M., Chau, D., Chhea, C., and Ir, P. (2023). The Barriers and Facilitators of Implementing a National Laboratory-Based AMR Surveillance System in Cambodia: Key Informants\u2019 Perspectives and Assessments of Microbiology Laboratories. Front. Public Health, 11.","DOI":"10.3389\/fpubh.2023.1332423"},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"9","DOI":"10.4102\/ajlm.v11i1.1476","article-title":"Implementation of a Customised Antimicrobial Resistance Laboratory Scorecard in Cameroon, Ethiopia and Kenya","volume":"11","author":"Trollip","year":"2022","journal-title":"Afr. J. Lab. Med."},{"key":"ref_155","unstructured":"WOAH (2025, November 30). Terrestrial Animal Health Code. Available online: https:\/\/rr-europe.woah.org\/app\/uploads\/2020\/08\/oie-terrestrial-code-1_2019_en.pdf."},{"key":"ref_156","unstructured":"WOAH (2025, November 30). Annual Report on Antimicrobial Agents Intended for Use in Animals 8 Th Report Contents. Available online: https:\/\/www.woah.org\/app\/uploads\/2024\/05\/woah-amu-report-2024-final.pdf."},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"S93","DOI":"10.1086\/340246","article-title":"Antimicrobial Use and Resistance in Animals","volume":"34","author":"McEwen","year":"2002","journal-title":"Clin. Infect. Dis."},{"key":"ref_158","unstructured":"EC (2025, November 30). A European One Health Action Plan Against Antimicrobial Resistance. Available online: https:\/\/health.ec.europa.eu\/system\/files\/2020-01\/amr_2017_action-plan_0.pdf."},{"key":"ref_159","first-page":"e04666","article-title":"EMA and EFSA Joint Scientific Opinion on Measures to Reduce the Need to Use Antimicrobial Agents in Animal Husbandry in the European Union, and the Resulting Impacts on Food Safety (RONAFA)","volume":"15","author":"Murphy","year":"2017","journal-title":"EFSA J."},{"key":"ref_160","unstructured":"(2025, November 30). Regulation-2019\/6-EN-EUR-Lex. Available online: https:\/\/eur-lex.europa.eu\/eli\/reg\/2019\/6\/oj\/eng."},{"key":"ref_161","doi-asserted-by":"crossref","unstructured":"Ajulo, S., and Awosile, B. (2024). Global Antimicrobial Resistance and Use Surveillance System (GLASS 2022): Investigating the Rela-tionship between Antimicrobial Resistance and Antimicrobial Consumption Data across the Participating Countries. PLoS ONE, 19.","DOI":"10.1371\/journal.pone.0297921"},{"key":"ref_162","unstructured":"EC (2025, November 30). EU Steps up the Fight against Antimicrobial Resistance. Available online: https:\/\/ec.europa.eu\/commission\/presscorner\/detail\/en\/ip_23_3187."},{"key":"ref_163","doi-asserted-by":"crossref","unstructured":"EFSA (2025). The European Union Summary Report on Antimicrobial Resistance in Zoonotic and Indicator Bacteria from Humans, Animals and Food in 2022\u20132023. EFSA J., 23, e9237.","DOI":"10.2903\/j.efsa.2025.p230301"},{"key":"ref_164","unstructured":"EMA (2025, November 30). Categorisation of Antibiotics Used in Animals Promotes Responsible Use to Protect Public and Animal Health. Available online: https:\/\/www.ema.europa.eu\/en\/news\/categorisation-antibiotics-used-animals-promotes-responsible-use-protect-public-and-animal-health."},{"key":"ref_165","unstructured":"WHO (2025, November 30). Evaluation of Certain Veterinary Drug Residues in Food. Available online: https:\/\/www.who.int\/publications\/i\/item\/9789240095533."}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/15\/1\/29\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,26]],"date-time":"2025-12-26T05:27:18Z","timestamp":1766726838000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/15\/1\/29"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,24]]},"references-count":165,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,1]]}},"alternative-id":["pathogens15010029"],"URL":"https:\/\/doi.org\/10.3390\/pathogens15010029","relation":{},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,24]]}}}