2510001699
  • Open Access
  • Review
Environmental Antimicrobial Resistance: Current Status and Future Prospects
  • Naixiang Zhai *,   
  • Kevin V. Thomas,   
  • Jinglong Li,   
  • Jake W. O’Brien

Received: 19 Jun 2025 | Revised: 28 Sep 2025 | Accepted: 10 Oct 2025 | Published: 04 Nov 2025

Abstract

Antibiotics underpin modern medicine and food production, but their indiscriminate use has accelerated antimicrobial resistance (AMR). Here we profile ARG dissemination in water, soil, air and anthropogenic niches such as wastewater treatment plants, intensive farms and landfills. We show that sulfonamide resistance genes (sul1/sul2) dominate aquatic systems, while tetracycline and macrolide genes prevail in livestock environments. Emerging evidence links airborne ARGs to seasonal PM2.5 peaks and long range dust transport. We evaluate state of the art detection platforms—high throughput qPCR, Hi-C metagenomics, nanopore long reads and CRISPR-Cas diagnostics—and discuss their complementarity. Finally, we outline integrated One Health policies that couple real time genomic surveillance with antibiotic stewardship incentives, and spotlight novel agents such as gepotidacin and sulopenem that help address the innovation gap. Coordinated adoption of these strategies is essential to avert a post-antibiotic era. Global cooperation and forward-looking One Health frameworks will be crucial to meeting this challenge.

References 

  • 1.
    Ho, C.S.; Wong, C.T.; Aung, T.T.; et al. Antimicrobial resistance: A concise update. Lancet Microbe 2025, 6, 100947.
  • 2.
    O’Neill, J. Tackling Drug-Resistant Infections Globally: Final Report and Recommendations; Wellcome Trust: London, UK, 2016.
  • 3.
    Collaborators, A.R. Global burden of bacterial antimicrobial resistance in 2019: A systematic analysis. Lancet 2022, 399, 629–655.
  • 4.
    Organization, W.H. Global Strategy and Action Plan on Oral Health 2023–2030; World Health Organization: Geneva, Switzerland, 2024.
  • 5.
    Jonas, O.B.; Irwin, A.; Berthe, F.C.J.; et al. Drug-resistant infections: A threat to our economic future. World Rep. 2017, 2, 1–132.
  • 6.
    Browne, A.J.; Chipeta, M.G.; Haines-Woodhouse, G.; et al. Global antibiotic consumption and usage in humans, 2000–2018: A spatial modelling study. Lancet Health 2021, 5, e893–e904.
  • 7.
    Porter, G.; Kotwani, A.; Bhullar, L.; et al. Over-the-counter sales of antibiotics for human use in India: The challenges and opportunities for regulation. Law. Int. 2021, 21, 147–173.
  • 8.
    Van Boeckel, T.P.; Brower, C.; Gilbert, M.; et al. Global trends in antimicrobial use in food animals. Natl. Acad. Sci. USA 2015, 112, 5649–5654.
  • 9.
    Van Boeckel, T.P.; Glennon, E.E.; Chen, D.; et al. Reducing antimicrobial use in food animals. Science 2017, 357, 1350–1352.
  • 10.
    Mullard, A. 2023 FDA approvals. Rev. Drug Discov. 2024, 23, 88–95.
  • 11.
    Valiakos, G.; Kapna, I. Colistin resistant mcr genes prevalence in livestock animals (swine, bovine, poultry) from a multinational perspective. A systematic review. Sci. 2021, 8, 265.
  • 12.
    Van Bavel, B.; Berrang-Ford, L.; Moon, K.; et al. Intersections between climate change and antimicrobial resistance: A systematic scoping review. Lancet Health 2024, 8, e1118–e1128.
  • 13.
    Von Wintersdorff, C.J.; Penders, J.; Van Niekerk, J.M.; et al. Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer. Microbiol. 2016, 7, 173.
  • 14.
    Pärnänen, K.M.; Narciso-da-Rocha, C.; Kneis, D.; et al. Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence. Adv. 2019, 5, eaau9124.
  • 15.
    Foysal, M.J.; Neilan, B.A.; Timms, V. The impact of anthropogenic activities on antimicrobial and heavy metal resistance in aquatic environments. Environ. Microbiol. 2025, 91, e02317-24.
  • 16.
    Ding, Y.; Hao, J.; Xiao, W.; et al. Role of efflux pumps, their inhibitors, and regulators in colistin resistance. Microbiol. 2023, 14, 1207441.
  • 17.
    Cabral, D.J.; Wurster, J.I.; Belenky, P. Antibiotic persistence as a metabolic adaptation: Stress, metabolism, the host, and new directions. Pharmaceuticals 2018, 11, 14.
  • 18.
    Barman, S.; Kurnaz, L.B.; Leighton, R.; et al. Intrinsic antimicrobial resistance: Molecular biomaterials to combat microbial biofilms and bacterial persisters. Biomaterials 2024, 311, 122690.
  • 19.
    Zaidi, S.; Ali, K.; Khan, A.U. It’s all relative: Analyzing microbiome compositions, its significance, pathogenesis and microbiota derived biofilms: Challenges and opportunities for disease intervention. Microbiol. 2023, 205, 257.
  • 20.

    Ferreira, M.; Sousa, C.F.; Gameiro, P. Fluoroquinolone Metalloantibiotics to Bypass Antimicrobial Resistance Mechanisms: Decreased Permeation through Porins. Membranes 2020, 11, 3.

  • 21.
    Miguel-Arribas, A.; Wu, L.J.; Michaelis, C.; et al. Conjugation operons in Gram-positive bacteria with and without antitermination systems. Microorganisms 2022, 10, 587.
  • 22.
    Hinnekens, P.; Fayad, N.; Gillis, A.; et al. Conjugation across Bacillus cereus and kin: A review. Microbiol. 2022, 13, 1034440.
  • 23.
    Johnsborg, O.; Eldholm, V.; Håvarstein, L.S. Natural genetic transformation: Prevalence, mechanisms and function. Microbiol. 2007, 158, 767–778.
  • 24.
    Durrant, M.G.; Li, M.M.; Siranosian, B.A.; et al. A bioinformatic analysis of integrative mobile genetic elements highlights their role in bacterial adaptation. Cell Host Microbe 2020, 27, 140–153.e9.
  • 25.
    Peng, K.; Liu, Y.X.; Sun, X.; et al. Long-read metagenomic sequencing reveals that high-copy small plasmids shape the highly prevalent antibiotic resistance genes in animal fecal microbiome. Total Environ. 2023, 893, 164585.
  • 26.
    Blake, K.S.; Choi, J.; Dantas, G. Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria. Mol. Life Sci. 2021, 78, 2585–2606.
  • 27.
    Bonomo, R.A. β-Lactamases: A focus on current challenges. Cold Spring Perspect. Med. 2017, 7, a025239.
  • 28.
    Cui, C.Y.; He, Q.; Jia, Q.L.; et al. Evolutionary trajectory of the Tet (X) family: Critical residue changes towards high-level tigecycline resistance. Msystems 2021, 6, 00050-21.
  • 29.
    Sun, L.; Sun, L.; Li, X.; et al. A novel tigecycline adjuvant ML-7 reverses the susceptibility of tigecycline-resistant Klebsiella pneumoniae. Cell. Infect. Microbiol. 2022, 11, 809542.
  • 30.
    Lade, H.; Kim, J.-S. Molecular determinants of β-lactam resistance in methicillin-resistant Staphylococcus aureus (MRSA): An updated review. Antibiotics 2023, 12, 1362.
  • 31.
    Svetlov, M.S.; Syroegin, E.A.; Aleksandrova, E.V.; et al. Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance. Chem. Biol. 2021, 17, 412–420.
  • 32.

    Guffey, A.A.; Loll, P.J. Regulation of resistance in vancomycin-resistant enterococci: The VanRS two-component system. Microorganisms 2021, 9, 2026.

  • 33.
    O'Toole, R.F.; Leong, K.W.; Cumming, V.; et al. Vancomycin-resistant Enterococcus faecium and the emergence of new sequence types associated with hospital infection. Microbiol. 2023, 174, 104046.
  • 34.
    Rodríguez-Martínez, J.M.; Cano, M.E.; Velasco, C.; et al. Plasmid-mediated quinolone resistance: An update. Infect. Chemother. 2011, 17, 149–182.
  • 35.
    Mingardon, F.; Clement, C.; Hirano, K. Improving olefin tolerance and production in E. coli using native and evolved AcrB. Bioeng. 2015, 112, 879–888.
  • 36.
    Masuda, N.; Sakagawa, E.; Ohya, S.; et al. Substrate specificities of MexAB-OprM, MexCD-OprJ, and MexXY-oprM efflux pumps in Pseudomonas aeruginosa. Agents Chemother. 2000, 44, 3322–3327.
  • 37.
    Kumar, S.; Floyd, J.T.; He, G.; et al. Bacterial antimicrobial efflux pumps of the MFS and MATE transporter families: A review. Res. Dev. Antimicrob. Agents Chemother. 2013, 7, 1–21.
  • 38.
    Biswas, R.; et al. Overview on the role of heavy metals tolerance on developing antibiotic resistance in both Gram-negative and Gram-positive bacteria. Microbiol. 2021, 203, 2761–2770.
  • 39.
    Wales, A.D.; Davies, R.H. Co-Selection of Resistance to Antibiotics, Biocides and Heavy Metals, and Its Relevance to Foodborne Pathogens. Antibiotics 2015, 4, 567–604.
  • 40.
    Davies, R.; Wales, A. Antimicrobial resistance on farms: A review including biosecurity and the potential role of disinfectants in resistance selection. Rev. Food Sci. Food Saf. 2019, 18, 753–774.
  • 41.
    Wang, D.; Ning, Q.; Deng, Z.; et al. Role of environmental stresses in elevating resistance mutations in bacteria: Phenomena and mechanisms. Pollut. 2022, 307, 119603.
  • 42.
    Mo, C.Y.; Manning, S.A.; Roggiani, M.; et al. Systematically altering bacterial SOS activity under stress reveals therapeutic strategies for potentiating antibiotics. MSphere 2016, 1, 00163–16.
  • 43.
    Abdullah, S.; Almusallam, A.; Li, M.; et al. Whole genome-based genetic insights of bla NDM producing clinical E. coli isolates in hospital settings of Pakistant. Spectr. 2023, 11, e00584-23.
  • 44.
    Moses, I.B.; Santos, F.F.; Gales, A.C. Human colonization and infection by Staphylococcus pseudintermedius: An emerging and underestimated zoonotic pathogen. Microorganisms 2023, 11, 581.
  • 45.
    Cave, R.; Ter-Stepanyan, M.M.; Mkrtchyan, H.V. Short-and Long-Read Sequencing Reveals the Presence and Evolution of an IncF Plasmid Harboring bla CTX-M-15 and bla CTX-M-27 Genes in Escherichia coli ST131. Spectr. 2023, 11, e00356-23.
  • 46.
    Fuentes-Castillo, D.; Castro-Tardón, D.; Esposito, F.; et al. Genomic evidences of gulls as reservoirs of critical priority CTX-M-producing Escherichia coli in Corcovado Gulf, Patagonia. Total Environ. 2023, 874, 162564.
  • 47.
    Rodó, X.; Pozdniakova, S.; Borràs, S.; et al. Microbial richness and air chemistry in aerosols above the PBL confirm 2,000-km long-distance transport of potential human pathogens. Natl. Acad. Sci. USA 2024, 121, e2404191121.
  • 48.
    Cassini, A.; Högberg, L.D.; Plachouras, D.; et al. Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: A population-level modelling analysis. Lancet Dis. 2019, 19, 56–66.
  • 49.
    MacFadden, D.R.; McGough, S.F.; Fisman, D.; et al. Antibiotic resistance increases with local temperature. Clim. Chang. 2018, 8, 510–514.
  • 50.
    Roope, L.S.; Smith, R.D.; Pouwels, K.B.; et al. The challenge of antimicrobial resistance: What economics can contribute. Science 2019, 364, eaau4679.
  • 51.
    Stewardson, A.J.; Marimuthu, K.; Sengupta, S.; et al. Effect of carbapenem resistance on outcomes of bloodstream infection caused by Enterobacteriaceae in low-income and middle-income countries (PANORAMA): A multinational prospective cohort study. Lancet Dis. 2019, 19, 601–610.
  • 52.
    Iwashyna, T.J.; Ely, E.W.; Smith, D.M.; et al. Long-term cognitive impairment and functional disability among survivors of severe sepsis. JAMA 2010, 304, 1787–1794.
  • 53.
    Prescott, H.C.; Angus, D.C. Enhancing recovery from sepsis: A review. JAMA 2018, 319, 62–75.
  • 54.
    Hatch, R.; Young, D.; Barber, V.; et al. Anxiety, depression and post traumatic stress disorder after critical illness: A UK-wide prospective cohort study. Care 2018, 22, 310.
  • 55.
    Nelson, R.E.; Hyun, D.; Jezek, A.; et al. Mortality, length of stay, and healthcare costs associated with multidrug-resistant bacterial infections among elderly hospitalized patients in the United States. Infect. Dis. 2022, 74, 1070–1080.
  • 56.
    Venkatesan, P. WHO 2020 report on the antibacterial production and development pipeline. Lancet Microbe 2021, 2, e239.
  • 57.
    Furlan, J.P.R.; Sellera, F.P.; Lincopan, N.; et al. Catastrophic floods and antimicrobial resistance: Interconnected threats with wide-ranging impacts. One Health 2024, 19, 100891.
  • 58.
    Dabo, S.; Taylor, J.; Confer, A. Pasteurella multocida and bovine respiratory disease. Health Res. Rev. 2007, 8, 129–150.
  • 59.
    Snyder, E.; Credille, B. Mannheimia haemolytica and Pasteurella multocida in bovine respiratory disease: How are they changing in response to efforts to control them? Clin. Food Anim. Pract. 2020, 36, 253–268.
  • 60.
    Ström, G.H.; Björklund, H.; Barnes, A.C.; et al. Antibiotic use by small-scale farmers for freshwater aquaculture in the Upper Mekong Delta, Vietnam. Aquat. Anim. Health 2019, 31, 290–298.
  • 61.
    Ofori, S.; Di Leto, Y.; Smrčková, Š.; et al. Treated wastewater reuse for crop irrigation: A comprehensive health risk assessment. Sci. Adv. 2025, 4, 252–269.
  • 62.
    Ahmed, S.; Ahmed, M.W.; Hasan, M.Z.; et al. Assessing the incidence of catastrophic health expenditure and impoverishment from out-of-pocket payments and their determinants in Bangladesh: Evidence from the nationwide Household Income and Expenditure Survey 2016. Health 2022, 14, 84–96.
  • 63.
    Molla, A.A.; Chi, C. Who pays for healthcare in Bangladesh? An analysis of progressivity in health systems financing. J. Equity Health 2017, 16, 1–10.
  • 64.
    Bhuiyan, M.U.; Luby, S.P.; Alamgir, N.I.; et al. Costs of hospitalization with respiratory syncytial virus illness among children aged< 5 years and the financial impact on households in Bangladesh, 2010. Glob. Health 2017, 7, 010412.
  • 65.
    Greene, J.; Samuel-Jakubos, H. Building patient trust in hospitals: A combination of hospital-related factors and health care clinician behaviors. Comm. J. Qual. Patient Saf. 2021, 47, 768–774.
  • 66.
    Abu-Rub, L.I.; Abdelrahman, H.A.; Johar, A.R.A.; et al. Antibiotics prescribing in intensive care settings during the COVID-19 era: A systematic review. Antibiotics 2021, 10, 935.
  • 67.
    Langford, B.J.; Leung, V.; Lo, J.; et al. Antibiotic prescribing guideline recommendations in COVID-19: A systematic survey. Eclinicalmedicine 2023, 65,
  • 68.
    Petazzoni, G.; Bellinzona, G.; Merla, C.; et al. The COVID-19 pandemic sparked off a large-scale outbreak of carbapenem-resistant Acinetobacter baumannii from the endemic strains at an Italian hospital. Spectr. 2023, 11, e04505-22.
  • 69.
    Embracing a One Health Framework to Fight Antimicrobial Resistance; OECD Publishing: Paris, France, 2023.
  • 70.
    Vankelegom, M.; Burke, D.; Mohammed, A.M.F.; et al. Cost-effectiveness of a rapid point-of-care test for diagnosing patients with suspected bloodstream infection in Ireland. Med. Unlocked 2022, 32, 101056.
  • 71.
    Lewnard, J.A.; Charani, E.; Gleason, A.; et al. Burden of bacterial antimicrobial resistance in low-income and middle-income countries avertible by existing interventions: An evidence review and modelling analysis. Lancet 2024, 403, 2439–2454.
  • 72.
    Haenelt, S.; Wang, G.; Kasmanas, J.C.; et al. The fate of sulfonamide resistance genes and anthropogenic pollution marker intI1 after discharge of wastewater into a pristine river stream. Microbiol. 2023, 14, 1058350.
  • 73.
    Hendriksen, R.S.; Munk, P.; Njage, P.; et al. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Commun. 2019, 10, 1124.
  • 74.
    Wang, H.; Song, J.; Yan, M.; et al. Waste lignin-based cationic flocculants treating dyeing wastewater: Fabrication, performance, and mechanism. Total Environ. 2023, 874, 162383.
  • 75.

    Riechel, M.; Matzinger, A.; Pawlowsky-Reusing, E.; et al. Impacts of combined sewer overflows on a large urban river–Understanding the effect of different management strategies. Water 2016, 105, 264–273.

  • 76.
    Frey, S.K.; Topp, E.; Khan, I.U.; et al. Quantitative Campylobacter spp., antibiotic resistance genes, and veterinary antibiotics in surface and ground water following manure application: Influence of tile drainage control. Total Environ. 2015, 532, 138–153.
  • 77.
    Tian, H.; Liu, J.; Sun, J.; et al. Cross-media migration behavior of antibiotic resistance genes (ARGs) from municipal wastewater treatment systems (MWTSs): Fugitive characteristics, sharing mechanisms, and aerosolization behavior. Total Environ. 2023, 893, 164710.
  • 78.
    Drane, K.; Sheehan, M.; Whelan, A.; et al. The role of wastewater treatment plants in dissemination of antibiotic resistance: Source, measurement, removal and risk assessment. Antibiotics 2024, 13, 668.
  • 79.
    Zhang, L.; Adyari, B.; Hou, L.; et al. Mass-immigration shapes the antibiotic resistome of wastewater treatment plants. Total Environ. 2024, 908, 168193.
  • 80.
    Mulchandani, R.; Wang, Y.; Gilbert, M.; et al. Global trends in antimicrobial use in food-producing animals: 2020 to 2030. PLOS Public Health 2023, 3, e0001305.
  • 81.
    Tiseo, K.; Huber, L.; Gilbert, M.; et al. Global trends in antimicrobial use in food animals from 2017 to 2030. Antibiotics 2020, 9, 918.
  • 82.
    Wang, Z.; Lu, Q.; Mao, X.; et al. Prevalence of extended-Spectrum β-lactamase-resistant genes in Escherichia coli isolates from Central China during 2016–2019. Animals 2022, 12, 3191.
  • 83.
    Yang, J.T.; Zhang, L.J.; Lu, Y.; et al. Genomic insights into global bla CTX-M-55-positive Escherichia coli epidemiology and transmission characteristics. Spectr. 2023, 11, e01089-23.
  • 84.
    Caracciolo, A.B.; Visca, A.; Rauseo, J.; et al. Bioaccumulation of antibiotics and resistance genes in lettuce following cattle manure and digestate fertilization and their effects on soil and phyllosphere microbial communities. Pollut. 2022, 315, 120413.
  • 85.
    Sanz, C.; Casado, M.; Navarro-Martin, L.; et al. Implications of the use of organic fertilizers for antibiotic resistance gene distribution in agricultural soils and fresh food products. A plot-scale study. Total Environ. 2022, 815, 151973.
  • 86.
    Liu, Z.T.; Ma, R.A.; Zhu, D.; et al. Organic fertilization co-selects genetically linked antibiotic and metal (loid) resistance genes in global soil microbiome. Commun. 2024, 15, 5168.
  • 87.
    Amarasekara, N.R.; Mafiz, A.I.; Qian, X.; et al. Exploring the co-occurrence of antibiotic, metal, and biocide resistance genes in the urban agricultural environment. Agric. Food Res. 2023, 11, 100474.
  • 88.
    Kim, D.-H.; Oh, S.-E. Continuous high-solids anaerobic co-digestion of organic solid wastes under mesophilic conditions. Waste 2011, 31, 1943–1948.
  • 89.
    Ritchie, H.; Spooner, F. Large Amounts of Antibiotics Are Used in Livestock, but Several Countries Have Shown This Doesn’t Have to Be the Case; Our World in Data: Oxford, UK,
  • 90.
    Wang, Y.-X.; Sun, Y.; Huang, Z.; et al. Associations of urinary metal levels with serum hormones, spermatozoa apoptosis and sperm DNA damage in a Chinese population. Int. 2016, 94, 177–188.
  • 91.
    Larsson, D.J.; de Pedro, C.; Paxeus, N. Effluent from drug manufactures contains extremely high levels of pharmaceuticals. Hazard. Mater. 2007, 148, 751–755.
  • 92.
    Li, J.; Cao, J.; Zhu, Y.G.; et al. Global survey of antibiotic resistance genes in air. Sci. Technol. 2018, 52, 10975–10984.
  • 93.
    Mesquita, E.; Ribeiro, R.; Silva, C.J.; et al. An update on wastewater multi-resistant bacteria: Identification of clinical pathogens such as Escherichia coli O25b: H4-B2-ST131-producing CTX-M-15 ESBL and KPC-3 carbapenemase-producing Klebsiella oxytoca. Microorganisms 2021, 9, 576.
  • 94.
    Pilote, J.; Létourneau, V.; Girard, M.; et al. Quantification of airborne dust, endotoxins, human pathogens and antibiotic and metal resistance genes in Eastern Canadian swine confinement buildings. Aerobiologia 2019, 35, 283–296.
  • 95.
    Kormos, D.; Lin, K.; Pruden, A.; et al. Critical review of antibiotic resistance genes in the atmosphere. Sci. Process. Impacts 2022, 24, 870–883.
  • 96.
    Hellberg, R.S.; Haney, C.J.; Shen, Y.; et al. Development of a custom 16S rRNA gene library for the identification and molecular subtyping of Salmonella enterica. Microbiol. Methods 2012, 91, 448–458.
  • 97.
    Zhou, J.; He, Z.; Yang, Y.; et al. High-throughput metagenomic technologies for complex microbial community analysis: Open and closed formats. MBio 2015, 6, 02288-14.
  • 98.
    Forsberg, K.J.; Reyes, A.; Wang, B.; et al. The shared antibiotic resistome of soil bacteria and human pathogens. Science 2012, 337, 1107–1111.
  • 99.
    Kuleshov, V.; Jiang, C.; Zhou, W.; et al. Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Biotechnol. 2016, 34, 64–69.
  • 100.
    Brito, I.L.; Yilmaz, S.; Huang, K.; et al. Mobile genes in the human microbiome are structured from global to individual scales. Nature 2016, 535, 435–439.
  • 101.
    Humphries, R.; Bobenchik, A.M.; Hindler, J.A.; et al. Overview of changes to the clinical and laboratory standards institute performance standards for antimicrobial susceptibility testing, M100. Clin. Microbiol. 2021, 59, 00213-21.
  • 102.
    Hachich, E.M.; Di Bari, M.; Christ, A.P.G.; et al. Comparison of thermotolerant coliforms and Escherichia coli densities in freshwater bodies. J. Microbiol. 2012, 43, 675–681.
  • 103.
    Athamanolap, P.; Hsieh, K.; Chen, L.; et al. Integrated bacterial identification and antimicrobial susceptibility testing using PCR and high-resolution melt. Chem. 2017, 89, 11529–11536.
  • 104.
    Li, B.; Yan, T. Next generation sequencing reveals limitation of qPCR methods in quantifying emerging antibiotic resistance genes (ARGs) in the environment. Microbiol. Biotechnol. 2021, 105, 2925–2936.
  • 105.
    Kojabad, A.A.; Farzanehpour, M.; Galeh, H.E.G.; et al. Droplet digital PCR of viral‎ DNA/RNA, current progress, challenges, and future perspectives. Med. Virol. 2021, 93, 4182–4197.
  • 106.
    Cavé, L.; Brothier, E.; Abrouk, D.; et al. Efficiency and sensitivity of the digital droplet PCR for the quantification of antibiotic resistance genes in soils and organic residues. Microbiol. Biotechnol. 2016, 100, 10597–10608.
  • 107.
    Hoshino, T.; Inagaki, F. Molecular quantification of environmental DNA using microfluidics and digital PCR. Appl. Microbiol. 2012, 35, 390–395.
  • 108.
    Hindson, B.J.; Ness, K.D.; Masquelier, D.A.; et al. High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Chem. 2011, 83, 8604–8610.
  • 109.
    Avesar, J.; Rosenfeld, D.; Truman-Rosentsvit, M.; et al. Rapid phenotypic antimicrobial susceptibility testing using nanoliter arrays. Natl. Acad. Sci. USA 2017, 114, E5787–E5795.
  • 110.
    Ma, J.; Wang, J.; Yang, H.; et al. IncHI1 plasmids mediated the tet (X4) gene spread in Enterobacteriaceae in porcine. Microbiol. 2023, 14, 1128905.
  • 111.
    Mohsin, M.; Hassan, B.; Martins, W.M.; et al. Emergence of plasmid-mediated tigecycline resistance tet (X4) gene in Escherichia coli isolated from poultry, food and the environment in South Asia. Total Environ. 2021, 787, 147613.
  • 112.
    Stalder, T.; Press, M.O.; Sullivan, S.; et al. Linking the resistome and plasmidome to the microbiome. ISME 2019, 13, 2437–2446.
  • 113.
    Kalmar, L.; Gupta, S.; Kean, I.R.; et al. HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities. PLoS 2022, 18, e1009776.
  • 114.
    Spencer, S.J.; Tamminen, M.V.; Preheim, S.P.; et al. Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. ISME 2016, 10, 427–436.
  • 115.
    Liu, S.; Dai, S.; Deng, Y.; et al. Long-read epicPCR enhances species-level host identification of clinically relevant antibiotic resistance genes in environmental microbial communities. Int. 2025, 197, 109337.
  • 116.
    Yin, X.; Jiang, X.T.; Chai, B.; et al. ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes. Bioinformatics 2018, 34, 2263–2270.
  • 117.
    Bortolaia, V.; Kaas, R.S.; Ruppe, E.; et al. ResFinder 4.0 for predictions of phenotypes from genotypes. Antimicrob. Chemother. 2020, 75, 3491–3500.
  • 118.
    Blaak, H.; Kemper, M.A.; de Man, H.; et al. Nationwide surveillance reveals frequent detection of carbapenemase-producing Enterobacterales in Dutch municipal wastewater. Total Environ. 2021, 776, 145925.
  • 119.
    Knight, M.E.; Webster, G.; Perry, W.B.; et al. National-scale antimicrobial resistance surveillance in wastewater: A comparative analysis of HT qPCR and metagenomic approaches. Water Res. 2024, 262, 121989.
  • 120.
    Cansdale, A.; Chong, J.P. MAGqual: A stand-alone pipeline to assess the quality of metagenome-assembled genomes. Microbiome 2024, 12, 226.
  • 121.
    Behavioural Economics Team of the Australian Government (BETA). Nudge vs. Superbugs: 12 Months on, DoH; Behavioural Economics Team of the Australian Government (BETA): Barton, ACT, Australia, 2020.
  • 122.
    Dupont, N.; Diness, L.H.; Fertner, M.; et al. Antimicrobial reduction measures applied in Danish pig herds following the introduction of the “Yellow Card” antimicrobial scheme. Vet. Med. 2017, 138, 9–16.
  • 123.
    Unicomb, L.E.; Nizame, F.A.; Uddin, M.R.; et al. Motivating antibiotic stewardship in Bangladesh: Identifying audiences and target behaviours using the behaviour change wheel. BMC Health 2021, 21, 968.
  • 124.
    Zhang, X.Y.; Liu, T.S.; Hu, J.Y. Antibiotics removal and antimicrobial resistance control by ozone/peroxymonosulfate-biological activated carbon: A novel treatment process. Water 2024, 261, 122069.
  • 125.
    Hodges, J.C.; Bilderback, A.L.; Bridge, C.M.; et al. Assessment of the effectiveness of ultraviolet-C disinfection on transmission of hospital-acquired pathogens from prior room occupants. Steward. Healthc. Epidemiol. 2022, 2, e110.
  • 126.
    Liu, Y.; Matsuyama, H.; Jin, P.; et al. Tailored design of nanofiltration membrane for endocrine disrupting compounds removal: Mechanisms, current advancements, and future perspectives. Purif. Technol. 2025, 361, 131471.
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Zhai, N.; Thomas, K. V.; Li, J.; O’Brien, J. W. Environmental Antimicrobial Resistance: Current Status and Future Prospects. Environmental Contamination: Causes and Solutions 2025, 1 (1), 6. https://doi.org/10.53941/eccs.2025.100006.
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