International Journal of Advance Research Publication and Reviews

International Journal of Advance Research Publication and Reviews
Peer-Reviewed | Multi-Disciplinary Journal

Antibiotic Pollution and Environmental Antimicrobial Resistance: Resistomes, Gene Transfer and One Health Implications

Author

Thatipamula Renuka, Gaddam Sahithi, Erukala Bhanuprasad, G. Swetha, Nishat Fathima

Abstract

 Antimicrobial resistance (AMR) is conventionally framed as a clinical problem, yet its evolutionary origins and many of its transmission routes lie in the environment. Antibiotics are released into soils, rivers, sediments, and coastal waters through human and veterinary excretion, inadequately treated municipal and hospital wastewater, manure application, aquaculture, and discharges from drug manufacturing. These emissions, together with co-pollutants such as metals and biocides, exert selective pressure on microbial communities and enrich antibiotic resistance genes (ARGs) in environmental reservoirs collectively termed the environmental resistome. Horizontal gene transfer (HGT), mediated by plasmids, integrons, transposons, integrative and conjugative elements, and bacteriophages, connects these reservoirs with human and animal pathogens. This review synthesizes current evidence on the sources and fate of antibiotic pollution, the composition and origins of environmental resistomes, the mechanisms and environmental modulators of gene transfer, and the implications for human, animal, and ecosystem health within a One Health framework. It also evaluates risk assessment concepts and mitigation options, including manufacturing effluent controls, advanced wastewater treatment, stewardship in agriculture, sanitation, and integrated surveillance. Pharmacologists are well placed to contribute to this agenda by linking pharmacokinetics, excretion, environmental concentration thresholds, and stewardship. Key knowledge gaps remain in quantifying transmission risk, defining enforceable environmental concentration limits, and standardizing surveillance.

Keywords

antimicrobial resistance; antibiotic pollution; resistome; horizontal gene transfer; mobile genetic elements; wastewater; One Health

Full Text:

Download Paper PDF

References

Allen, H. K., Donato, J., Wang, H. H., Cloud-Hansen, K. A., Davies, J., & Handelsman, J. (2010). Call of the wild: Antibiotic resistance genes in natural environments. Nature Reviews Microbiology, 8(4), 251–259. https://doi.org/10.1038/nrmicro2312

Andersson, D. I., & Hughes, D. (2014). Microbiological effects of sublethal levels of antibiotics. Nature Reviews Microbiology, 12(7), 465–478. https://doi.org/10.1038/nrmicro3270

Ashbolt, N. J., Amézquita, A., Backhaus, T., Borriello, P., Brandt, K. K., Collignon, P., Coors, A., Finley, R., Gaze, W. H., Heberer, T., Lawrence, J. R., Larsson, D. G. J., McEwen, S. A., Ryan, J. J., Schönfeld, J., Silley, P., Snape, J. R., Van den Eede, C., & Topp, E. (2013). Human health risk assessment (HHRA) for environmental development and transfer of antibiotic resistance. Environmental Health Perspectives, 121(9), 993–1001. https://doi.org/10.1289/ehp.1206316

Balcázar, J. L. (2014). Bacteriophages as vehicles for antibiotic resistance genes in the environment. PLoS Pathogens, 10(7), e1004219. https://doi.org/10.1371/journal.ppat.1004219

Beaber, J. W., Hochhut, B., & Waldor, M. K. (2004). SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature, 427(6969), 72–74. https://doi.org/10.1038/nature02241

Bengtsson-Palme, J., Kristiansson, E., & Larsson, D. G. J. (2018). Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiology Reviews, 42(1), fux053. https://doi.org/10.1093/femsre/fux053

Bengtsson-Palme, J., & Larsson, D. G. J. (2016). Concentrations of antibiotics predicted to select for resistant bacteria: Proposed limits for environmental regulation. Environment International, 86, 140–149. https://doi.org/10.1016/j.envint.2015.10.015

Berendonk, T. U., Manaia, C. M., Merlin, C., Fatta-Kassinos, D., Cytryn, E., Walsh, F., Bürgmann, H., Sørum, H., Norström, M., Pons, M.-N., Kreuzinger, N., Huovinen, P., Stefani, S., Schwartz, T., Kisand, V., Baquero, F., & Martinez, J. L. (2015). Tackling antibiotic resistance: The environmental framework. Nature Reviews Microbiology, 13(5), 310–317. https://doi.org/10.1038/nrmicro3439

Blair, J. M. A., Webber, M. A., Baylay, A. J., Ogbolu, D. O., & Piddock, L. J. V. (2015). Molecular mechanisms of antibiotic resistance. Nature Reviews Microbiology, 13(1), 42–51. https://doi.org/10.1038/nrmicro3380

Brandt, K. K., Amézquita, A., Backhaus, T., Boxall, A., Coors, A., Heberer, T., Lawrence, J. R., Lazorchak, J., Schönfeld, J., Snape, J. R., Zhu, Y.-G., & Topp, E. (2015). Ecotoxicological assessment of antibiotics: A call for improved consideration of microorganisms. Environment International, 85, 189–205. https://doi.org/10.1016/j.envint.2015.09.013

Bürgmann, H., Frigon, D., Gaze, W. H., Manaia, C. M., Pruden, A., Singer, A. C., Smets, B. F., & Zhang, T. (2018). Water and sanitation: An essential battlefront in the war on antimicrobial resistance. FEMS Microbiology Ecology, 94(9), fiy101. https://doi.org/10.1093/femsec/fiy101

D'Costa, V. M., King, C. E., Kalan, L., Morar, M., Sung, W. W. L., Schwarz, C., Froese, D., Zazula, G., Calmels, F., Debruyne, R., Golding, G. B., Poinar, H. N., & Wright, G. D. (2011). Antibiotic resistance is ancient. Nature, 477(7365), 457–461. https://doi.org/10.1038/nature10388

Ebmeyer, S., Kristiansson, E., & Larsson, D. G. J. (2021). A framework for identifying the recent origins of mobile antibiotic resistance genes. Communications Biology, 4, 8. https://doi.org/10.1038/s42003-020-01545-5

Fick, J., Söderström, H., Lindberg, R. H., Phan, C., Tysklind, M., & Larsson, D. G. J. (2009). Contamination of surface, ground, and drinking water from pharmaceutical production. Environmental Toxicology and Chemistry, 28(12), 2522–2527. https://doi.org/10.1897/09-073.1

Food and Agriculture Organization of the United Nations, United Nations Environment Programme, World Health Organization, & World Organisation for Animal Health. (2022). One Health joint plan of action (2022–2026): Working together for the health of humans, animals, plants and the environment. FAO, UNEP, WHO, & WOAH.

Forsberg, K. J., Reyes, A., Wang, B., Selleck, E. M., Sommer, M. O. A., & Dantas, G. (2012). The shared antibiotic resistome of soil bacteria and human pathogens. Science, 337(6098), 1107–1111. https://doi.org/10.1126/science.1220761

Gaze, W. H., Krone, S. M., Larsson, D. G. J., Li, X.-Z., Robinson, J. A., Simonet, P., Smalla, K., Timinouni, M., Topp, E., Wellington, E. M., Wright, G. D., & Zhu, Y.-G. (2013). Influence of humans on evolution and mobilization of environmental antibiotic resistome. Emerging Infectious Diseases, 19(7), e120871. https://doi.org/10.3201/eid1907.120871

Gillings, M. R. (2014). Integrons: Past, present, and future. Microbiology and Molecular Biology Reviews, 78(2), 257–277. https://doi.org/10.1128/MMBR.00056-13

Gillings, M. R., Gaze, W. H., Pruden, A., Smalla, K., Tiedje, J. M., & Zhu, Y.-G. (2015). Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. The ISME Journal, 9(6), 1269–1279. https://doi.org/10.1038/ismej.2014.226

Gullberg, E., Cao, S., Berg, O. G., Ilbäck, C., Sandegren, L., Hughes, D., & Andersson, D. I. (2011). Selection of resistant bacteria at very low antibiotic concentrations. PLoS Pathogens, 7(7), e1002158. https://doi.org/10.1371/journal.ppat.1002158

Hendriksen, R. S., Munk, P., Njage, P., van Bunnik, B., McNally, L., Lukjancenko, O., Röder, T., Nieuwenhuijse, D., Pedersen, S. K., Kjeldgaard, J., Kaas, R. S., Clausen, P. T. L. C., Vogt, J. K., Leekitcharoenphon, P., van de Schans, M. G. M., Zuidema, T., de Roda Husman, A. M., Rasmussen, S., Petersen, B., … Aarestrup, F. M. (2019). Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nature Communications, 10, 1124. https://doi.org/10.1038/s41467-019-08853-3

Hernando-Amado, S., Coque, T. M., Baquero, F., & Martínez, J. L. (2019). Defining and combating antibiotic resistance from One Health and Global Health perspectives. Nature Microbiology, 4(9), 1432–1442. https://doi.org/10.1038/s41564-019-0503-9

Hiltunen, T., Virta, M., & Laine, A.-L. (2017). Antibiotic resistance in the wild: An eco-evolutionary perspective. Philosophical Transactions of the Royal Society B, 372(1712), 20160039. https://doi.org/10.1098/rstb.2016.0039

Johnston, C., Martin, B., Fichant, G., Polard, P., & Claverys, J.-P. (2014). Bacterial transformation: Distribution, shared mechanisms and divergent control. Nature Reviews Microbiology, 12(3), 181–196. https://doi.org/10.1038/nrmicro3199

Karkman, A., Do, T. T., Walsh, F., & Virta, M. P. J. (2018). Antibiotic-resistance genes in waste water. Trends in Microbiology, 26(3), 220–228. https://doi.org/10.1016/j.tim.2017.09.005

Klümper, U., Recker, M., Zhang, L., Yin, X., Zhang, T., Buckling, A., & Gaze, W. H. (2019). Selection for antimicrobial resistance is reduced when embedded in a natural microbial community. The ISME Journal, 13(12), 2927–2937. https://doi.org/10.1038/s41396-019-0483-z

Kolpin, D. W., Furlong, E. T., Meyer, M. T., Thurman, E. M., Zaugg, S. D., Barber, L. B., & Buxton, H. T. (2002). Pharmaceuticals, hormones, and other organic wastewater contaminants in U.S. streams, 1999–2000: A national reconnaissance. Environmental Science & Technology, 36(6), 1202–1211. https://doi.org/10.1021/es011055j

Kraemer, S. A., Ramachandran, A., & Perron, G. G. (2019). Antibiotic pollution in the environment: From microbial ecology to public policy. Microorganisms, 7(6), 180. https://doi.org/10.3390/microorganisms7060180

Kristiansson, E., Fick, J., Janzon, A., Grabic, R., Rutgersson, C., Weijdegård, B., Söderström, H., & Larsson, D. G. J. (2011). Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements. PLoS ONE, 6(2), e17038. https://doi.org/10.1371/journal.pone.0017038

Larsson, D. G. J. (2014). Pollution from drug manufacturing: Review and perspectives. Philosophical Transactions of the Royal Society B, 369(1656), 20130571. https://doi.org/10.1098/rstb.2013.0571

Larsson, D. G. J., de Pedro, C., & Paxeus, N. (2007). Effluent from drug manufactures contains extremely high levels of pharmaceuticals. Journal of Hazardous Materials, 148(3), 751–755. https://doi.org/10.1016/j.jhazmat.2007.07.008

Larsson, D. G. J., & Flach, C.-F. (2022). Antibiotic resistance in the environment. Nature Reviews Microbiology, 20(5), 257–269. https://doi.org/10.1038/s41579-021-00649-x

Leonard, A. F. C., Zhang, L., Balfour, A. J., Garside, R., Hawkey, P. M., Murray, A. K., Ukoumunne, O. C., & Gaze, W. H. (2018). Exposure to and colonisation by antibiotic-resistant E. coli in UK coastal water users: Environmental surveillance, exposure assessment, and epidemiological study (Beach Bum Survey). Environment International, 114, 326–333. https://doi.org/10.1016/j.envint.2017.11.003

Li, B., Yang, Y., Ma, L., Ju, F., Guo, F., Tiedje, J. M., & Zhang, T. (2015). Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. The ISME Journal, 9(11), 2490–2502. https://doi.org/10.1038/ismej.2015.59

Liu, Y.-Y., Wang, Y., Walsh, T. R., Yi, L.-X., Zhang, R., Spencer, J., Doi, Y., Tian, G., Dong, B., Huang, X., Yu, L.-F., Gu, D., Ren, H., Chen, X., Lv, L., He, D., Zhou, H., Liang, Z., Liu, J.-H., & Shen, J. (2016). Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: A microbiological and molecular biological study. The Lancet Infectious Diseases, 16(2), 161–168. https://doi.org/10.1016/S1473-3099(15)00424-7

Lopatkin, A. J., Huang, S., Smith, R. P., Srimani, J. K., Sysoeva, T. A., Bewick, S., Karig, D. K., & You, L. (2016). Antibiotics as a selective driver for conjugation dynamics. Nature Microbiology, 1, 16044. https://doi.org/10.1038/nmicrobiol.2016.44

Lübbert, C., Baars, C., Dayakar, A., Lippmann, N., Rodloff, A. C., Kinzig, M., & Sörgel, F. (2017). Environmental pollution with antimicrobial agents from bulk drug manufacturing industries in Hyderabad, South India, is associated with dissemination of extended-spectrum beta-lactamase and carbapenemase-producing pathogens. Infection, 45(4), 479–491. https://doi.org/10.1007/s15010-017-1007-2

Manaia, C. M. (2017). Assessing the risk of antibiotic resistance transmission from the environment to humans: Non-direct proportionality between abundance and risk. Trends in Microbiology, 25(3), 173–181. https://doi.org/10.1016/j.tim.2016.11.014

Modi, S. R., Lee, H. H., Spina, C. S., & Collins, J. J. (2013). Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature, 499(7457), 219–222. https://doi.org/10.1038/nature12212

Munk, P., Brinch, C., Møller, F. D., Petersen, T. N., Hendriksen, R. S., Seyfarth, A. M., Kjeldgaard, J. S., Svendsen, C. A., van Bunnik, B., Berglund, F., Global Sewage Surveillance Consortium, Larsson, D. G. J., Koopmans, M., Woolhouse, M., & Aarestrup, F. M. (2022). Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance. Nature Communications, 13, 7251. https://doi.org/10.1038/s41467-022-34312-7

Murray, C. J. L., Ikuta, K. S., Sharara, F., Swetschinski, L., Robles Aguilar, G., Gray, A., Han, C., Bisignano, C., Rao, P., Wool, E., Johnson, S. C., Browne, A. J., Chipeta, M. G., Fell, F., Hackett, S., Haines-Woodhouse, G., Kashef Hamadani, B. H., Kumaran, E. A. P., McManigal, B., … Naghavi, M. (2022). Global burden of bacterial antimicrobial resistance in 2019: A systematic analysis. The Lancet, 399(10325), 629–655. https://doi.org/10.1016/S0140-6736(21)02724-0

Nadimpalli, M. L., Marks, S. J., Montealegre, M. C., Gilman, R. H., Pajuelo, M. J., Saito, M., Tsukayama, P., Njenga, S. M., Kiiru, J., Swarthout, J., Islam, M. A., Julian, T. R., & Pickering, A. J. (2020). Urban informal settlements as hotspots of antimicrobial resistance and the need to curb environmental transmission. Nature Microbiology, 5(6), 787–795. https://doi.org/10.1038/s41564-020-0722-0

Ochman, H., Lawrence, J. G., & Groisman, E. A. (2000). Lateral gene transfer and the nature of bacterial innovation. Nature, 405(6784), 299–304. https://doi.org/10.1038/35012500

Pal, C., Bengtsson-Palme, J., Kristiansson, E., & Larsson, D. G. J. (2015). Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential. BMC Genomics, 16, 964. https://doi.org/10.1186/s12864-015-2153-5

Pärnänen, K. M. M., Narciso-da-Rocha, C., Kneis, D., Berendonk, T. U., Cacace, D., Do, T. T., Elpers, C., Fatta-Kassinos, D., Henriques, I., Jaeger, T., Karkman, A., Martinez, J. L., Michael, S. G., Michael-Kordatou, I., O'Sullivan, K., Rodriguez-Mozaz, S., Schwartz, T., Sheng, H., Sørum, H., … Manaia, C. M. (2019). Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence. Science Advances, 5(3), eaau9124. https://doi.org/10.1126/sciadv.aau9124

Partridge, S. R., Kwong, S. M., Firth, N., & Jensen, S. O. (2018). Mobile genetic elements associated with antimicrobial resistance. Clinical Microbiology Reviews, 31(4), e00088-17. https://doi.org/10.1128/CMR.00088-17

Pehrsson, E. C., Tsukayama, P., Patel, S., Mejía-Bautista, M., Sosa-Soto, G., Navarrete, K. M., Calderon, M., Cabrera, L., Hoyos-Arango, W., Bertoli, M. T., Berg, D. E., Gilman, R. H., & Dantas, G. (2016). Interconnected microbiomes and resistomes in low-income human habitats. Nature, 533(7602), 212–216. https://doi.org/10.1038/nature17672

Poirel, L., Rodriguez-Martinez, J.-M., Mammeri, H., Liard, A., & Nordmann, P. (2005). Origin of plasmid-mediated quinolone resistance determinant QnrA. Antimicrobial Agents and Chemotherapy, 49(8), 3523–3525. https://doi.org/10.1128/AAC.49.8.3523-3525.2005

Qiu, Z., Yu, Y., Chen, Z., Jin, M., Yang, D., Zhao, Z., Wang, J., Shen, Z., Wang, X., Qian, D., Huang, A., Zhang, B., & Li, J.-W. (2012). Nanoalumina promotes the horizontal transfer of multiresistance genes mediated by plasmids across genera. Proceedings of the National Academy of Sciences, 109(13), 4944–4949. https://doi.org/10.1073/pnas.1107254109

Rizzo, L., Manaia, C., Merlin, C., Schwartz, T., Dagot, C., Ploy, M. C., Michael, I., & Fatta-Kassinos, D. (2013). Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: A review. Science of the Total Environment, 447, 345–360. https://doi.org/10.1016/j.scitotenv.2013.01.032

Robinson, T. P., Bu, D. P., Carrique-Mas, J., Fèvre, E. M., Gilbert, M., Grace, D., Hay, S. I., Jiwakanon, J., Kakkar, M., Kariuki, S., Laxminarayan, R., Lubroth, J., Magnusson, U., Thi Ngoc, P., Van Boeckel, T. P., & Woolhouse, M. E. J. (2016). Antibiotic resistance is the quintessential One Health issue. Transactions of the Royal Society of Tropical Medicine and Hygiene, 110(7), 377–380. https://doi.org/10.1093/trstmh/trw048

Singer, A. C., Shaw, H., Rhodes, V., & Hart, A. (2016). Review of antimicrobial resistance in the environment and its relevance to environmental regulators. Frontiers in Microbiology, 7, 1728. https://doi.org/10.3389/fmicb.2016.01728

Smillie, C. S., Smith, M. B., Friedman, J., Cordero, O. X., David, L. A., & Alm, E. J. (2011). Ecology drives a global network of gene exchange connecting the human microbiome. Nature, 480(7376), 241–244. https://doi.org/10.1038/nature10571

Thanner, S., Drissner, D., & Walsh, F. (2016). Antimicrobial resistance in agriculture. mBio, 7(2), e02227-15. https://doi.org/10.1128/mBio.02227-15

United Nations Environment Programme. (2023). Bracing for superbugs: Strengthening environmental action in the One Health response to antimicrobial resistance. UNEP.

Van Boeckel, T. P., Brower, C., Gilbert, M., Grenfell, B. T., Levin, S. A., Robinson, T. P., Teillant, A., & Laxminarayan, R. (2015). Global trends in antimicrobial use in food animals. Proceedings of the National Academy of Sciences, 112(18), 5649–5654. https://doi.org/10.1073/pnas.1503141112

Van Boeckel, T. P., Pires, J., Silvester, R., Zhao, C., Song, J., Criscuolo, N. G., Gilbert, M., Bonhoeffer, S., & Laxminarayan, R. (2019). Global trends in antimicrobial resistance in animals in low- and middle-income countries. Science, 365(6459), eaaw1944. https://doi.org/10.1126/science.aaw1944

von Wintersdorff, C. J. H., Penders, J., van Niekerk, J. M., Mills, N. D., Majumder, S., van Alphen, L. B., Savelkoul, P. H. M., & Wolffs, P. F. G. (2016). Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer. Frontiers in Microbiology, 7, 173. https://doi.org/10.3389/fmicb.2016.00173

Wang, Y., Lu, J., Engelstädter, J., Zhang, S., Ding, P., Mao, L., Yuan, Z., Bond, P. L., & Guo, J. (2020). Non-antibiotic pharmaceuticals enhance the transmission of exogenous antibiotic resistance genes through bacterial transformation. The ISME Journal, 14(8), 2179–2196. https://doi.org/10.1038/s41396-020-0679-2

Wright, G. D. (2007). The antibiotic resistome: The nexus of chemical and genetic diversity. Nature Reviews Microbiology, 5(3), 175–186. https://doi.org/10.1038/nrmicro1614

Zhang, Q.-Q., Ying, G.-G., Pan, C.-G., Liu, Y.-S., & Zhao, J.-L. (2015). Comprehensive evaluation of antibiotics emission and fate in the river basins of China: Source analysis, multimedia modeling, and linkage to bacterial resistance. Environmental Science & Technology, 49(11), 6772–6782. https://doi.org/10.1021/acs.est.5b00729

Zhu, Y.-G., Gillings, M., Penuelas, J., Ok, Y. S., Wang, H.-T., & Rillig, M. C. (2019). Soil biota, antimicrobial resistance and planetary health. Environment International, 131, 105059. https://doi.org/10.1016/j.envint.2019.105059

Zhu, Y.-G., Johnson, T. A., Su, J.-Q., Qiao, M., Guo, G.-X., Stedtfeld, R. D., Hashsham, S. A., & Tiedje, J. M. (2013). Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proceedings of the National Academy of Sciences, 110(9), 3435–3440. https://doi.org/10.1073/pnas.1222743110

 

 

Top