D’Costa, V. M. et al. Antibiotic resistance is ancient. Nature 477, 457–461 (2011). This study shows that different ARGs are present in 30,000-year-old permafrost.
Bhullar, K. et al. Antibiotic resistance is prevalent in an isolated cave microbiome. PLoS ONE 7, e34953 (2012).
Google Scholar
Lugli, G. A. et al. Ancient bacteria of the Ötzi’s microbiome: a genomic tale from the Copper Age. Microbiome 5, 5 (2017).
Google Scholar
Perry, J., Waglechner, N. & Wright, G. The prehistory of antibiotic resistance. Cold Spring Harb. Perspect. Med. 6, a025197 (2016).
Google Scholar
Davies, J. & Davies, D. Origins and evolution of antibiotic resistance. Microbiol. Mol. Biol. Rev. 74, 417–433 (2010). This authoritative and educational review discusses in an insightful way the evolution of resistance, including its origins and future implications.
Google Scholar
Allen, H. K. et al. Call of the wild: antibiotic resistance genes in natural environments. Nat. Rev. Microbiol. 8, 251–259 (2010).
Google Scholar
Martinez, J. L. The role of natural environments in the evolution of resistance traits in pathogenic bacteria. Proc. R. Soc. B Biol. Sci. 276, 2521–2530 (2009).
Alcock, B. P. et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. https://doi.org/10.1093/nar/gkz935 (2019).
Google Scholar
Mackenzie, J. S. & Jeggo, M. The one health approach — why is it so important? Trop. Med. Infect. Dis. 4, 88 (2019).
Google Scholar
Buschhardt, T. et al. A one health glossary to support communication and information exchange between the human health, animal health and food safety sectors. One Health 13, 100263 (2021).
Google Scholar
Berendonk, T. U. et al. Tackling antibiotic resistance: the environmental framework. Nat. Rev. Microbiol. 13, 310–317 (2015).
Google Scholar
Wellington, E. M. et al. The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria. Lancet Infect. Dis. 13, 155–165 (2013).
Google Scholar
Bengtsson-Palme, J., Kristiansson, E. & Larsson, D. G. J. Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiol. Rev. https://doi.org/10.1093/femsre/fux053 (2017).
Google Scholar
Chow, L. K. M., Ghaly, T. M. & Gillings, M. R. A survey of sub-inhibitory concentrations of antibiotics in the environment. J. Environ. Sci. 99, 21–27 (2021).
Andersson, D. I. et al. Antibiotic resistance: turning evolutionary principles into clinical reality. FEMS Microbiol. Rev. 44, 171–188 (2020).
Google Scholar
Singer, A. C., Shaw, H., Rhodes, V. & Hart, A. Review of antimicrobial resistance in the environment and its relevance to environmental regulators. Front. Microbiol. https://doi.org/10.3389/fmicb.2016.01728 (2016).
Google Scholar
United Nations Environment Programme. Frontiers 2017: emerging issues of environmental concern, https://www.unenvironment.org/resources/frontiers-2017-emerging-issues-environmental-concern (2017).
Access to Medicines Foundation. 2020 antimicrobial resistance benchmark, https://accesstomedicinefoundation.org/publications/2020-antimicrobial-resistance-benchmark (2020).
Review on Antimicrobial Resistance. Antimicrobials in agriculture and the environment: reducing unnecessary waste, https://amr-review.org/Publications.html (2015).
European Parliament. Strategic approach to pharmaceuticals in the environment, https://www.europarl.europa.eu/doceo/document/TA-9-2020-0226_EN.pdf (2020).
WHO. Technical brief on water, sanitation, hygiene (WASH) and wastewater management to prevent infections and reduce the spread of antimicrobial resistance (AMR)., https://www.who.int/water_sanitation_health/publications/wash-wastewater-management-to-prevent-infections-and-reduce-amr/en/ (2020).
Graham, D. W. et al. Complexities in understanding antimicrobial resistance across domesticated animal, human, and environmental systems. Ann. N. Y. Acad. Sci. 1441, 17–30 (2019).
Google Scholar
Smalla, K., Cook, K., Djordjevic, S. P., Klümper, U. & Gillings, M. Environmental dimensions of antibiotic resistance: assessment of basic science gaps. FEMS Microbiol. Ecol. https://doi.org/10.1093/femsec/fiy195 (2018).
Google Scholar
Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013).
Google Scholar
Schulz, F. et al. Towards a balanced view of the bacterial tree of life. Microbiome https://doi.org/10.1186/s40168-017-0360-9 (2017).
Google Scholar
Forsberg, K. J. et al. The shared antibiotic resistome of soil bacteria and human pathogens. Science 337, 1107–1111 (2012). This study demonstrates numerous identical resistance gene loci between multiresistant soil bacteria and diverse human pathogens, providing evidence for recent gene exchange across species and environments.
Google Scholar
Berglund, F. et al. Identification of 76 novel B1 metallo-beta-lactamases through large-scale screening of genomic and metagenomic data. Microbiome 5, 134 (2017).
Google Scholar
Dantas, G., Sommer, M. O. A., Oluwasegun, R. D. & Church, G. M. Bacteria subsisting on antibiotics. Science 320, 100–103 (2008).
Google Scholar
Berglund, F. et al. Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes. Microb. Genomics https://doi.org/10.1099/mgen.0.000455 (2020).
Google Scholar
Pawlowski, A. C. et al. A diverse intrinsic antibiotic resistome from a cave bacterium. Nat. Commun. 7, 13803 (2016).
Google Scholar
Morar, M. & Wright, G. D. The genomic enzymology of antibiotic resistance. Annu. Rev. Genet. 44, 25–51 (2010).
Google Scholar
Andersson, D. I., Jerlström-Hultqvist, J. & Näsvall, J. Evolution of new functions de novo and from preexisting genes. Cold Spring Harb. Perspect. Biol. 7, a017996 (2015).
Google Scholar
Razavi, M., Kristiansson, E., Flach, C.-F. & Larsson, D. G. J. The association between insertion sequences and antibiotic resistance genes. mSphere https://doi.org/10.1128/msphere.00418-20 (2020).
Google Scholar
Partridge, S. R., Kwong, S. M., Firth, N. & Jensen, S. O. Mobile genetic elements associated with antimicrobial resistance. Clin. Microbiol. Rev. https://doi.org/10.1128/cmr.00088-17 (2018).
Google Scholar
Gillings, M. et al. The evolution of class 1 integrons and the rise of antibiotic resistance. J. Bacteriol. 190, 5095–5100 (2008).
Google Scholar
Razavi, M. et al. Discovery of the fourth mobile sulfonamide resistance gene. Microbiome https://doi.org/10.1186/s40168-017-0379-y (2017).
Google Scholar
Flach, C.-F. et al. Does antifouling paint select for antibiotic resistance? Sci. Total Environ. 590–591, 461–468 (2017).
Google Scholar
Shintani, M. et al. Plant species-dependent increased abundance and diversity of IncP-1 plasmids in the rhizosphere: new insights into their role and ecology. Front. Microbiol. 11, 590776 (2020).
Google Scholar
Baquero, F., Coque, T. M., Martínez, J.-L., Aracil-Gisbert, S. & Lanza, V. F. Gene transmission in the one health microbiosphere and the channels of antimicrobial resistance. Front. Microbiol. https://doi.org/10.3389/fmicb.2019.02892 (2019).
Google Scholar
Vandecraen, J., Chandler, M., Aertsen, A. & Van Houdt, R. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit. Rev. Microbiol. 43, 709–730 (2017).
Google Scholar
Depardieu, F., Podglajen, I., Leclercq, R., Collatz, E. & Courvalin, P. Modes and modulations of antibiotic resistance gene expression. Clin. Microbiol. Rev. 20, 79–114 (2007).
Google Scholar
Jutkina, J., Marathe, N. P., Flach, C. F. & Larsson, D. G. J. Antibiotics and common antibacterial biocides stimulate horizontal transfer of resistance at low concentrations. Sci. Total Environ. 616-617, 172–178 (2018).
Google Scholar
Scornec, H., Bellanger, X., Guilloteau, H., Groshenry, G. & Merlin, C. Inducibility of Tn916 conjugative transfer in Enterococcus faecalis by subinhibitory concentrations of ribosome-targeting antibiotics. J. Antimicrob. Chemother. 72, 2722–2728 (2017).
Google Scholar
Aminov, R. I. Horizontal gene exchange in environmental microbiota. Front. Microbiol. https://doi.org/10.3389/fmicb.2011.00158 (2011).
Google Scholar
Knöppel, A., Näsvall, J. & Andersson, D. I. Evolution of antibiotic resistance without antibiotic exposure. Antimicrob. Agents Chemother. https://doi.org/10.1128/aac.01495-17 (2017).
Google Scholar
Kimura, M. & Ohta, T. The average number of generations until fixation of a mutant gene in a finite population. Genetics 61, 763–771 (1969).
Google Scholar
Letten, A. D., Hall, A. R. & Levine, J. M. Using ecological coexistence theory to understand antibiotic resistance and microbial competition. Nat. Ecol. Evol. 5, 431–441 (2021).
Google Scholar
Waglechner, N. & Wright, G. D. Antibiotic resistance: it’s bad, but why isn’t it worse? BMC Biol. https://doi.org/10.1186/s12915-017-0423-1 (2017).
Google Scholar
Ebmeyer, S., Erik, K. & Larsson, D. G. J. A framework for identifying the recent origins of mobile antibiotic resistance genes. Commun. Biol. https://doi.org/10.1038/s42003-020-01545-5 (2021). This study amends, summarizes and scrutinizes current evidence for proposed recent origin species for mobile ARGs.
Google Scholar
Andersson, D. I. & Hughes, D. Persistence of antibiotic resistance in bacterial populations. FEMS Microbiol. Rev. 35, 901–911 (2011).
Google Scholar
Wang, J., Chu, L., Wojnárovits, L. & Takács, E. Occurrence and fate of antibiotics, antibiotic resistant genes (ARGs) and antibiotic resistant bacteria (ARB) in municipal wastewater treatment plant: an overview. Sci. Total. Environ. 744, 140997 (2020).
Google Scholar
Tran, N. H., Reinhard, M. & Gin, K. Y.-H. Occurrence and fate of emerging contaminants in municipal wastewater treatment plants from different geographical regions-a review. Water Res. 133, 182–207 (2018).
Google Scholar
Szymańska, U. et al. Presence of antibiotics in the aquatic environment in Europe and their analytical monitoring: recent trends and perspectives. Microchem. J. 147, 729–740 (2019).
Anwar, M., Iqbal, Q. & Saleem, F. Improper disposal of unused antibiotics: an often overlooked driver of antimicrobial resistance. Expert Rev. Antiinfect Ther. https://doi.org/10.1080/14787210.2020.1754797 (2020).
Google Scholar
Cabello, F. C. et al. Antimicrobial use in aquaculture re-examined: its relevance to antimicrobial resistance and to animal and human health. Environ. Microbiol. 15, 1917–1942 (2013).
Google Scholar
Cabello, F. C., Godfrey, H. P., Buschmann, A. H. & Dölz, H. J. Aquaculture as yet another environmental gateway to the development and globalisation of antimicrobial resistance. Lancet Infect. Dis. 16, e127–e133 (2016).
Google Scholar
Taylor, P. & Reeder, R. Antibiotic use on crops in low and middle-income countries based on recommendations made by agricultural advisors. CABI Agric. Biosci. https://doi.org/10.1186/s43170-020-00001-y (2020).
Google Scholar
Larsson, D. G. J. Pollution from drug manufacturing: review and perspectives. Philos. Trans. R. Soc. B Biol. Sci. 369, 20130571 (2014).
Larsson, D. G. J., De Pedro, C. & Paxeus, N. Effluent from drug manufactures contains extremely high levels of pharmaceuticals. J. Hazard. Mater. 148, 751–755 (2007).
Google Scholar
Milaković, M. et al. Pollution from azithromycin-manufacturing promotes macrolide-resistance gene propagation and induces spatial and seasonal bacterial community shifts in receiving river sediments. Environ. Int. 123, 501–511 (2019).
Google Scholar
Bielen, A. et al. Negative environmental impacts of antibiotic-contaminated effluents from pharmaceutical industries. Water Res. 126, 79–87 (2017).
Google Scholar
Fick, J. et al. Contamination of surface, ground, and drinking water from pharmaceutical production. Environ. Toxicol. Chem. 28, 2522–2527 (2009).
Google Scholar
Bengtsson-Palme, J. & Larsson, D. G. J. Concentrations of antibiotics predicted to select for resistant bacteria: proposed limits for environmental regulation. Environ. Int. 86, 140–149 (2016). This study uses a simplified approach based on available MIC data for many species to predict concentrations of 111 antibiotics that are not likely to select for resistance.
Google Scholar
Gullberg, E. et al. Selection of resistant bacteria at very low antibiotic concentrations. PLoS Pathog. 7, e1002158 (2011).
Google Scholar
Karkman, A., Pärnänen, K. & Larsson, D. G. J. Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments. Nat. Commun. https://doi.org/10.1038/s41467-018-07992-3 (2019).
Google Scholar
Yang, Y., Li, B., Zou, S., Fang, H. H. P. & Zhang, T. Fate of antibiotic resistance genes in sewage treatment plant revealed by metagenomic approach. Water Res. 62, 97–106 (2014).
Google Scholar
Bengtsson-Palme, J. et al. Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics. Sci. Total Environ. 572, 697–712 (2016).
Google Scholar
Manaia, C. M. et al. Antibiotic resistance in wastewater treatment plants: tackling the black box. Environ. Int. 115, 312–324 (2018).
Google Scholar
Flach, C. F., Genheden, M., Fick, J. & Joakim Larsson, D. G. A comprehensive screening of Escherichia coli isolates from Scandinavia’s largest sewage treatment plant indicates no selection for antibiotic resistance. Environ. Sci. Technol. 52, 11419–11428 (2018).
Google Scholar
Kraupner, N. et al. Evidence for selection of multi-resistant E. coli by hospital effluent. Environ. Int. 150, 106436 (2021).
Google Scholar
Flach, C. F. et al. Isolation of novel IncA/C and IncN fluoroquinolone resistance plasmids from an antibiotic-polluted lake. J. Antimicrob. Chemother. 70, 2709–2717 (2015).
Google Scholar
Bengtsson-Palme, J., Boulund, F., Fick, J., Kristiansson, E. & Larsson, D. G. J. Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Front. Microbiol. https://doi.org/10.3389/fmicb.2014.00648 (2014).
Google Scholar
Marathe, N. P. et al. Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste. Environ. Int. 112, 279–286 (2018).
Google Scholar
Thiele-Bruhn, S. Pharmaceutical antibiotic compounds in soils–a review. J. Plant Nutr. Soil Sci. 166, 145–167 (2003).
Google Scholar
Li, W., Shi, Y., Gao, L., Liu, J. & Cai, Y. Occurrence, distribution and potential affecting factors of antibiotics in sewage sludge of wastewater treatment plants in China. Sci. Total. Environ. 445–446, 306–313 (2013).
Google Scholar
Reinthaler, F. F. et al. Resistance patterns of Escherichia coli isolated from sewage sludge in comparison with those isolated from human patients in 2000 and 2009. J. Water Health 11, 13–20 (2013).
Google Scholar
Rutgersson, C. et al. Long-term application of Swedish sewage sludge on farmland does not cause clear changes in the soil bacterial resistome. Environ. Int. 137, 105339 (2020).
Google Scholar
Jechalke, S., Heuer, H., Siemens, J., Amelung, W. & Smalla, K. Fate and effects of veterinary antibiotics in soil. Trends Microbiol. 22, 536–545 (2014).
Google Scholar
Boxall, A. B. et al. Pharmaceuticals and personal care products in the environment: what are the big questions? Environ. Health Perspect. 120, 1221–1229 (2012).
Google Scholar
Song, J., Rensing, C., Holm, P. E., Virta, M. & Brandt, K. K. Comparison of metals and tetracycline as selective agents for development of tetracycline resistant bacterial communities in agricultural soil. Environ. Sci. Technol. 51, 3040–3047 (2017).
Google Scholar
Jechalke, S. et al. Plasmid-mediated fitness advantage of Acinetobacter baylyi in sulfadiazine-polluted soil. FEMS Microbiol. Lett. 348, 127–132 (2013). This study shows that a commonly used antibiotic in pig farming has the potential to select for a resistant Acinetobacter strain in manure-amended soils.
Google Scholar
Pal, C. et al. Metal resistance and its association with antibiotic resistance. Adv. Microb. Physiol. 70, 261–313 (2017).
Google Scholar
Wales, A. & Davies, R. Co-selection of resistance to antibiotics, biocides and heavy metals, and its relevance to foodborne pathogens. Antibiotics 4, 567–604 (2015).
Google Scholar
Pal, C., Bengtsson-Palme, J., Kristiansson, E. & Larsson, D. G. J. Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential. BMC Genomics https://doi.org/10.1186/s12864-015-2153-5 (2015).
Google Scholar
Klümper, U. et al. Metal stressors consistently modulate bacterial conjugal plasmid uptake potential in a phylogenetically conserved manner. ISME J. 11, 152–165 (2017).
Google Scholar
Jutkina, J., Rutgersson, C., Flach, C. F. & Joakim Larsson, D. G. An assay for determining minimal concentrations of antibiotics that drive horizontal transfer of resistance. Sci. Total. Environ. 548–549, 131–138 (2016).
Google Scholar
Wang, Y. et al. Non-antibiotic pharmaceuticals enhance the transmission of exogenous antibiotic resistance genes through bacterial transformation. ISME J. 14, 2179–2196 (2020).
Google Scholar
Klumper, U. et al. Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community. ISME J. 9, 934–945 (2015). This study shows that plasmids that are common in pathogens can easily be taken up by diverse environmental bacteria, thereby providing pathways for the exchange of resistance genes.
Google Scholar
Gillings, M. R., Paulsen, I. T. & Tetu, S. G. Genomics and the evolution of antibiotic resistance. Ann. N. Y. Acad. Sci. 1388, 92–107 (2017).
Google Scholar
Heuer, H. & Smalla, K. Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol. Rev. 36, 1083–1104 (2012).
Google Scholar
Bengtsson-Palme, J. & Larsson, D. G. Antibiotic resistance genes in the environment: prioritizing risks. Nat. Rev. Microbiol. 13, 396 (2015).
Google Scholar
Leonard, A. F. C. et al. Exposure to and colonisation by antibiotic-resistant E. coli in UK coastal water users: environmental surveillance, exposure assessment, and epidemiological study (Beach Bum Survey). Environ. Int. 114, 326–333 (2018). This is one of few studies showing that people more likely to ingest surface waters are also more prone to be carriers of resistant bacteria compared with matched controls.
Google Scholar
Manaia, C. M. Assessing the risk of antibiotic resistance transmission from the environment to humans: non-direct proportionality between abundance and risk. Trends Microbiol. 25, 173–181 (2017).
Google Scholar
Schijven, J. F., Blaak, H., Schets, F. M. & De Roda Husman, A. M. Fate of extended-spectrum β-lactamase-producing Escherichia coli from faecal sources in surface water and probability of human exposure through swimming. Environ. Sci. Technol. 49, 11825–11833 (2015).
Google Scholar
Collignon, P., Beggs, J. J., Walsh, T. R., Gandra, S. & Laxminarayan, R. Anthropological and socioeconomic factors contributing to global antimicrobial resistance: a univariate and multivariable analysis. Lancet Planet. Health 2, e398–e405 (2018).
Google Scholar
Dancer, S. J. Controlling hospital-acquired infection: focus on the role of the environment and new technologies for decontamination. Clin. Microbiol. Rev. 27, 665–690 (2014).
Google Scholar
Weber, D. J., Anderson, D. & Rutala, W. A. The role of the surface environment in healthcare-associated infections. Curr. Opin. Infect. Dis. 26, 338–344 (2013).
Google Scholar
Søraas, A., Sundsfjord, A., Sandven, I., Brunborg, C. & Jenum, P. A. Risk factors for community-acquired urinary tract infections caused by ESBL-producing Enterobacteriaceae –a case–control study in a low prevalence country. PLoS ONE 8, e69581 (2013).
Google Scholar
Zhou, S.-Y.-D. et al. Prevalence of antibiotic resistome in ready-to-eat salad. Front. Public Health https://doi.org/10.3389/fpubh.2020.00092 (2020).
Google Scholar
Uyttendaele, M. et al. Microbial hazards in irrigation water: standards, norms, and testing to manage use of water in fresh produce primary production. Compr. Rev. Food Sci. Food Saf. 14, 336–356 (2015).
Reid, C. J., Blau, K., Jechalke, S., Smalla, K. & Djordjevic, S. P. Whole genome sequencing of Escherichia coli from store-bought produce. Front. Microbiol. 10, 3050 (2020).
Google Scholar
Blau, K. et al. The transferable resistome of produce. mBio 9, e01300-18 (2018).
Google Scholar
Zhu, Y.-G. et al. Soil biota, antimicrobial resistance and planetary health. Environ. Int. 131, 105059 (2019).
Google Scholar
Pal, C., Bengtsson-Palme, J., Kristiansson, E. & Larsson, D. G. J. The structure and diversity of human, animal and environmental resistomes. Microbiome 4, 54 (2016).
Google Scholar
Kozajda, A., Jeżak, K. & Kapsa, A. Airborne Staphylococcus aureus in different environments — a review. Environ. Sci. Pollut. Res. 26, 34741–34753 (2019).
Google Scholar
Ashbolt, N. J. et al. Human health risk assessment (HHRA) for environmental development and transfer of antibiotic resistance. Environ. Health Perspect. 121, 993–1001 (2013).
Google Scholar
Franz, E., Schijven, J., De Roda Husman, A. M. & Blaak, H. Meta-regression analysis of commensal and pathogenic Escherichia coli survival in soil and water. Environ. Sci. Technol. 48, 6763–6771 (2014).
Google Scholar
Lewis, K. Platforms for antibiotic discovery. Nat. Rev. Drug. Discov. 12, 371–387 (2013).
Google Scholar
Linton, K. B., Richmond, M. H., Bevan, R. & Gillespie, W. A. Antibiotic resistance and R factors in coliform bacilli isolated from hospital and domestic sewage. J. Med. Microbiol. 7, 91–103 (1974).
Google Scholar
Huijbers, P., Joakim Larsson, D. G. & Flach, C. F. Surveillance of antibiotic resistant Escherichia coli in human populations through urban wastewater in ten European countries. Environ. Pollut. 261, 114200 (2020).
Google Scholar
Hutinel, M. et al. Population-level surveillance of antibiotic resistance in Escherichia coli through sewage analysis. Euro Surveill. https://doi.org/10.2807/1560-7917.es.2019.24.37.1800497 (2019).
Google Scholar
Aarestrup, F. M. & Woolhouse, M. E. J. Using sewage for surveillance of antimicrobial resistance. Science 367, 630–632 (2020).
Google Scholar
Kwak, Y. K. et al. Surveillance of antimicrobial resistance among Escherichia coli in wastewater in Stockholm during 1 year: does it reflect the resistance trends in the society? Int. J. Antimicrob. Agents 45, 25–32 (2015).
Google Scholar
Parnanen, K. M. M. et al. Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence. Sci. Adv. 5, eaau9124 (2019).
Google Scholar
Hendriksen, R. S. et al. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nat. Commun. 10, 1124 (2019). This is the most comprehensive survey of ARGs in sewage across the world to date, showing distinct differences between regions.
Google Scholar
Huijbers, P. M. C., Flach, C. F. & Larsson, D. G. J. A conceptual framework for the environmental surveillance of antibiotics and antibiotic resistance. Environ. Int. 130, 104880 (2019).
Google Scholar
Böhm, M.-E., Razavi, M., Marathe, N. P., Flach, C.-F. & Larsson, D. G. J. Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities. Microbiome https://doi.org/10.1186/s40168-020-00814-z (2020). Using a functional assay targeting mobile genes, this study explores environment communities and finds a completely novel resistance gene that had escaped discovery in clinics despite its presence in pathogens on different continents.
Google Scholar
Flach, C.-F., Hutinel, M., Razavi, M., Åhrén, C. & Larsson, D. G. J. Monitoring of hospital sewage shows both promise and limitations as an early-warning system for carbapenemase-producing Enterobacterales in a low-prevalence setting. Water Res. 200, 117261 (2021).
Google Scholar
Karkman, A., Berglund, F., Flach, C.-F., Kristiansson, E. & Larsson, D. G. J. Predicting clinical resistance prevalence using sewage metagenomic data. Commun. Biol. https://doi.org/10.1038/s42003-020-01439-6 (2020).
Google Scholar
European Centre for Disease Prevention and Control. Surveillance of antimicrobial resistance in Europe 2017 (Stockholm, Sweden, 2018).
Hovi, T. et al. Role of environmental poliovirus surveillance in global polio eradication and beyond. Epidemiol. Infect. 140, 1–13 (2012).
Google Scholar
Agrawal, S., Orschler, L. & Lackner, S. Long-term monitoring of SARS-CoV-2 RNA in wastewater of the Frankfurt metropolitan area in southern Germany. Sci. Rep. https://doi.org/10.1038/s41598-021-84914-2 (2021).
Google Scholar
Medema, G., Heijnen, L., Elsinga, G., Italiaander, R. & Brouwer, A. Presence of SARS-coronavirus-2 RNA in sewage and correlation with reported COVID-19 prevalence in the early stage of the epidemic in the Netherlands. Environ. Sci. Technol. Lett. 7, 511–516 (2020).
Google Scholar
Lundstrom, S. V. et al. Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms. Sci. Total Environ. 553, 587–595 (2016).
Google Scholar
McCann, C. M. et al. Understanding drivers of antibiotic resistance genes in High Arctic soil ecosystems. Environ. Int. 125, 497–504 (2019).
Google Scholar
Pruden, A., Arabi, M. & Storteboom, H. N. Correlation between upstream human activities and riverine antibiotic resistance genes. Environ. Sci. Technol. 46, 11541–11549 (2012).
Google Scholar
Zhu, Y.-G. et al. Continental-scale pollution of estuaries with antibiotic resistance genes. Nat. Microbiol. 2, 16270 (2017).
Google Scholar
Zhu, Y.-G. et al. Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proc. Natl Acad. Sci. USA 110, 3435–3440 (2013).
Google Scholar
Knapp, C. W., Dolfing, J., Ehlert, P. A. I. & Graham, D. W. Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940. Environ. Sci. Technol. 44, 580–587 (2010).
Google Scholar
Nesme, J. & Simonet, P. The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria. Environ. Microbiol. 17, 913–930 (2015).
Google Scholar
Finley, R. L. et al. The scourge of antibiotic resistance: the important role of the environment. Clin. Infect. Dis. 57, 704–710 (2013).
Google Scholar
Sjölund, M. et al. Dissemination of multidrug-resistant bacteria into the Arctic. Emerg. Infect. Dis. 14, 70–72 (2008).
Google Scholar
Zhu, G. et al. Air pollution could drive global dissemination of antibiotic resistance genes. ISME J. https://doi.org/10.1038/s41396-020-00780-2 (2020).
Google Scholar
Nichols, D. et al. Use of Ichip for high-throughput in situ cultivation of “Uncultivable” microbial species. Appl. Environ. Microbiol. 76, 2445–2450 (2010).
Google Scholar
Ashton, P. M. et al. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat. Biotechnol. 33, 296–300 (2015).
Google Scholar
Spencer, S. J. et al. Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. ISME J. 10, 427–436 (2016).
Google Scholar
Rice, E. W., Wang, P., Smith, A. L. & Stadler, L. B. Determining hosts of antibiotic resistance genes: a review of methodological advances. Environ. Sci. Technol. Lett. 7, 282–291 (2020).
Google Scholar
Sivalingam, P., Poté, J. & Prabakar, K. Extracellular DNA (eDNA): neglected and potential sources of antibiotic resistant genes (ARGs) in the aquatic environments. Pathogens 9, 874 (2020).
Google Scholar
Bengtsson-Palme, J., Larsson, D. G. J. & Kristiansson, E. Using metagenomics to investigate human and environmental resistomes. J. Antimicrob. Chemother. 72, 2690–2703 (2017).
Google Scholar
Karkman, A. et al. High-throughput quantification of antibiotic resistance genes from an urban wastewater treatment plant. FEMS Microbiol. Ecol. 92, https://doi.org/10.1093/femsec/fiw014 (2016).
Gillings, M. R. et al. Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. ISME J. 9, 1269–1279 (2015).
Google Scholar
Gaze, W. H., Abdouslam, N., Hawkey, P. M. & Wellington, E. M. H. Incidence of Class 1 integrons in a quaternary ammonium compound-polluted environment. Antimicrob. Agents Chemother. 49, 1802–1807 (2005).
Google Scholar
Sommer, M. O. A., Munck, C., Toft-Kehler, R. V. & Andersson, D. I. Prediction of antibiotic resistance: time for a new preclinical paradigm? Nat. Rev. Microbiol. 15, 689–696 (2017). This article highlights the needs to consider the environmental gene reservoir and other factors influencing resistance evolution in the development process for new antibiotics.
Google Scholar
Pehrsson, E. C., Forsberg, K. J., Gibson, M. K., Ahmadi, S. & Dantas, G. Novel resistance functions uncovered using functional metagenomic investigations of resistance reservoirs. Front. Microbiol. https://doi.org/10.3389/fmicb.2013.00145 (2013).
Google Scholar
Kim, C., Ryu, H.-D., Chung, E. G., Kim, Y. & Lee, J.-K. A review of analytical procedures for the simultaneous determination of medically important veterinary antibiotics in environmental water: sample preparation, liquid chromatography, and mass spectrometry. J. Environ. Manag. 217, 629–645 (2018).
Google Scholar
Fahrenfeld, N. & Bisceglia, K. J. Emerging investigators series: sewer surveillance for monitoring antibiotic use and prevalence of antibiotic resistance: urban sewer epidemiology. Environ. Sci. Water Res. Technol. 2, 788–799 (2016).
Google Scholar
Anliker, S. et al. Assessing emissions from pharmaceutical manufacturing based on temporal high-resolution mass spectrometry data. Environ. Sci. Technol. 54, 4110–4120 (2020). This recent study elegantly uses the erratic emission profiles of drugs from manufacturing plants to attribute a large portion of the pharmaceutical residues found in a Swiss river to industrial emissions, further showing that curbing such pollution is an ongoing, worldwide challenge.
Google Scholar
Klümper, U. et al. Selection for antimicrobial resistance is reduced when embedded in a natural microbial community. ISME J. 13, 2927–2937 (2019).
Google Scholar
Kraupner, N. et al. Selective concentrations for trimethoprim resistance in aquatic environments. Environ. Int. 144, 106083 (2020).
Google Scholar
Murray, A. K. et al. Novel insights into selection for antibiotic resistance in complex microbial communities. mBio https://doi.org/10.1128/mbio.00969-18 (2018).
Google Scholar
Government of India. Environment (Protection) Amendment Rules, 2020 – Inviting comments/suggestions on Environmental Standards for Bulk Drug and Formulation (Pharmaceutical) Industry, http://moef.gov.in/g-s-r-44-e-date-23-01-2020-environment-protection-amendment-rules-2020-inviting-commentssuggestions-on-environmental-standards-for-bulk-drug-and-formulation-pharmaceutical-indu/ (2020).
Tell, J. et al. Science-based targets for antibiotics in receiving waters from pharmaceutical manufacturing operations. Integr. Environ. Assess. Manag. 15, 312–319 (2019).
Google Scholar
Greenfield, B. K. et al. Modeling the emergence of antibiotic resistance in the environment: an analytical solution for the minimum selection concentration. Antimicrob. Agents Chemother. https://doi.org/10.1128/aac.01686-17 (2018).
Google Scholar
Murray, A. K. et al. The ‘Selection end points in Communities of bacTeria’ (SELECT) method: a novel experimental assay to facilitate risk assessment of selection for antimicrobial resistance in the environment. Environ. Health Perspect. 128, 107007 (2020).
Google Scholar
Andersson, D. I. & Hughes, D. Antibiotic resistance and its cost: is it possible to reverse resistance? Nat. Rev. Microbiol. 8, 260–271 (2010).
Google Scholar
Stanton, I. C., Murray, A. K., Zhang, L., Snape, J. & Gaze, W. H. Evolution of antibiotic resistance at low antibiotic concentrations including selection below the minimal selective concentration. Commun. Biol. https://doi.org/10.1038/s42003-020-01176-w (2020).
Google Scholar
Nijsingh, N., Munthe, C. & Larsson, D. G. J. Managing pollution from antibiotics manufacturing: charting actors, incentives and disincentives. Environ. Health 18, 95 (2019).
Google Scholar
Sundin, G. W. & Wang, N. Antibiotic resistance in plant-pathogenic bacteria. Annu. Rev. Phytopathol. 56, 161–180 (2018).
Google Scholar
Government of Sweden. Uppdrag angående försöksverksamhet för en miljöpremie i läkemedelsförmånssystemet, https://www.regeringen.se/499677/contentassets/36dcec65be904fd58e5e6b01c2f99709/uppdrag-angaende-forsoksverksamhet-for-en-miljopremie-i-lakemedelsformanssystemet-tlv.pdf (2021).
Norwegian Hospital Procurement Trust. New environmental criteria for the procurement of pharmaceuticals, https://sykehusinnkjop.no/nyheter/new-environmental-criteria-for-the-procurement-of-pharmaceuticals (2019).
Swedish Procurement Agency. Pharmaceuticals, https://www.upphandlingsmyndigheten.se/kriterier/sjukvard-och-omsorg/lakemedel/ (2021).
G7. G7 Health Ministers’ Declaration, Oxford, 4 June 2021, https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/992268/G7-health_ministers-communique-oxford-4-june-2021_5.pdf (2021).
Årdal, C. et al. Supply chain transparency and the availability of essential medicines. Bull. World Health Organ. 99, 319–320 (2021).
Google Scholar
Graham, D., Giesen, M. & Bunce, J. Strategic approach for prioritising local and regional sanitation interventions for reducing global antibiotic resistance. Water 11, 27 (2018).
Margot, J. et al. Treatment of micropollutants in municipal wastewater: ozone or powdered activated carbon? Sci. Total. Environ. 461–462, 480–498 (2013).
Google Scholar
Larsson, D. G. J. et al. Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance. Environ. Int. 117, 132–138 (2018).
Google Scholar
Laxminarayan, R. et al. The Lancet Infectious Diseases Commission on antimicrobial resistance: 6 years later. Lancet Infect. Dis. 20, e51–e60 (2020).
Google Scholar
Ahammad, Z. S., Sreekrishnan, T. R., Hands, C. L., Knapp, C. W. & Graham, D. W. Increased waterborne blaNDM-1 resistance gene abundances associated with seasonal human pilgrimages to the upper Ganges River. Environ. Sci. Technol. 48, 3014–3020 (2014).
Google Scholar
Kookana, R. S. et al. Potential ecological footprints of active pharmaceutical ingredients: an examination of risk factors in low-, middle- and high-income countries. Philos. Trans. R. Soc. B Biol. Sci. 369, 20130586 (2014).
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