1.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.
Google Scholar
2.Bhullar, K. et al. Antibiotic resistance is prevalent in an isolated cave microbiome. PLoS ONE 7, e34953 (2012).CAS
PubMed
PubMed Central
Google Scholar
3.Lugli, G. A. et al. Ancient bacteria of the Ötzi’s microbiome: a genomic tale from the Copper Age. Microbiome 5, 5 (2017).PubMed
PubMed Central
Google Scholar
4.Perry, J., Waglechner, N. & Wright, G. The prehistory of antibiotic resistance. Cold Spring Harb. Perspect. Med. 6, a025197 (2016).PubMed
PubMed Central
Google Scholar
5.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.CAS
PubMed
PubMed Central
Google Scholar
6.Allen, H. K. et al. Call of the wild: antibiotic resistance genes in natural environments. Nat. Rev. Microbiol. 8, 251–259 (2010).CAS
PubMed
Google Scholar
7.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).
Google Scholar
8.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).Article
PubMed Central
Google Scholar
9.Mackenzie, J. S. & Jeggo, M. The one health approach — why is it so important? Trop. Med. Infect. Dis. 4, 88 (2019).PubMed Central
Google Scholar
10.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).PubMed
PubMed Central
Google Scholar
11.Berendonk, T. U. et al. Tackling antibiotic resistance: the environmental framework. Nat. Rev. Microbiol. 13, 310–317 (2015).CAS
PubMed
Google Scholar
12.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).CAS
PubMed
Google Scholar
13.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).Article
PubMed Central
Google Scholar
14.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).
Google Scholar
15.Andersson, D. I. et al. Antibiotic resistance: turning evolutionary principles into clinical reality. FEMS Microbiol. Rev. 44, 171–188 (2020).CAS
PubMed
Google Scholar
16.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).Article
PubMed
PubMed Central
Google Scholar
17.United Nations Environment Programme. Frontiers 2017: emerging issues of environmental concern, https://www.unenvironment.org/resources/frontiers-2017-emerging-issues-environmental-concern (2017).18.Access to Medicines Foundation. 2020 antimicrobial resistance benchmark, https://accesstomedicinefoundation.org/publications/2020-antimicrobial-resistance-benchmark (2020).19.Review on Antimicrobial Resistance. Antimicrobials in agriculture and the environment: reducing unnecessary waste, https://amr-review.org/Publications.html (2015).20.European Parliament. Strategic approach to pharmaceuticals in the environment, https://www.europarl.europa.eu/doceo/document/TA-9-2020-0226_EN.pdf (2020).21.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).22.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).PubMed
PubMed Central
Google Scholar
23.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).Article
PubMed
Google Scholar
24.Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013).CAS
PubMed
Google Scholar
25.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).Article
PubMed
PubMed Central
Google Scholar
26.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.CAS
PubMed
PubMed Central
Google Scholar
27.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).PubMed
PubMed Central
Google Scholar
28.Dantas, G., Sommer, M. O. A., Oluwasegun, R. D. & Church, G. M. Bacteria subsisting on antibiotics. Science 320, 100–103 (2008).CAS
PubMed
Google Scholar
29.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).Article
Google Scholar
30.Pawlowski, A. C. et al. A diverse intrinsic antibiotic resistome from a cave bacterium. Nat. Commun. 7, 13803 (2016).CAS
PubMed
PubMed Central
Google Scholar
31.Morar, M. & Wright, G. D. The genomic enzymology of antibiotic resistance. Annu. Rev. Genet. 44, 25–51 (2010).CAS
PubMed
Google Scholar
32.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).PubMed
PubMed Central
Google Scholar
33.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).Article
PubMed
PubMed Central
Google Scholar
34.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).Article
PubMed
PubMed Central
Google Scholar
35.Gillings, M. et al. The evolution of class 1 integrons and the rise of antibiotic resistance. J. Bacteriol. 190, 5095–5100 (2008).CAS
PubMed
PubMed Central
Google Scholar
36.Razavi, M. et al. Discovery of the fourth mobile sulfonamide resistance gene. Microbiome https://doi.org/10.1186/s40168-017-0379-y (2017).Article
PubMed
PubMed Central
Google Scholar
37.Flach, C.-F. et al. Does antifouling paint select for antibiotic resistance? Sci. Total Environ. 590–591, 461–468 (2017).PubMed
Google Scholar
38.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).PubMed
PubMed Central
Google Scholar
39.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).Article
PubMed
PubMed Central
Google Scholar
40.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).CAS
PubMed
Google Scholar
41.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).CAS
PubMed
PubMed Central
Google Scholar
42.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).CAS
PubMed
Google Scholar
43.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).CAS
PubMed
Google Scholar
44.Aminov, R. I. Horizontal gene exchange in environmental microbiota. Front. Microbiol. https://doi.org/10.3389/fmicb.2011.00158 (2011).Article
PubMed
PubMed Central
Google Scholar
45.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).Article
PubMed
PubMed Central
Google Scholar
46.Kimura, M. & Ohta, T. The average number of generations until fixation of a mutant gene in a finite population. Genetics 61, 763–771 (1969).CAS
PubMed
PubMed Central
Google Scholar
47.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).PubMed
Google Scholar
48.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).Article
PubMed
PubMed Central
Google Scholar
49.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.Article
PubMed
PubMed Central
Google Scholar
50.Andersson, D. I. & Hughes, D. Persistence of antibiotic resistance in bacterial populations. FEMS Microbiol. Rev. 35, 901–911 (2011).CAS
PubMed
Google Scholar
51.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).CAS
PubMed
Google Scholar
52.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).CAS
PubMed
Google Scholar
53.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).
Google Scholar
54.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).Article
Google Scholar
55.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).PubMed
Google Scholar
56.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).PubMed
Google Scholar
57.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).Article
Google Scholar
58.Larsson, D. G. J. Pollution from drug manufacturing: review and perspectives. Philos. Trans. R. Soc. B Biol. Sci. 369, 20130571 (2014).
Google Scholar
59.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).CAS
PubMed
Google Scholar
60.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).PubMed
Google Scholar
61.Bielen, A. et al. Negative environmental impacts of antibiotic-contaminated effluents from pharmaceutical industries. Water Res. 126, 79–87 (2017).CAS
PubMed
Google Scholar
62.Fick, J. et al. Contamination of surface, ground, and drinking water from pharmaceutical production. Environ. Toxicol. Chem. 28, 2522–2527 (2009).CAS
PubMed
Google Scholar
63.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.CAS
PubMed
Google Scholar
64.Gullberg, E. et al. Selection of resistant bacteria at very low antibiotic concentrations. PLoS Pathog. 7, e1002158 (2011).CAS
PubMed
PubMed Central
Google Scholar
65.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).Article
PubMed
PubMed Central
Google Scholar
66.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).CAS
PubMed
Google Scholar
67.Bengtsson-Palme, J. et al. Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics. Sci. Total Environ. 572, 697–712 (2016).CAS
PubMed
Google Scholar
68.Manaia, C. M. et al. Antibiotic resistance in wastewater treatment plants: tackling the black box. Environ. Int. 115, 312–324 (2018).CAS
PubMed
Google Scholar
69.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).CAS
PubMed
Google Scholar
70.Kraupner, N. et al. Evidence for selection of multi-resistant E. coli by hospital effluent. Environ. Int. 150, 106436 (2021).CAS
PubMed
Google Scholar
71.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).CAS
PubMed
Google Scholar
72.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).Article
PubMed
PubMed Central
Google Scholar
73.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).CAS
PubMed
Google Scholar
74.Thiele-Bruhn, S. Pharmaceutical antibiotic compounds in soils–a review. J. Plant Nutr. Soil Sci. 166, 145–167 (2003).CAS
Google Scholar
75.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).PubMed
Google Scholar
76.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).PubMed
Google Scholar
77.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).CAS
PubMed
Google Scholar
78.Jechalke, S., Heuer, H., Siemens, J., Amelung, W. & Smalla, K. Fate and effects of veterinary antibiotics in soil. Trends Microbiol. 22, 536–545 (2014).CAS
PubMed
Google Scholar
79.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).PubMed
PubMed Central
Google Scholar
80.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).CAS
PubMed
Google Scholar
81.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.CAS
PubMed
Google Scholar
82.Pal, C. et al. Metal resistance and its association with antibiotic resistance. Adv. Microb. Physiol. 70, 261–313 (2017).CAS
PubMed
Google Scholar
83.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).PubMed
PubMed Central
Google Scholar
84.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).Article
PubMed
PubMed Central
Google Scholar
85.Klümper, U. et al. Metal stressors consistently modulate bacterial conjugal plasmid uptake potential in a phylogenetically conserved manner. ISME J. 11, 152–165 (2017).PubMed
Google Scholar
86.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).PubMed
Google Scholar
87.Wang, Y. et al. Non-antibiotic pharmaceuticals enhance the transmission of exogenous antibiotic resistance genes through bacterial transformation. ISME J. 14, 2179–2196 (2020).CAS
PubMed
PubMed Central
Google Scholar
88.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.CAS
PubMed
Google Scholar
89.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).PubMed
Google Scholar
90.Heuer, H. & Smalla, K. Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol. Rev. 36, 1083–1104 (2012).CAS
PubMed
Google Scholar
91.Bengtsson-Palme, J. & Larsson, D. G. Antibiotic resistance genes in the environment: prioritizing risks. Nat. Rev. Microbiol. 13, 396 (2015).CAS
PubMed
Google Scholar
92.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.PubMed
Google Scholar
93.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).CAS
PubMed
Google Scholar
94.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).CAS
PubMed
Google Scholar
95.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).PubMed
Google Scholar
96.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).PubMed
PubMed Central
Google Scholar
97.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).PubMed
Google Scholar
98.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).PubMed
PubMed Central
Google Scholar
99.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).Article
PubMed
PubMed Central
Google Scholar
100.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).
Google Scholar
101.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).PubMed
PubMed Central
Google Scholar
102.Blau, K. et al. The transferable resistome of produce. mBio 9, e01300-18 (2018).PubMed
PubMed Central
Google Scholar
103.Zhu, Y.-G. et al. Soil biota, antimicrobial resistance and planetary health. Environ. Int. 131, 105059 (2019).PubMed
Google Scholar
104.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).PubMed
PubMed Central
Google Scholar
105.Kozajda, A., Jeżak, K. & Kapsa, A. Airborne Staphylococcus aureus in different environments — a review. Environ. Sci. Pollut. Res. 26, 34741–34753 (2019).CAS
Google Scholar
106.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).PubMed
PubMed Central
Google Scholar
107.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).CAS
PubMed
Google Scholar
108.Lewis, K. Platforms for antibiotic discovery. Nat. Rev. Drug. Discov. 12, 371–387 (2013).CAS
PubMed
Google Scholar
109.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).CAS
PubMed
Google Scholar
110.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).CAS
PubMed
Google Scholar
111.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).Article
PubMed
PubMed Central
Google Scholar
112.Aarestrup, F. M. & Woolhouse, M. E. J. Using sewage for surveillance of antimicrobial resistance. Science 367, 630–632 (2020).CAS
PubMed
Google Scholar
113.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).CAS
PubMed
Google Scholar
114.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).CAS
PubMed
PubMed Central
Google Scholar
115.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.PubMed
PubMed Central
Google Scholar
116.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).CAS
PubMed
Google Scholar
117.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.Article
PubMed
PubMed Central
Google Scholar
118.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).CAS
PubMed
Google Scholar
119.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).Article
PubMed
PubMed Central
Google Scholar
120.European Centre for Disease Prevention and Control. Surveillance of antimicrobial resistance in Europe 2017 (Stockholm, Sweden, 2018).121.Hovi, T. et al. Role of environmental poliovirus surveillance in global polio eradication and beyond. Epidemiol. Infect. 140, 1–13 (2012).CAS
PubMed
Google Scholar
122.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).Article
PubMed
PubMed Central
Google Scholar
123.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).CAS
Google Scholar
124.Lundstrom, S. V. et al. Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms. Sci. Total Environ. 553, 587–595 (2016).PubMed
Google Scholar
125.McCann, C. M. et al. Understanding drivers of antibiotic resistance genes in High Arctic soil ecosystems. Environ. Int. 125, 497–504 (2019).CAS
PubMed
Google Scholar
126.Pruden, A., Arabi, M. & Storteboom, H. N. Correlation between upstream human activities and riverine antibiotic resistance genes. Environ. Sci. Technol. 46, 11541–11549 (2012).CAS
PubMed
Google Scholar
127.Zhu, Y.-G. et al. Continental-scale pollution of estuaries with antibiotic resistance genes. Nat. Microbiol. 2, 16270 (2017).CAS
PubMed
Google Scholar
128.Zhu, Y.-G. et al. Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proc. Natl Acad. Sci. USA 110, 3435–3440 (2013).CAS
PubMed
PubMed Central
Google Scholar
129.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).CAS
PubMed
Google Scholar
130.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).PubMed
Google Scholar
131.Finley, R. L. et al. The scourge of antibiotic resistance: the important role of the environment. Clin. Infect. Dis. 57, 704–710 (2013).PubMed
Google Scholar
132.Sjölund, M. et al. Dissemination of multidrug-resistant bacteria into the Arctic. Emerg. Infect. Dis. 14, 70–72 (2008).PubMed
PubMed Central
Google Scholar
133.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).Article
PubMed
PubMed Central
Google Scholar
134.Nichols, D. et al. Use of Ichip for high-throughput in situ cultivation of “Uncultivable” microbial species. Appl. Environ. Microbiol. 76, 2445–2450 (2010).CAS
PubMed
PubMed Central
Google Scholar
135.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).CAS
PubMed
Google Scholar
136.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).CAS
PubMed
Google Scholar
137.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).CAS
Google Scholar
138.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).CAS
PubMed Central
Google Scholar
139.Bengtsson-Palme, J., Larsson, D. G. J. & Kristiansson, E. Using metagenomics to investigate human and environmental resistomes. J. Antimicrob. Chemother. 72, 2690–2703 (2017).CAS
PubMed
Google Scholar
140.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).141.Gillings, M. R. et al. Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution. ISME J. 9, 1269–1279 (2015).CAS
PubMed
Google Scholar
142.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).CAS
PubMed
PubMed Central
Google Scholar
143.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.CAS
PubMed
Google Scholar
144.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).Article
PubMed
PubMed Central
Google Scholar
145.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).CAS
Google Scholar
146.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).CAS
Google Scholar
147.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.CAS
PubMed
Google Scholar
148.Klümper, U. et al. Selection for antimicrobial resistance is reduced when embedded in a natural microbial community. ISME J. 13, 2927–2937 (2019).PubMed
PubMed Central
Google Scholar
149.Kraupner, N. et al. Selective concentrations for trimethoprim resistance in aquatic environments. Environ. Int. 144, 106083 (2020).CAS
PubMed
Google Scholar
150.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).Article
PubMed
PubMed Central
Google Scholar
151.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).152.Tell, J. et al. Science-based targets for antibiotics in receiving waters from pharmaceutical manufacturing operations. Integr. Environ. Assess. Manag. 15, 312–319 (2019).CAS
PubMed
PubMed Central
Google Scholar
153.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).Article
PubMed
PubMed Central
Google Scholar
154.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).PubMed
PubMed Central
Google Scholar
155.Andersson, D. I. & Hughes, D. Antibiotic resistance and its cost: is it possible to reverse resistance? Nat. Rev. Microbiol. 8, 260–271 (2010).CAS
PubMed
Google Scholar
156.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).Article
PubMed
PubMed Central
Google Scholar
157.Nijsingh, N., Munthe, C. & Larsson, D. G. J. Managing pollution from antibiotics manufacturing: charting actors, incentives and disincentives. Environ. Health 18, 95 (2019).PubMed
PubMed Central
Google Scholar
158.Sundin, G. W. & Wang, N. Antibiotic resistance in plant-pathogenic bacteria. Annu. Rev. Phytopathol. 56, 161–180 (2018).CAS
PubMed
Google Scholar
159.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).160.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).161.Swedish Procurement Agency. Pharmaceuticals, https://www.upphandlingsmyndigheten.se/kriterier/sjukvard-och-omsorg/lakemedel/ (2021).162.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).163.Årdal, C. et al. Supply chain transparency and the availability of essential medicines. Bull. World Health Organ. 99, 319–320 (2021).PubMed
PubMed Central
Google Scholar
164.Graham, D., Giesen, M. & Bunce, J. Strategic approach for prioritising local and regional sanitation interventions for reducing global antibiotic resistance. Water 11, 27 (2018).
Google Scholar
165.Margot, J. et al. Treatment of micropollutants in municipal wastewater: ozone or powdered activated carbon? Sci. Total. Environ. 461–462, 480–498 (2013).PubMed
Google Scholar
166.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).PubMed
Google Scholar
167.Laxminarayan, R. et al. The Lancet Infectious Diseases Commission on antimicrobial resistance: 6 years later. Lancet Infect. Dis. 20, e51–e60 (2020).PubMed
Google Scholar
168.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).CAS
PubMed
PubMed Central
Google Scholar
169.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).
Google Scholar More