Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era

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  • Murray, C. J. et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629–655 (2022).

    Article 
    CAS 

    Google Scholar 

  • Centers for Disease Control and Prevention. Antibiotic resistance threats in the United States, 2019. CDC https://stacks.cdc.gov/view/cdc/82532 (2019).

  • European Centre for Disease Prevention and Control. Antimicrobial resistance surveillance in Europe 2022−2020 data. ECDC. https://www.ecdc.europa.eu/en/publications-data/antimicrobial-resistance-surveillance-europe-2022-2020-data (2022).

  • World Health Organization. Global Antimicrobial Resistance and Use Surveillance System (GLASS) Report: 2021. WHO https://www.who.int/publications-detail-redirect/9789240027336 (2021).

  • Jonas, O. B., Irwin, A., Berthe, F. C. J., Le Gall, F. G. & Marquez, P. V. Drug-Resistant Infections: A Threat To Our Economic Future Vol. 2 (World Bank, 2017).

  • European Centre for Disease Prevention and Control. Antimicrobial resistance in the EU/EEA (EARS-Net) — Annual Epidemiological Report for 2021. ECDC https://www.ecdc.europa.eu/en/publications-data/surveillance-antimicrobial-resistance-europe-2021 (2022).

  • Liu, Y.-Y. et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect. Dis. 16, 161–168 (2016).

    Article 
    PubMed 

    Google Scholar 

  • Graham, D. W., Knapp, C. W., Christensen, B. T., McCluskey, S. & Dolfing, J. Appearance of β-lactam resistance genes in agricultural soils and clinical isolates over the 20th century. Sci. Rep. 6, 21550 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Forsberg, K. J. et al. The shared antibiotic resistome of soil bacteria and human pathogens. Science 337, 1107–1111 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Allen, H. K. et al. Call of the wild: antibiotic resistance genes in natural environments. Nat. Rev. Microbiol. 8, 251–259 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Perry, J., Waglechner, N. & Wright, G. The prehistory of antibiotic resistance. Cold Spring Harb. Perspect. Med. 6, a025197 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Larsson, D. G. J. & Flach, C.-F. Antibiotic resistance in the environment. Nat. Rev. Microbiol. 20, 257–269 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Andersson, D. I. et al. Antibiotic resistance: turning evolutionary principles into clinical reality. FEMS Microbiol. Rev. 44, 171–188 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Levy, S. B., Fitzgerald, G. B. & Macone, A. B. Spread of antibiotic-resistant plasmids from chicken to chicken and from chicken to man. Nature 260, 40–42 (1976).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Pehrsson, E. C. et al. Interconnected microbiomes and resistomes in low-income human habitats. Nature 533, 212–216 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Smillie, C. S. et al. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480, 241–244 (2011).

    Article 
    CAS 
    PubMed 

    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. 10, 02892 (2019).

    Article 

    Google Scholar 

  • Mackenzie, J. S. & Jeggo, M. The One Health approach — Why is it so important? Trop. Med. Infect. Dis. 4, 88 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • One Health High-Level Expert Panel (OHHLEP) et al. One Health: a new definition for a sustainable and healthy future. PLoS Pathog. 18, e1010537 (2022).

    Article 

    Google Scholar 

  • Hernando-Amado, S., Coque, T. M., Baquero, F. & Martínez, J. L. Defining and combating antibiotic resistance from One Health and Global Health perspectives. Nat. Microbiol. 4, 1432–1442 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Muehlenbein, M. P. Human–wildlife contact and emerging infectious diseases. Hum. Environ. Interact. 1, 79–94 (2012).

    Google Scholar 

  • Rodríguez-Beltrán, J., DelaFuente, J., León-Sampedro, R., MacLean, R. C. & San Millán, Á. Beyond horizontal gene transfer: the role of plasmids in bacterial evolution. Nat. Rev. Microbiol. 19, 347–359 (2021).

    Article 
    PubMed 

    Google Scholar 

  • Watanabe, T. & Fukasawa, T. Episome-mediated transfer of drug resistance in Enterobacteriaceae. I. J. Bacteriol. 81, 669–678 (1961).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Datta, N. Transmissible drug resistance in an epidemic strain of Salmonella typhimurium. J. Hyg. 60, 301–310 (1962).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hawkey, P. M. & Jones, A. M. The changing epidemiology of resistance. J. Antimicrob. Chemother. 64, i3–i10 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • When the drugs don’t work. Nat. Microbiol. 1, 16003 (2016).

  • Mathers, A. J., Peirano, G. & Pitout, J. D. D. The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae. Clin. Microbiol. Rev. 28, 565–591 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wang, R. et al. The global distribution and spread of the mobilized colistin resistance gene mcr-1. Nat. Commun. 9, 1179 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Evans, D. R. Genomic epidemiology of horizontal plasmid transfer among healthcare-associated bacterial pathogens in a tertiary hospital. Thesis, Univ. of Pittsburgh (2021).

  • Groussin, M. et al. Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell 184, 2053–2067 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Redondo-Salvo, S. et al. Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids. Nat. Commun. 11, 3602 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Acman, M., van Dorp, L., Santini, J. M. & Balloux, F. Large-scale network analysis captures biological features of bacterial plasmids. Nat. Commun. 11, 2452 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Thomas, C. M. & Nielsen, K. M. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 3, 711–721 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Partridge, S. R., Kwong, S. M., Firth, N. & Jensen, S. O. Mobile genetic elements associated with antimicrobial resistance. Clin. Microbiol. Rev. 31, e00088-17 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Che, Y. et al. Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes. Proc. Natl Acad. Sci. USA 118, e2008731118 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Matlock, W. et al. Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK. eLife 12, e85302 (2023).

    Article 
    PubMed 

    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).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Blau, K. et al. The transferable resistome of produce. mBio 9, e01300–e01318 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Heuer, H. et al. IncP-1ε plasmids are important vectors of antibiotic resistance genes in agricultural systems: diversification driven by class 1 integron gene cassettes. Front. Microbiol. 3, 2 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kyselková, M. et al. Characterization of tet(Y)-carrying LowGC plasmids exogenously captured from cow manure at a conventional dairy farm. FEMS Microbiol. Ecol. 92, fiw075 (2016).

    Article 
    PubMed 

    Google Scholar 

  • Law, A. et al. Biosolids as a source of antibiotic resistance plasmids for commensal and pathogenic bacteria. Front. Microbiol. 12, 606409 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, Q., Chang, W., Zhang, H., Hu, D. & Wang, X. The role of plasmids in the multiple antibiotic resistance transfer in ESBLs-producing Escherichia coli isolated from wastewater treatment plants. Front. Microbiol. 10, 633 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Rahube, T. O., Viana, L. S., Koraimann, G. & Yost, C. K. Characterization and comparative analysis of antibiotic resistance plasmids isolated from a wastewater treatment plant. Front. Microbiol. 5, 558 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • De la Cruz Barrón, M., Merlin, C., Guilloteau, H., Montargès-Pelletier, E. & Bellanger, X. Suspended materials in river waters differentially enrich class 1 integron- and IncP-1 plasmid-carrying bacteria in sediments. Front. Microbiol. 9, 1443 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sriswasdi, S., Yang, C. & Iwasaki, W. Generalist species drive microbial dispersion and evolution. Nat. Commun. 8, 1162 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Berry, D. & Widder, S. Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Front. Microbiol. 5, 219 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Stalder, T., Press, M. O., Sullivan, S., Liachko, I. & Top, E. M. Linking the resistome and plasmidome to the microbiome. ISME J. 13, 2437–2446 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Che, Y. et al. Mobile antibiotic resistome in wastewater treatment plants revealed by nanopore metagenomic sequencing. Microbiome 7, 44 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hultman, J. et al. Host range of antibiotic resistance genes in wastewater treatment plant influent and effluent. FEMS Microbiol 94, fiy038 (2018).

    Google Scholar 

  • Li, L. et al. Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes. ISME J. 14, 1170–1181 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Galata, V., Fehlmann, T., Backes, C. & Keller, A. PLSDB: a resource of complete bacterial plasmids. Nucleic Acids Res. 47, D195–D202 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Nation, R. L. & Li, J. Colistin in the 21st century. Curr. Opin. Infect. Dis. 22, 535–543 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Snesrud, E. et al. A model for transposition of the colistin resistance gene mcr-1 by ISApl1. Antimicrob. Agents Chemother. 60, 6973–6976 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Xiaomin, S. et al. Global impact of mcr-1-positive Enterobacteriaceae bacteria on “One Health”. Crit. Rev. Microbiol. 46, 565–577 (2020).

    Article 
    PubMed 

    Google Scholar 

  • Munoz-Price, L. S. et al. Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases. Lancet Infect. Dis. 13, 785–796 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cui, X., Zhang, H. & Du, H. Carbapenemases in enterobacteriaceae: detection and antimicrobial therapy. Front. Microbiol. 10, 1823 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Brink, A. J. Epidemiology of carbapenem-resistant Gram-negative infections globally. Curr. Opin. Infect. Dis. 32, 609–616 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Cassini, A. et al. Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: a population-level modelling analysis. Lancet Infect. Dis. 19, 56–66 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Papp-Wallace, K. M., Endimiani, A., Taracila, M. A. & Bonomo, R. A. Carbapenems: past, present, and future. Antimicrob. Agents Chemother. 55, 4943–4960 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Farfour, E. et al. Carbapenemase-producing Enterobacterales outbreak: another dark side of COVID-19. Am. J. Infect. Control. 48, 1533–1536 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Schweizer, C. et al. Plasmid-mediated transmission of KPC-2 carbapenemase in Enterobacteriaceae in critically ill patients. Front. Microbiol. 10, 276 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Tofteland, S., Naseer, U., Lislevand, J. H., Sundsfjord, A. & Samuelsen, Ø. A long-term low-frequency hospital outbreak of KPC-producing Klebsiella pneumoniae involving intergenus plasmid diffusion and a persisting environmental reservoir. PLoS ONE 8, e59015 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Evans, D. R. et al. Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital. eLife 9, e53886 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sheppard, A. E. et al. Nested Russian doll-like genetic mobility drives rapid dissemination of the carbapenem resistance gene blaKPC. Antimicrob. Agents Chemother. 60, 3767–3778 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • He, S. et al. Mechanisms of evolution in high-consequence drug resistance plasmids. mBio 7, 01987-16 (2016).

    Article 

    Google Scholar 

  • Weingarten, R. A. et al. Genomic analysis of hospital plumbing reveals diverse reservoir of bacterial plasmids conferring carbapenem resistance. mBio 9, e02011-17 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Mathers, A. J. et al. Klebsiella quasipneumoniae provides a window into carbapenemase gene transfer, plasmid rearrangements, and patient interactions with the hospital environment. Antimicrob. Agents Chemother. 63, e02513-18 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bevan, E. R., Jones, A. M. & Hawkey, P. M. Global epidemiology of CTX-M β-lactamases: temporal and geographical shifts in genotype. J. Antimicrob. Chemother. 72, 2145–2155 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Poirel, L., Cattoir, V. & Nordmann, P. Plasmid-mediated quinolone resistance; interactions between human, animal, and environmental ecologies. Front. Microbiol. 3, 24 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hiltunen, T., Virta, M. & Laine, A.-L. Antibiotic resistance in the wild: an eco-evolutionary perspective. Phil. Trans. R. Soc. 372, 20160039 (2017).

    Article 

    Google Scholar 

  • Baquero, F. et al. Evolutionary pathways and trajectories in antibiotic resistance. Clin. Microbiol. Rev. https://doi.org/10.1128/CMR.00050-19 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Stewart, F. M. & Levin, B. R. The population biology of bacterial plasmids: a priori conditions for the existence of conjugationally transmitted factors. Genetics 87, 209–228 (1977).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lopatkin, A. J. et al. Persistence and reversal of plasmid-mediated antibiotic resistance. Nat. Commun. 8, 1689 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • San Millan, A., Heilbron, K. & MacLean, R. C. Positive epistasis between co-infecting plasmids promotes plasmid survival in bacterial populations. ISME J. 8, 601–612 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Dionisio, F., Zilhão, R. & Gama, J. A. Interactions between plasmids and other mobile genetic elements affect their transmission and persistence. Plasmid 102, 29–36 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Gama, J. A., Zilhão, R. & Dionisio, F. Plasmid interactions can improve plasmid persistence in bacterial populations. Front. Microbiol. 11, 2033 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Horne, T., Orr, V. T. & Hall, J. P. How do interactions between mobile genetic elements affect horizontal gene transfer? Curr. Opin. Microbiol. 73, 102282 (2023).

    Article 
    PubMed 

    Google Scholar 

  • Zhou, J. & Ning, D. Stochastic community assembly: does it matter in microbial ecology? Microbiol. Molec. Biol. Rev. 81, e00002–e00017 (2017).

    Article 

    Google Scholar 

  • Wein, T., Hülter, N. F., Mizrahi, I. & Dagan, T. Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance. Nat. Commun. 10, 2595 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hall, J. P. J., Wright, R. C. T., Guymer, D., Harrison, E. & Brockhurst, M. A. Y. Extremely fast amelioration of plasmid fitness costs by multiple functionally diverse pathways. Microbiology 166, 56–62 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Brockhurst, M. A. & Harrison, E. Ecological and evolutionary solutions to the plasmid paradox. Trends Microbiol. 30, 534–543 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • MacLean, R. C. & Millan, A. S. Microbial evolution: towards resolving the plasmid paradox. Curr. Biol. 25, R764–R767 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • van Elsas, J. D. & Bailey, M. J. The ecology of transfer of mobile genetic elements. FEMS Microbiol. Ecol. 42, 187–197 (2002).

    Article 
    PubMed 

    Google Scholar 

  • Van Elsas, J. D., Fry, J., Hirsch, P. R. & Molin, S. in The Horizontal Gene Pool; Bacterial Plasmids And Gene Spread (ed. Thomas, C. M.) 175–206 (Harwood Academic, 2000).

  • Heuer, H. & Smalla, K. Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol. Rev. 36, 1083–1104 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Smalla, K., Jechalke, S. & Top, E. M. Plasmid detection, characterization and ecology. Microbiol. Spectr. https://doi.org/10.1128/microbiolspec.PLAS-00382014 (2015).

    Article 
    PubMed 

    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).

    Article 
    PubMed 

    Google Scholar 

  • Wegrzyn, G. & Wegrzyn, A. Stress responses and replication of plasmids in bacterial cells. Microb. Cell Fact. 1, 2 (2002).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Saraswat, V., Kim, D. Y., Lee, J. & Park, Y.-H. Effect of specific production rate of recombinant protein on multimerization of plasmid vector and gene expression level. FEMS Microbiol. Lett. 179, 367–373 (1999).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Caulcott, C. A. et al. Investigation of the effect of growth environment on the stability of low-copy-number plasmids in Escherichia coli. Microbiology 133, 1881–1889 (1987).

    Article 
    CAS 

    Google Scholar 

  • Cyriaque, V. et al. Lead drives complex dynamics of a conjugative plasmid in a bacterial community. Front. Microbiol. 12, 655903 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Flemming, H.-C. & Wuertz, S. Bacteria and archaea on Earth and their abundance in biofilms. Nat. Rev. Microbiol. 17, 247–260 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Stepanauskas, R. et al. Coselection for microbial resistance to metals and antibiotics in freshwater microcosms. Environ. Microbiol. 8, 1510–1514 (2006).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Gómez-Sanz, E. et al. Novel erm(T)-carrying multiresistance plasmids from porcine and human isolates of methicillin-resistant Staphylococcus aureus ST398 that also harbor cadmium and copper resistance determinants. Antimicrob. Agents Chemother. 57, 3275–3282 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Levison, M. E. & Levison, J. H. Pharmacokinetics and pharmacodynamics of antibacterial agents. Infect. Dis. Clin. North Am. 23, 791–815.vii (2009).

    Article 
    PubMed 

    Google Scholar 

  • Paulus, G. K. et al. The impact of on-site hospital wastewater treatment on the downstream communal wastewater system in terms of antibiotics and antibiotic resistance genes. Int. J. Hyg. Environ. Health 222, 635–644 (2019).

    Article 
    CAS 
    PubMed 

    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).

    Article 
    CAS 

    Google Scholar 

  • Kaplan, E., Marano, R. B. M., Jurkevitch, E. & Cytryn, E. Enhanced bacterial fitness under residual fluoroquinolone concentrations is associated with increased gene expression in wastewater-derived, qnr plasmid-harboring strains. Front. Microbiol. 9, 1176 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cairns, J. et al. Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes. Commun. Biol. 1, 1–8 (2018).

    Article 
    CAS 

    Google Scholar 

  • Gullberg, E., Albrecht, L. M., Karlsson, C., Sandegren, L. & Andersson, D. I. Selection of a multidrug resistance plasmid by sublethal levels of antibiotics and heavy metals. mBio 5, e01918-14 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ngigi, A. N., Magu, M. M. & Muendo, B. M. Occurrence of antibiotics residues in hospital wastewater, wastewater treatment plant, and in surface water in Nairobi County, Kenya. Environ. Monit. Assess. 192, 18 (2019).

    Article 
    PubMed 

    Google Scholar 

  • Rodriguez-Mozaz, S. et al. Antibiotic residues in final effluents of European wastewater treatment plants and their impact on the aquatic environment. Environ. Int. 140, 105733 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • He, Y. et al. Antibiotic resistance genes from livestock waste: occurrence, dissemination, and treatment. npj Clean Water 3, 4 (2020).

    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. 3, 467 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Andersson, D. I. & Hughes, D. Microbiological effects of sublethal levels of antibiotics. Nat. Rev. Microbiol. 12, 465–478 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kraupner, N. et al. Selective concentrations for trimethoprim resistance in aquatic environments. Environ. Int. 144, 106083 (2020).

    Article 
    CAS 
    PubMed 

    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).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Clarke, L., Pelin, A., Phan, M. & Wong, A. The effect of environmental heterogeneity on the fitness of antibiotic resistance mutations in Escherichia coli. Evol. Ecol. 34, 379–390 (2020).

    Article 

    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).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Yao, Y. et al. Intra- and interpopulation transposition of mobile genetic elements driven by antibiotic selection. Nat. Ecol. Evol. https://doi.org/10.1038/s41559-022-01705-2 (2022).

    Article 
    PubMed 

    Google Scholar 

  • Lehtinen, S., Huisman, J. S. & Bonhoeffer, S. Evolutionary mechanisms that determine which bacterial genes are carried on plasmids. Evol. Lett. 5, 290–301 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wang, Y., Batra, A., Schulenburg, H. & Dagan, T. Gene sharing among plasmids and chromosomes reveals barriers for antibiotic resistance gene transfer. Phil. Trans. R. Soc. 377, 20200467 (2021).

    Article 

    Google Scholar 

  • Rodríguez-Beltrán, J. et al. Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria. Proc. Natl Acad. Sci. USA 117, 15755–15762 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Schneiders, S. et al. Spatiotemporal variations in growth rate and virulence plasmid copy number during Yersinia pseudotuberculosis infection. Infect. Immun. 89, e00710–e00720 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Näsvall, J., Sun, L., Roth, J. R. & Andersson, D. I. Real-time evolution of new genes by innovation, amplification, and divergence. Science 338, 384–387 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kasagaki, S., Hashimoto, M. & Maeda, S. Subminimal inhibitory concentrations of ampicillin and mechanical stimuli cooperatively promote cell-to-cell plasmid transformation in Escherichia coli. Curr. Res. Microb. Sci. 3, 100130 (2022).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Xiao, X., Zeng, F., Li, R., Liu, Y. & Wang, Z. Subinhibitory concentration of colistin promotes the conjugation frequencies of Mcr-1- and blaNDM-5-positive plasmids. Microbiol. Spectr. 10, e02160-21 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lopatkin, A. J. et al. Antibiotics as a selective driver for conjugation dynamics. Nat. Microbiol. 1, 16044 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Liu, G., Thomsen, L. E. & Olsen, J. E. Antimicrobial-induced horizontal transfer of antimicrobial resistance genes in bacteria: a mini-review. J. Antimicrob. Chemother. 77, 556–567 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Yu, Z., Wang, Y., Lu, J., Bond, P. L. & Guo, J. Nonnutritive sweeteners can promote the dissemination of antibiotic resistance through conjugative gene transfer. ISME J. https://doi.org/10.1038/s41396-021-00909-x (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hu, X. et al. Plasmid binding to metal oxide nanoparticles inhibited lateral transfer of antibiotic resistance genes. Environ. Sci. Nano 6, 1310–1322 (2019).

    Article 
    CAS 

    Google Scholar 

  • Parra, B., Tortella, G. R., Cuozzo, S. & Martínez, M. Negative effect of copper nanoparticles on the conjugation frequency of conjugative catabolic plasmids. Ecotoxicol. Environ. Saf. 169, 662–668 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Xiong, R. et al. Indole inhibits IncP-1 conjugation system mainly through promoting korA and korB expression. Front. Microbiol. 12, 628133 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kosterlitz, O. et al. Estimating the transfer rates of bacterial plasmids with an adapted Luria–Delbrück fluctuation analysis. PLoS Biol. 20, e3001732 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Huisman, J. S. et al. Estimating plasmid conjugation rates: a new computational tool and a critical comparison of methods. Plasmid 121, 102627 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Cabezón, E., de la Cruz, F. & Arechaga, I. Conjugation inhibitors and their potential use to prevent dissemination of antibiotic resistance genes in bacteria. Front. Microbiol. 8, 2329 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Karkman, A., Pärnänen, K. & Larsson, D. G. J. Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments. Nat. Commun. 10, 80 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nahum, J. R. et al. A tortoise–hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria. Proc. Natl Acad. Sci. USA 112, 7530–7535 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Perfeito, L., Pereira, M. I., Campos, P. R. A. & Gordo, I. The effect of spatial structure on adaptation in Escherichia coli. Biol. Lett. 4, 57–59 (2008).

    Article 
    PubMed 

    Google Scholar 

  • France, M. T. & Forney, L. J. The relationship between spatial structure and the maintenance of diversity in microbial populations. Am. Nat. 193, 503–513 (2019).

    Article 
    PubMed 

    Google Scholar 

  • Yang, Y., Liu, G., Ye, C. & Liu, W. Bacterial community and climate change implication affected the diversity and abundance of antibiotic resistance genes in wetlands on the Qinghai-Tibetan Plateau. J. Hazard. Mater. 361, 283–293 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Maciel-Guerra, A. et al. Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock. ISME J. https://doi.org/10.1038/s41396-022-01315-7 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • MacFadden, D. R., McGough, S. F., Fisman, D., Santillana, M. & Brownstein, J. S. antibiotic resistance increases with local temperature. Nat. Clim. Change 8, 510–514 (2018).

    Article 
    CAS 

    Google Scholar 

  • Louvet, J. N. et al. Vancomycin sorption on activated sludge Gram+ bacteria rather than on EPS; 3D confocal laser scanning microscopy time-lapse imaging. Water Res. 124, 290–297 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Borer, B. & Or, D. Bacterial age distribution in soil — generational gaps in adjacent hot and cold spots. PLoS Comput. Biol. 18, e1009857 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kloos, J., Gama, J. A., Hegstad, J., Samuelsen, Ø. & Johnsen, P. J. Piggybacking on niche adaptation improves the maintenance of multidrug‐resistance plasmids. Mol. Biol. Evol. 38, 3188–3201 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Stalder, T. et al. Evolving populations in biofilms contain more persistent plasmids. Mol. Biol. Evol. 37, 1563–1576 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ponciano, J. M., La, H.-J., Joyce, P. & Forney, L. J. Evolution of diversity in spatially structured Escherichia coli populations. Appl. Environ. Microbiol. 75, 6047–6054 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Boles, B. R., Thoendel, M. & Singh, P. K. Self-generated diversity produces “insurance effects” in biofilm communities. Proc. Natl Acad. Sci. USA 101, 16630–16635 (2004).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Eastman, J. M., Harmon, L. J., La, H.-J., Joyce, P. & Forney, L. J. The onion model, a simple neutral model for the evolution of diversity in bacterial biofilms. J. Evol. Biol. 24, 2496–2504 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Santos-Lopez, A., Marshall, C. W., Scribner, M. R., Snyder, D. J. & Cooper, V. S. Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle. eLife 8, e47612 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lewis, K. Riddle of biofilm resistance. Antimicrob. Agents Chemother. 45, 999–1007 (2001).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Donlan, R. M. Biofilms: microbial life on surfaces. Emerg. Infect. Dis. 8, 881–890 (2002).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Galié, S., García-Gutiérrez, C., Miguélez, E. M., Villar, C. J. & Lombó, F. Biofilms in the food industry: health aspects and control methods. Front. Microbiol. 9, 898 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Chan, S. et al. Bacterial release from pipe biofilm in a full-scale drinking water distribution system. npj Biofilms Microbiomes 5, 9 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Ridenhour, B. J. et al. Persistence of antibiotic resistance plasmids in bacterial biofilms. Evol. Appl. 10, 640–647 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Metzger, G. A. et al. Biofilms preserve transmissibility of a multi-drug resistance plasmid. npj Biofilms Microbiomes 8, 95 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • De Gelder, L., Ponciano, J. M., Joyce, P. & Top, E. M. Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship. Microbiology 153, 452–463 (2007).

    Article 
    PubMed 

    Google Scholar 

  • Røder, H. L. et al. Biofilms can act as plasmid reserves in the absence of plasmid specific selection. npj Biofilms Microbiomes 7, 1–6 (2021).

    Article 

    Google Scholar 

  • Teal, T. K., Lies, D. P., Wold, B. J. & Newman, D. K. Spatiometabolic stratification of Shewanella oneidensis biofilms. Appl. Environ. Microbiol. 72, 7324–7330 (2006).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Werner, E. et al. Stratified growth in Pseudomonas aeruginosa biofilms. Appl. Environ. Microbiol. 70, 6188–6196 (2004).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wood, T. K., Knabel, S. J. & Kwan, B. W. Bacterial persister cell formation and dormancy. Appl. Environ. Microbiol. 79, 7116–7121 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Coutu, S., Rossi, L., Barry, D. A., Rudaz, S. & Vernaz, N. Temporal variability of antibiotics fluxes in wastewater and contribution from hospitals. PLoS ONE 8, e53592 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Marti, E., Variatza, E. & Balcazar, J. L. The role of aquatic ecosystems as reservoirs of antibiotic resistance. Trends Microbiol. 22, 36–41 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Schwartz, D. J., Langdon, A. E. & Dantas, G. Understanding the impact of antibiotic perturbation on the human microbiome. Genome Med. 12, 82 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • San Millan, A. et al. Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids. Nat. Commun. 5, 5208 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Stevenson, C., Hall, J. P. J., Brockhurst, M. A. & Harrison, E. Plasmid stability is enhanced by higher-frequency pulses of positive selection. Proc. Natl Acad. Sci. USA 285, 20172497 (2018).

    Google Scholar 

  • Forsyth, V. S. et al. Rapid growth of uropathogenic Escherichia coli during human urinary tract infection. mBio 9, e00186-18 (2018).

  • Gibson, B., Wilson, D. J., Feil, E. & Eyre-Walker, A. The distribution of bacterial doubling times in the wild. Proc. Biol. Sci. 285, 20180789 (2018).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Harris, D. & Paul, E. A. Measurement of bacterial growth rates in soil. Appl. Soil. Ecol. 1, 277–290 (1994).

    Article 

    Google Scholar 

  • Bottery, M. J. Ecological dynamics of plasmid transfer and persistence in microbial communities. Curr. Opin. Microbiol. 68, 102152 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • De Gelder, L., Vandecasteele, F. P. J., Brown, C. J., Forney, L. J. & Top, E. M. Plasmid donor affects host range of promiscuous IncP-1 plasmid pB10 in an activated-sludge microbial community. Appl. Environ. Microbiol. 71, 5309–5317 (2005).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Heß, S., Kneis, D., Virta, M. & Hiltunen, T. The spread of the plasmid RP4 in a synthetic bacterial community is dependent on the particular donor strain. FEMS Microbiol. Ecol. https://doi.org/10.1093/femsec/fiab147 (2021).

    Article 
    PubMed 

    Google Scholar 

  • Musovic, S., Klümper, U., Dechesne, A., Magid, J. & Smets, B. F. Long-term manure exposure increases soil bacterial community potential for plasmid uptake. Environ. Microbiol. Rep. 6, 125–130 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Li, L. et al. Estimating the transfer range of plasmids encoding antimicrobial resistance in a wastewater treatment plant microbial community. Environ. Sci. Technol. Lett. 5, 260–265 (2018).

    Article 
    CAS 

    Google Scholar 

  • Olesen, A. K. et al. IncHI1A plasmids potentially facilitate horizontal flow of antibiotic resistance genes to pathogens in microbial communities of urban residential sewage. Mol. Ecol. 31, 1595–1608 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Pinilla-Redondo, R. et al. Broad dissemination of plasmids across groundwater-fed rapid sand filter microbiomes. mBio 12, e03068-21 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Klümper, U. et al. Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community. ISME J. 9, 934–945 (2015).

    Article 
    PubMed 

    Google Scholar 

  • Kottara, A., Carrilero, L., Harrison, E., Hall, J. P. J. & Brockhurst, M. A. Y. The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities. Microbiology 167, 001086 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Alonso-del Valle, A. et al. Variability of plasmid fitness effects contributes to plasmid persistence in bacterial communities. Nat. Commun. 12, 2653 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bottery, M. J., Pitchford, J. W. & Friman, V.-P. Ecology and evolution of antimicrobial resistance in bacterial communities. ISME J. 15, 939–948 (2021).

    Article 
    PubMed 

    Google Scholar 

  • Hall, J. P. J., Wood, A. J., Harrison, E. & Brockhurst, M. A. Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities. Proc. Natl Acad. Sci. USA 113, 8260–8265 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Loftie-Eaton, W. et al. Contagious antibiotic resistance: plasmid transfer among bacterial residents of the zebrafish gut. Appl. Environ. Microbiol. 87, e02735-20 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Noyes, N. R. et al. Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing. Microbiome 5, 142 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Slizovskiy, I. B. et al. Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes. Microbiome 10, 185 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Björkman, J., Nagaev, I., Berg, O. G., Hughes, D. & Andersson, D. I. Effects of environment on compensatory mutations to ameliorate costs of antibiotic resistance. Science 287, 1479–1482 (2000).

    Article 
    PubMed 

    Google Scholar 

  • Topp, E., Larsson, D. G. J., Miller, D. N., Van den Eede, C. & Virta, M. P. J. Antimicrobial resistance and the environment: assessment of advances, gaps and recommendations for agriculture, aquaculture and pharmaceutical manufacturing. FEMS Microbiol. Ecol. 94, fix185 (2018).

    Article 

    Google Scholar 

  • Bürgmann, H. et al. Water and sanitation: an essential battlefront in the war on antimicrobial resistance. FEMS Microbiol. Ecol. 94, fiy101 (2018).

    Article 

    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. 94, fiy195 (2018).

    Article 
    CAS 

    Google Scholar 

  • Pospíšil, J. et al. Bacterial nanotubes as a manifestation of cell death. Nat. Commun. 11, 4963 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Schmartz, G. P. et al. PLSDB: advancing a comprehensive database of bacterial plasmids. Nucleic Acids Res. 50, D273–D278 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Cabezón, E., Ripoll-Rozada, J., Peña, A., de la Cruz, F. & Arechaga, I. Towards an integrated model of bacterial conjugation. FEMS Microbiol. Rev. 39, 81–95 (2015).

    PubMed 

    Google Scholar 

  • Szpirer, C., Top, E., Couturier, M. & Mergeay, M. Y. Retrotransfer or gene capture: a feature of conjugative plasmids, with ecological and evolutionary significance. Microbiology 145, 3321–3329 (1999).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Smillie, C., Garcillán-Barcia, M. P., Francia, M. V., Rocha, E. P. C. & de la Cruz, F. Mobility of plasmids. Microbiol. Mol. Biol. Rev. 74, 434–452 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Coluzzi, C., Garcillán-Barcia, M. P., de la Cruz, F. & Rocha, E. P. C. Evolution of plasmid mobility: origin and fate of conjugative and nonconjugative plasmids. Mol. Biol. Evol. 39, msac115 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Thomas, C. M. & Summers, D. Bacterial plasmids. In Encyclopedia of Life Sciences (American Cancer Society, 2008).

  • Pesesky, M. W., Tilley, R. & Beck, D. A. C. Mosaic plasmids are abundant and unevenly distributed across prokaryotic taxa. Plasmid 102, 10–18 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Brito, I. L. Examining horizontal gene transfer in microbial communities. Nat. Rev. Microbiol. 19, 442–453 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kent, A. G., Vill, A. C., Shi, Q., Satlin, M. J. & Brito, I. L. Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C. Nat. Commun. 11, 4379 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Yaffe, E. & Relman, D. A. Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation. Nat. Microbiol. 5, 343–353 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Kalmar, L. et al. HAM-ART: an optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities. PLoS Genet. 18, e1009776 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Beaulaurier, J. et al. Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nat. Biotechnol. 36, 61–69 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Diebold, P. J., New, F. N., Hovan, M., Satlin, M. J. & Brito, I. L. Linking plasmid-based β-lactamases to their bacterial hosts using single-cell fusion PCR. eLife 10, e66834 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Roman, V. L., Merlin, C., Virta, M. P. J. & Bellanger, X. EpicPCR 2.0: technical and methodological improvement of a cutting-edge single-cell genomic approach. Microorganisms 9, 1649 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    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).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Musovic, S., Oregaard, G., Kroer, N. & Sørensen, S. J. Cultivation-independent examination of horizontal transfer and host range of an IncP-1 plasmid among Gram-positive and Gram-negative bacteria indigenous to the barley rhizosphere. Appl. Environ. Microbiol. 72, 6687–6692 (2006).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Batani, G., Bayer, K., Böge, J., Hentschel, U. & Thomas, T. Fluorescence in situ hybridization (FISH) and cell sorting of living bacteria. Sci. Rep. 9, 18618 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Macedo, G. et al. Horizontal gene transfer of an IncP1 plasmid to soil bacterial community introduced by Escherichia coli through manure amendment in soil microcosms. Environ. Sci. Technol. 56, 11398–11408 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Arias-Andres, M., Klümper, U., Rojas-Jimenez, K. & Grossart, H.-P. Microplastic pollution increases gene exchange in aquatic ecosystems. Environ. Pollut. 237, 253–261 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Vrancianu, C. O., Popa, L. I., Bleotu, C. & Chifiriuc, M. C. Targeting plasmids to limit acquisition and transmission of antimicrobial resistance. Front. Microbiol. 11, 761 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jalasvuori, M., Friman, V.-P., Nieminen, A., Bamford, J. K. H. & Buckling, A. Bacteriophage selection against a plasmid-encoded sex apparatus leads to the loss of antibiotic-resistance plasmids. Biol. Lett. 7, 902–905 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Novick, R. P. Plasmid incompatibility. Microbiol. Rev. 51, 381–395 (1987).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Buckner, M. M. C., Ciusa, M. L. & Piddock, L. J. V. Strategies to combat antimicrobial resistance: anti-plasmid and plasmid curing. FEMS Microbiol. Rev. 42, 781–804 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lazdins, A. et al. Potentiation of curing by a broad-host-range self-transmissible vector for displacing resistance plasmids to tackle AMR. PLoS ONE 15, e0225202 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kamruzzaman, M., Shoma, S., Thomas, C. M., Partridge, S. R. & Iredell, J. R. Plasmid interference for curing antibiotic resistance plasmids in vivo. PLoS ONE 12, e0172913 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lauritsen, I., Porse, A., Sommer, M. O. A. & Nørholm, M. H. H. A versatile one-step CRISPR–Cas9 based approach to plasmid-curing. Microb. Cell Fact. 16, 135 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hao, M. et al. CRISPR–Cas9-mediated carbapenemase gene and plasmid curing in carbapenem-resistant Enterobacteriaceae. Antimicrob. Agents Chemother. 64, e00843-20 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bikard, D. et al. Exploiting CRISPR–Cas nucleases to produce sequence-specific antimicrobials. Nat. Biotechnol. 32, 1146–1150 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    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).

    Article 
    PubMed 

    Google Scholar 

  • Hendriksen, R. S. et al. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nat. Commun. 10, 1124 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Micoli, F., Bagnoli, F., Rappuoli, R. & Serruto, D. The role of vaccines in combatting antimicrobial resistance. Nat. Rev. Microbiol. 19, 287–302 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Anjum, M. F. et al. The potential of using E. coli as an indicator for the surveillance of antimicrobial resistance (AMR) in the environment. Curr. Opin. Microbiol. 64, 152–158 (2021).

    Article 
    CAS 
    PubMed 

    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).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Liguori, K. et al. Antimicrobial resistance monitoring of water environments: a framework for standardized methods and quality control. Environ. Sci. Technol. 56, 9149–9160 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Joint Programming Initiative On Antimicrobial Resistance: Strategic Research And Innovation Agenda on Antimicrobial Resistance (JPIAMR, 2021).

  • ECDC, EFSA, EMA & OECD Antimicrobial Resistance In The EU/EEA: A One Health Response Vol. 15 (OECD, 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 https://doi.org/10.4060/cc2289en (2022).

  • Martínez, J. L., Coque, T. M. & Baquero, F. What is a resistance gene? Ranking risk in resistomes. Nat. Rev. Microbiol. 13, 116–123 (2015).

    Article 
    PubMed 

    Google Scholar 



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