Poirel, L. et al. Tn125-related acquisition of blaNDM-like genes in Acinetobacter baumannii. Antimicrob. Agents Chemother. 56, 1087–1089 (2012).
Google Scholar
Wang, R. et al. The global distribution and spread of the mobilized colistin resistance gene mcr-1. Nat. Commun. 9, 1179 (2018).
Google Scholar
Clark, N. C., Weigel, L. M., Patel, J. B. & Tenover, F. C. Comparison of Tn1546-like elements in vancomycin-resistant Staphylococcus aureus isolates from Michigan and Pennsylvania. Antimicrob. Agents Chemother. 49, 470–472 (2005).
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).
Google Scholar
Stokes, H. W. & Gillings, M. R. Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens. FEMS Microbiol. Rev. 35, 790–819 (2011).
Google Scholar
Ghaly, T. M. & Gillings, M. R. Mobile DNAs as ecologically and evolutionarily independent units of life. Trends Microbiol. 26, 904–912 (2018).
Google Scholar
Modi, S. R., Lee, H. H., Spina, C. S. & Collins, J. J. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499, 219–222 (2013).
Google Scholar
Brown-Jaque, M., Calero-Cáceres, W. & Muniesa, M. Transfer of antibiotic-resistance genes via phage-related mobile elements. Plasmid https://doi.org/10.1016/j.plasmid.2015.01.001 (2015).
Frantzeskakis, L. et al. Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen. BMC Genomics 19, 381 (2018).
Scott, K. P. The role of conjugative transposons in spreading antibiotic resistance between bacteria that inhabit the gastrointestinal tract. Cell. Mol. Life Sci. 59, 2071–2082 (2002).
Google Scholar
Pezzella, C., Ricci, A., DiGiannatale, E., Luzzi, I. & Carattoli, A. Tetracycline and streptomycin resistance genes, transposons, and plasmids in Salmonella enterica isolates from animals in Italy. Antimicrob. Agents Chemother. 48, 903–908 (2004).
Google Scholar
Bengtsson-Palme, J., Boulund, F., Fick, J., Kristiansson, E. & Larsson, D. G. Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Front. Microbiol. 5, 648 (2014).
Google Scholar
Imchen, M. & Kumavath, R. Shotgun metagenomics reveals a heterogeneous prokaryotic community and a wide array of antibiotic resistance genes in mangrove sediment. FEMS Microbiol. Ecol. 96, fiaa173 (2020).
Google Scholar
Zhang, T., Zhang, X.-X. & Ye, L. Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge. PLoS ONE 6, e26041 (2011).
Google Scholar
Hu, H. et al. Novel plasmid and its variant harboring both a blaNDM-1 gene and type IV secretion system in clinical isolates of Acinetobacter lwoffii. Antimicrob. Agents Chemother. 56, 1698–1702 (2012).
Google Scholar
Smet, A. et al. Complete nucleotide sequence of CTX-M-15-plasmids from clinical Escherichia coli isolates: insertional events of transposons and insertion sequences. PLoS ONE 5, e11202 (2010).
Google Scholar
Revilla, C. et al. Different pathways to acquiring resistance genes illustrated by the recent evolution of IncW plasmids. Antimicrob. Agents Chemother. 52, 1472–1480 (2008).
Google Scholar
Poirel, L., Dortet, L., Bernabeu, S. & Nordmann, P. Genetic features of blaNDM-1-positive Enterobacteriaceae. Antimicrob. Agents Chemother. 55, 5403–5407 (2011).
Google Scholar
Toleman, M. A., Spencer, J., Jones, L. & Walsh, T. R. blaNDM-1 is a chimera likely constructed in Acinetobacter baumannii. Antimicrob. Agents Chemother. 56, 2773–2776 (2012).
Google Scholar
Bonnin, R. A., Poirel, L. & Nordmann, P. New Delhi metallo-β-lactamase-producing Acinetobacter baumannii: a novel paradigm for spreading antibiotic resistance genes. Future Microbiol. 9, 33–41 (2014).
Google Scholar
Waterman, P. E. et al. Bacterial peritonitis due to Acinetobacter baumannii sequence type 25 with plasmid-borne New Delhi metallo-β-lactamase in Honduras. Antimicrob. Agents Chemother. 57, 4584–4586 (2013).
Google Scholar
McGann, P. et al. Detection of New Delhi metallo-β-lactamase (encoded by blaNDM-1) in Acinetobacter schindleri during routine surveillance. J. Clin. Microbiol. 51, 1942–1944 (2013).
Google Scholar
Forsberg, K. J. et al. The shared antibiotic resistome of soil bacteria and human pathogens. Science 337, 1107–1111 (2012).
Google Scholar
Jiang, X. et al. Dissemination of antibiotic resistance genes from antibiotic producers to pathogens. Nat. Commun. 8, 15784 (2017).
Google Scholar
Spanogiannopoulos, P., Waglechner, N., Koteva, K. & Wright, G. D. A rifamycin inactivating phosphotransferase family shared by environmental and pathogenic bacteria. Proc. Natl Acad. Sci. USA 111, 7102–7107 (2014).
Google Scholar
Yang, J. et al. Marine sediment bacteria harbor antibiotic resistance genes highly similar to those found in human pathogens. Microb. Ecol. 65, 975–981 (2013).
Google Scholar
D’Costa, V. M. et al. Antibiotic resistance is ancient. Nature 477, 457–461 (2011).
Google Scholar
Van Goethem, M. W. et al. A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils. Microbiome 6, 40 (2018).
Google Scholar
Mindlin, S., Soina, V. S., Petrova, M. A. & Gorlenko, Zh. M. Isolation of antibiotic resistance bacterial strains from Eastern Siberia permafrost sediments. Genetika 44, 36–44 (2008).
Google Scholar
Cohen, S. N. Transposable genetic elements and plasmid evolution. Nature 263, 731–738 (1976).
Google Scholar
Wright, G. D. Environmental and clinical antibiotic resistomes, same only different. Curr. Opin. Microbiol. 51, 57–63 (2019).
Google Scholar
von Wintersdorff, C. J. et al. Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer. Front. Microbiol. 7, 173 (2016).
Google Scholar
Rankin, D. J., Rocha, E. P. C. & Brown, S. P. What traits are carried on mobile genetic elements, and why? Heredity (Edinb) https://doi.org/10.1038/hdy.2010.24 (2011).
Kottara, A., Hall, J. P., Harrison, E. & Brockhurst, M. A. Variable plasmid fitness effects and mobile genetic element dynamics across Pseudomonas species. FEMS Microbiol. Ecol. 94, fix172 (2018).
Hall, J. P., 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).
Google Scholar
Hall, J. P. J., Williams, D., Paterson, S., Harrison, E. & Brockhurst, M. A. Positive selection inhibits gene mobilisation and transfer in soil bacterial communities. Nat. Ecol. Evol. 1, 1348–1353 (2017).
Google Scholar
Naumann, T. A. & Reznikoff, W. S. Tn5 transposase with an altered specificity for transposon ends. J. Bacteriol. 184, 233–240 (2002).
Google Scholar
Wang, H. et al. Increased plasmid copy number is essential for Yersinia T3SS function and virulence. Science 353, 492–495 (2016).
Google Scholar
Sandegren, L. & Andersson, D. I. Bacterial gene amplification: implications for the evolution of antibiotic resistance. Nat. Rev. Microbiol. 7, 578–588 (2009).
Google Scholar
Dimitriu, T., Mathews, A. C. & Buckling, A. Increased copy number couples the evolution of plasmid horizontal transmission and plasmid-encoded antibiotic resistance. Proc. Natl Acad. Sci. USA 118, e2107818118 (2021).
Google Scholar
De Lorenzo, V., Herrero, M., Jakubzik, U. & Timmis, K. N. Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria. J. Bacteriol. 172, 6568–6572 (1990).
Google Scholar
Lichtenstein, C. & Brenner, S. Site-specific properties of Tn7 transposition into the E. coli chromosome. Mol. Gen. Genet. 183, 380–387 (1981).
Google Scholar
Bethke, J. H. et al. Environmental and genetic determinants of plasmid mobility in pathogenic Escherichia coli. Sci. Adv. 6, eaax3173 (2020).
Google Scholar
Mahillon, J. & Chandler, M. Insertion sequences. Microbiol. Mol. Biol. Rev. 62, 725–774 (1998).
Google Scholar
Siguier, P., Perochon, J., Lestrade, L., Mahillon, J. & Chandler, M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 34, D32–D36 (2006).
Google Scholar
Seelke, R. W., Kline, B. C., Trawick, J. D. & Ritts, G. D. Genetic studies of F plasmid maintenance genes involved in copy number control, incompatability, and partitioning. Plasmid 7, 163–179 (1982).
Google Scholar
Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.0008 (2006).
Google Scholar
Watve, M. M., Dahanukar, N. & Watve, M. G. Sociobiological control of plasmid copy number in bacteria. PLoS ONE 5, e9328 (2010).
Google Scholar
Lehtinen, S. et al. Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae. Sci. Adv. 6, eaaz6137 (2020).
Google Scholar
Ubeda, C. et al. Antibiotic-induced SOS response promotes horizontal dissemination of pathogenicity island-encoded virulence factors in staphylococci. Mol. Microbiol. 56, 836–844 (2005).
Google Scholar
Beaber, J. W., Hochhut, B. & Waldor, M. K. SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature 427, 72–74 (2004).
Google Scholar
al‐Masaudi, S. B., Day, M. & Russell, A. D. Effect of some antibiotics and biocides on plasmid transfer in Staphylococcus aureus. J. Appl. Bacteriol. 71, 239–243 (1991).
Nichols, B. P. & Guay, G. G. Gene amplification contributes to sulfonamide resistance in Escherichia coli. Antimicrob. Agents Chemother. 33, 2042–2048 (1989).
Google Scholar
Normark, S., Edlund, T., Grundström, T., Bergström, S. & Wolf-Watz, H. Escherichia coli K-12 mutants hyperproducing chromosomal beta-lactamase by gene repetitions. J. Bacteriol. 132, 912–922 (1977).
Google Scholar
Zienkiewicz, M., Kern-Zdanowicz, I., Carattoli, A., Gniadkowski, M. & Cegłowski, P. Tandem multiplication of the IS 26-flanked amplicon with the blaSHV-5 gene within plasmid p1658/97. FEMS Microbiol. Lett. 341, 27–36 (2013).
Google Scholar
Matthews, P. R. & Stewart, P. R. Amplification of a section of chromosomal DNA in methicillin-resistant Staphylococcus aureus following growth in high concentrations of methicillin. J. Gen. Microbiol. 134, 1455–1464 (1988).
Google Scholar
Sun, S., Berg, O. G., Roth, J. R. & Andersson, D. I. Contribution of gene amplification to evolution of increased antibiotic resistance in Salmonella typhimurium. Genetics 182, 1183–1195 (2009).
Google Scholar
Andersson, D. I. & Hughes, D. Gene amplification and adaptive evolution in bacteria. Annu. Rev. Genet. 43, 167–195 (2009).
Google Scholar
Nicoloff, H., Perreten, V. & Levy, S. B. Increased genome instability in Escherichia coli lon mutants: relation to emergence of multiple-antibiotic-resistant (Mar) mutants caused by insertion sequence elements and large tandem genomic amplifications. Antimicrob. Agents Chemother. 51, 1293–1303 (2007).
Google Scholar
Bertini, A. et al. Multicopy blaOXA-58 gene as a source of high-level resistance to carbapenems in Acinetobacter baumannii. Antimicrob. Agents Chemother. 51, 2324–2328 (2007).
Google Scholar
Knapp, C. W. et al. Indirect evidence of transposon-mediated selection of antibiotic resistance genes in aquatic systems at low-level oxytetracycline exposures. Environ. Sci. Technol. 42, 5348–5353 (2008).
Google Scholar
San Millan, A., Escudero, J. A., Gifford, D. R., Mazel, D. & MacLean, R. C. Multicopy plasmids potentiate the evolution of antibiotic resistance in bacteria. Nat. Ecol. Evol. 1, 10 (2016).
Rodriguez-Beltran, J. et al. Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation. Nat. Ecol. Evol. 2, 873–881 (2018).
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).
Frost, L. S., Leplae, R., Summers, A. O. & Toussaint, A. Mobile genetic elements: the agents of open source evolution. Nat. Rev. Microbiol. 3, 722–732 (2005).
Google Scholar
You, L., Hoonlor, A. & Yin, J. Modeling biological systems using Dynetica—a simulator of dynamic networks. Bioinformatics 19, 435–436 (2003).
Google Scholar
Afgan, E. et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 46, W537–W544 (2018).
Google Scholar
Wingett, S. W. & Andrews, S. FastQ Screen: a tool for multi-genome mapping and quality control. F1000Res. 7, 1338 (2018).
Google Scholar
Blankenberg, D. et al. Manipulation of FASTQ data with Galaxy. Bioinformatics 26, 1783–1785 (2010).
Google Scholar
Magoč, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).
Google Scholar
Smith, T., Heger, A. & Sudbery, I. UMI-tools: modeling sequencing errors in unique molecular identifiers to improve quantification accuracy. Genome Res. 27, 491–499 (2017).
Google Scholar
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Google Scholar
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Google Scholar
Source: Ecology - nature.com