De Gelder, L., Ponciano, J. M., Joyce, P., & Top, E. M. (2007). Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship. Microbiology, 153(2), 452-463. doi:10.1099/mic.0.2006/001784-0
Norman, A., Hansen, L. H., & Sørensen, S. J. (2009). Conjugative plasmids: vessels of the communal gene pool. Philosophical Transactions of the Royal Society B: Biological Sciences, 364(1527), 2275-2289. doi:10.1098/rstb.2009.0037
Andam, C. P., Fournier, G. P., & Gogarten, J. P. (2011). Multilevel populations and the evolution of antibiotic resistance through horizontal gene transfer. FEMS Microbiology Reviews, 35(5), 756-767. doi:10.1111/j.1574-6976.2011.00274.x
[+]
De Gelder, L., Ponciano, J. M., Joyce, P., & Top, E. M. (2007). Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship. Microbiology, 153(2), 452-463. doi:10.1099/mic.0.2006/001784-0
Norman, A., Hansen, L. H., & Sørensen, S. J. (2009). Conjugative plasmids: vessels of the communal gene pool. Philosophical Transactions of the Royal Society B: Biological Sciences, 364(1527), 2275-2289. doi:10.1098/rstb.2009.0037
Andam, C. P., Fournier, G. P., & Gogarten, J. P. (2011). Multilevel populations and the evolution of antibiotic resistance through horizontal gene transfer. FEMS Microbiology Reviews, 35(5), 756-767. doi:10.1111/j.1574-6976.2011.00274.x
Baquero, F., Tedim, A. P., & Coque, T. M. (2013). Antibiotic resistance shaping multi-level population biology of bacteria. Frontiers in Microbiology, 4. doi:10.3389/fmicb.2013.00015
Wein, T., Hülter, N. F., Mizrahi, I., & Dagan, T. (2019). Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance. Nature Communications, 10(1). doi:10.1038/s41467-019-10600-7
Yano, H., Shintani, M., Tomita, M., Suzuki, H., & Oshima, T. (2019). Reconsidering plasmid maintenance factors for computational plasmid design. Computational and Structural Biotechnology Journal, 17, 70-81. doi:10.1016/j.csbj.2018.12.001
Gumpert, H., Kubicek-Sutherland, J. Z., Porse, A., Karami, N., Munck, C., Linkevicius, M., … Sommer, M. O. A. (2017). Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment. Frontiers in Microbiology, 8. doi:10.3389/fmicb.2017.01852
Durão, P., Balbontín, R., & Gordo, I. (2018). Evolutionary Mechanisms Shaping the Maintenance of Antibiotic Resistance. Trends in Microbiology, 26(8), 677-691. doi:10.1016/j.tim.2018.01.005
Campos, M., Llorens, C., Sempere, J. M., Futami, R., Rodriguez, I., Carrasco, P., … Baquero, F. (2015). A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES). Biology Direct, 10(1). doi:10.1186/s13062-015-0070-9
Campos, M., Capilla, R., Naya, F., Futami, R., Coque, T., Moya, A., … Baquero, F. (2019). Simulating Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model. mBio, 10(1), e02460-18. doi:10.1128/mbio.02460-18
13. Baquero F, Campos M, Llorens C, Sempere JM. 2018. A model of antibiotic resistance evolution dynamics through P systems with active membranes and communication rules, p 33–44. In Graciani C, Agustín Riscos-Núñez A, Păun Gh, Rozenberg G, Salomaa A (ed), Enjoying natural computing. Springer, Cham, Switzerland.
Leclerc, Q. J., Lindsay, J. A., & Knight, G. M. (2019). Mathematical modelling to study the horizontal transfer of antimicrobial resistance genes in bacteria: current state of the field and recommendations. Journal of The Royal Society Interface, 16(157), 20190260. doi:10.1098/rsif.2019.0260
Blanquart, F. (2019). Evolutionary epidemiology models to predict the dynamics of antibiotic resistance. Evolutionary Applications, 12(3), 365-383. doi:10.1111/eva.12753
16. Rozenberg G, Salomaa A, Păun G (ed). 2010. The Oxford handbook of membrane computing. Oxford University Press, Oxford, England.
17. Păun G. 2002. Membrane computing. An introduction. Springer-Verlag, Heidelberg, Germany.
Novais, A., Cantón, R., Moreira, R., Peixe, L., Baquero, F., & Coque, T. M. (2006). Emergence and Dissemination of Enterobacteriaceae Isolates Producing CTX-M-1-Like Enzymes in Spain Are Associated with IncFII (CTX-M-15) and Broad-Host-Range (CTX-M-1, -3, and -32) Plasmids. Antimicrobial Agents and Chemotherapy, 51(2), 796-799. doi:10.1128/aac.01070-06
Mathers, A. J., Peirano, G., & Pitout, J. D. D. (2015). The Role of Epidemic Resistance Plasmids and International High-Risk Clones in the Spread of Multidrug-Resistant Enterobacteriaceae. Clinical Microbiology Reviews, 28(3), 565-591. doi:10.1128/cmr.00116-14
20. Poirel L, Madec JY, Lupo A, Schink AK, Kieffer N, Nordmann P, Schwarz S. 2018. Antimicrobial resistance in Escherichia coli, p 289–316. In Schwarz S, Cavaco LM, Shen J (ed), Antimicrobial resistance in bacteria from livestock and companion animals. ASM Press, Washington, DC.
Livermore, D. M., & Hawkey, P. M. (2005). CTX-M: changing the face of ESBLs in the UK. Journal of Antimicrobial Chemotherapy, 56(3), 451-454. doi:10.1093/jac/dki239
23. European Centre for Disease Prevention and Control. 2015. Antimicrobial resistance surveillance in Europe 2015. Annual report of the European Antimicrobial Resistance Surveillance Network (EARS-Net). European Centre for Disease Prevention and Control, Stockholm, Sweden.
Bush, K., & Fisher, J. F. (2011). Epidemiological Expansion, Structural Studies, and Clinical Challenges of New β-Lactamases from Gram-Negative Bacteria. Annual Review of Microbiology, 65(1), 455-478. doi:10.1146/annurev-micro-090110-102911
Bush, K. (2018). Past and Present Perspectives on β-Lactamases. Antimicrobial Agents and Chemotherapy, 62(10). doi:10.1128/aac.01076-18
Hawser, S. P., Bouchillon, S. K., Hoban, D. J., Badal, R. E., Cantón, R., & Baquero, F. (2010). Incidence and Antimicrobial Susceptibility of Escherichia coli and Klebsiella pneumoniae with Extended-Spectrum β-Lactamases in Community- and Hospital-Associated Intra-Abdominal Infections in Europe: Results of the 2008 Study for Monitoring Antimicrobial Resistance Trends (SMART). Antimicrobial Agents and Chemotherapy, 54(7), 3043-3046. doi:10.1128/aac.00265-10
Simonsen, L., Gordon, D. M., Stewart, F. M., & Levin, B. R. (1990). Estimating the rate of plasmid transfer: an end-point method. Journal of General Microbiology, 136(11), 2319-2325. doi:10.1099/00221287-136-11-2319
Levin, B. R., Stewart, F. M., & Rice, V. A. (1979). The kinetics of conjugative plasmid transmission: Fit of a simple mass action model. Plasmid, 2(2), 247-260. doi:10.1016/0147-619x(79)90043-x
Turner, P. E., Williams, E. S. C. P., Okeke, C., Cooper, V. S., Duffy, S., & Wertz, J. E. (2014). Antibiotic resistance correlates with transmission in plasmid evolution. Evolution, 68(12), 3368-3380. doi:10.1111/evo.12537
Porse, A., Schønning, K., Munck, C., & Sommer, M. O. A. (2016). Survival and Evolution of a Large Multidrug Resistance Plasmid in New Clinical Bacterial Hosts. Molecular Biology and Evolution, 33(11), 2860-2873. doi:10.1093/molbev/msw163
Smillie, C., Garcillán-Barcia, M. P., Francia, M. V., Rocha, E. P. C., & de la Cruz, F. (2010). Mobility of Plasmids. Microbiology and Molecular Biology Reviews, 74(3), 434-452. doi:10.1128/mmbr.00020-10
38. Taylor DE, Gibreel A, Tracz DM, Lawley TD. 2004. Antibiotic resistance plasmids, p 473–492. In Funnell BE, Phillips GJ (ed), Plasmid biology. American Society of Microbiology, Washington, DC.
Million-Weaver, S., & Camps, M. (2014). Mechanisms of plasmid segregation: Have multicopy plasmids been overlooked? Plasmid, 75, 27-36. doi:10.1016/j.plasmid.2014.07.002
Lau, B. T. C., Malkus, P., & Paulsson, J. (2013). New quantitative methods for measuring plasmid loss rates reveal unexpected stability. Plasmid, 70(3), 353-361. doi:10.1016/j.plasmid.2013.07.007
Vogwill, T., & MacLean, R. C. (2014). The genetic basis of the fitness costs of antimicrobial resistance: a meta-analysis approach. Evolutionary Applications, 8(3), 284-295. doi:10.1111/eva.12202
Andersson, D. I., & Levin, B. R. (1999). The biological cost of antibiotic resistance. Current Opinion in Microbiology, 2(5), 489-493. doi:10.1016/s1369-5274(99)00005-3
Andersson, D. I., & Hughes, D. (2010). Antibiotic resistance and its cost: is it possible to reverse resistance? Nature Reviews Microbiology, 8(4), 260-271. doi:10.1038/nrmicro2319
Loftie-Eaton, W., Bashford, K., Quinn, H., Dong, K., Millstein, J., Hunter, S., … Top, E. M. (2017). Compensatory mutations improve general permissiveness to antibiotic resistance plasmids. Nature Ecology & Evolution, 1(9), 1354-1363. doi:10.1038/s41559-017-0243-2
Zwanzig, M., Harrison, E., Brockhurst, M. A., Hall, J. P. J., Berendonk, T. U., & Berger, U. (2019). Mobile Compensatory Mutations Promote Plasmid Survival. mSystems, 4(1). doi:10.1128/msystems.00186-18
Yang, Q. E., MacLean, C., Papkou, A., Pritchard, M., Powell, L., Thomas, D., … Walsh, T. R. (2020). Compensatory mutations modulate the competitiveness and dynamics of plasmid-mediated colistin resistance in Escherichia coli clones. The ISME Journal, 14(3), 861-865. doi:10.1038/s41396-019-0578-6
Gama, J. A., Zilhão, R., & Dionisio, F. (2018). Impact of plasmid interactions with the chromosome and other plasmids on the spread of antibiotic resistance. Plasmid, 99, 82-88. doi:10.1016/j.plasmid.2018.09.009
Harrison, E., Dytham, C., Hall, J. P. J., Guymer, D., Spiers, A. J., Paterson, S., & Brockhurst, M. A. (2016). Rapid compensatory evolution promotes the survival of conjugative plasmids. Mobile Genetic Elements, 6(3), e1179074. doi:10.1080/2159256x.2016.1179074
Hall, J. P. J., Brockhurst, M. A., Dytham, C., & Harrison, E. (2017). The evolution of plasmid stability: Are infectious transmission and compensatory evolution competing evolutionary trajectories? Plasmid, 91, 90-95. doi:10.1016/j.plasmid.2017.04.003
54. Shintani M, Suzuki H. 2019. Plasmids and their hosts, p 109–133. In Nishida H, Oshima T (ed), DNA traffic in the environment. Springer, Singapore.
Komp Lindgren, P., Karlsson, A., & Hughes, D. (2003). Mutation Rate and Evolution of Fluoroquinolone Resistance in Escherichia coli Isolates from Patients with Urinary Tract Infections. Antimicrobial Agents and Chemotherapy, 47(10), 3222-3232. doi:10.1128/aac.47.10.3222-3232.2003
Krone, S. M., Lu, R., Fox, R., Suzuki, H., & Top, E. M. (2007). Modelling the spatial dynamics of plasmid transfer and persistence. Microbiology, 153(8), 2803-2816. doi:10.1099/mic.0.2006/004531-0
Baquero, F., Coque, T. M., & de la Cruz, F. (2011). Ecology and Evolution as Targets: the Need for Novel Eco-Evo Drugs and Strategies To Fight Antibiotic Resistance. Antimicrobial Agents and Chemotherapy, 55(8), 3649-3660. doi:10.1128/aac.00013-11
Buckner, M. M. C., Ciusa, M. L., & Piddock, L. J. V. (2018). Strategies to combat antimicrobial resistance: anti-plasmid and plasmid curing. FEMS Microbiology Reviews, 42(6), 781-804. doi:10.1093/femsre/fuy031
Bush, K. (2008). Extended-spectrum β-lactamases in North America, 1987–2006. Clinical Microbiology and Infection, 14, 134-143. doi:10.1111/j.1469-0691.2007.01848.x
Jacoby, G. A., & Han, P. (1996). Detection of extended-spectrum beta-lactamases in clinical isolates of Klebsiella pneumoniae and Escherichia coli. Journal of clinical microbiology, 34(4), 908-911. doi:10.1128/jcm.34.4.908-911.1996
Valverde, A., Coque, T. M., Sanchez-Moreno, M. P., Rollan, A., Baquero, F., & Canton, R. (2004). Dramatic Increase in Prevalence of Fecal Carriage of Extended-Spectrum -Lactamase-Producing Enterobacteriaceae during Nonoutbreak Situations in Spain. Journal of Clinical Microbiology, 42(10), 4769-4775. doi:10.1128/jcm.42.10.4769-4775.2004
Hernández, J. R., Martínez-Martínez, L., Cantón, R., Coque, T. M., & Pascual, A. (2005). Nationwide Study of Escherichia coli and Klebsiella pneumoniae Producing Extended-Spectrum β-Lactamases in Spain. Antimicrobial Agents and Chemotherapy, 49(5), 2122-2125. doi:10.1128/aac.49.5.2122-2125.2005
PEREZ, F., ENDIMIANI, A., HUJER, K., & BONOMO, R. (2007). The continuing challenge of ESBLs. Current Opinion in Pharmacology, 7(5), 459-469. doi:10.1016/j.coph.2007.08.003
Hernández-García, M., Pérez-Viso, B., Navarro-San Francisco, C., Baquero, F., Morosini, M. I., Ruiz-Garbajosa, P., & Cantón, R. (2019). Intestinal co-colonization with different carbapenemase-producing Enterobacterales isolates is not a rare event in an OXA-48 endemic area. EClinicalMedicine, 15, 72-79. doi:10.1016/j.eclinm.2019.09.005
Jensen, R. B., & Gerdes, K. (1995). Programmed cell death in bacteria: proteic plasmid stabilization systems. Molecular Microbiology, 17(2), 205-210. doi:10.1111/j.1365-2958.1995.mmi_17020205.x
Stalder, T., Cornwell, B., Lacroix, J., Kohler, B., Dixon, S., Yano, H., … Top, E. M. (2020). Evolving Populations in Biofilms Contain More Persistent Plasmids. Molecular Biology and Evolution, 37(6), 1563-1576. doi:10.1093/molbev/msaa024
McNally, A., Oren, Y., Kelly, D., Pascoe, B., Dunn, S., Sreecharan, T., … Corander, J. (2016). Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations. PLOS Genetics, 12(9), e1006280. doi:10.1371/journal.pgen.1006280
Baquero, M.-R., Galán, J. C., del Carmen Turrientes, M., Cantón, R., Coque, T. M., Martínez, J. L., & Baquero, F. (2005). Increased Mutation Frequencies in Escherichia coli Isolates Harboring Extended-Spectrum β-Lactamases. Antimicrobial Agents and Chemotherapy, 49(11), 4754-4756. doi:10.1128/aac.49.11.4754-4756.2005
Baquero, F. (2004). From pieces to patterns: evolutionary engineering in bacterial pathogens. Nature Reviews Microbiology, 2(6), 510-518. doi:10.1038/nrmicro909
Andersson, D. I., Balaban, N. Q., Baquero, F., Courvalin, P., Glaser, P., Gophna, U., … Tønjum, T. (2020). Antibiotic resistance: turning evolutionary principles into clinical reality. FEMS Microbiology Reviews, 44(2), 171-188. doi:10.1093/femsre/fuaa001
Jernberg, C., Löfmark, S., Edlund, C., & Jansson, J. K. (2010). Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology, 156(11), 3216-3223. doi:10.1099/mic.0.040618-0
Sommer, F., Anderson, J. M., Bharti, R., Raes, J., & Rosenstiel, P. (2017). The resilience of the intestinal microbiota influences health and disease. Nature Reviews Microbiology, 15(10), 630-638. doi:10.1038/nrmicro.2017.58
Novais, C., Tedim, A. P., Lanza, V. F., Freitas, A. R., Silveira, E., Escada, R., … Coque, T. M. (2016). Co-diversification of Enterococcus faecium Core Genomes and PBP5: Evidences of pbp5 Horizontal Transfer. Frontiers in Microbiology, 7. doi:10.3389/fmicb.2016.01581
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