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Simulating the Influence of Conjugative-Plasmid Kinetic Values on the Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model

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Simulating the Influence of Conjugative-Plasmid Kinetic Values on the Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model

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Campos Frances, M.; San Millan, A.; Sempere Luna, JM.; Lanza, VF.; Coque, TM.; Llorens, C.; Baquero, F. (2020). Simulating the Influence of Conjugative-Plasmid Kinetic Values on the Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model. Antimicrobial Agents and Chemotherapy. 64(8):1-19. https://doi.org/10.1128/AAC.00593-20

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Title: Simulating the Influence of Conjugative-Plasmid Kinetic Values on the Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model
Author: Campos Frances, Marcelino San Millan, Alvaro Sempere Luna, José María Lanza, Val F. Coque, Teresa M. Llorens, Carlos Baquero, Fernando
UPV Unit: Universitat Politècnica de València. Departamento de Sistemas Informáticos y Computación - Departament de Sistemes Informàtics i Computació
Issued date:
Abstract:
[EN] Bacterial plasmids harboring antibiotic resistance genes are critical in the spread of antibiotic resistance. It is known that plasmids differ in their kinetic values, i.e., conjugation rate, segregation rate by copy ...[+]
Subjects: Antibiotic resistance , Complex systems , Computational biology , Computer modeling , Conjugation , Ecosystems , Membrane computing , Plasmids
Copyrigths: Reserva de todos los derechos
Source:
Antimicrobial Agents and Chemotherapy. (issn: 0066-4804 )
DOI: 10.1128/AAC.00593-20
Publisher:
American Society for Microbiology
Publisher version: https://doi.org/10.1128/AAC.00593-20
Project ID:
info:eu-repo/grantAgreement/MINECO//AC16%2F00043/ES/Escherichia coli ST131: a model for high-risk transmission dynamics of antimicrobial resistance/
info:eu-repo/grantAgreement/EC/H2020/757440/EU/Understanding the evolution of plasmid-mediated antibiotic resistance in real life scenarios/
info:eu-repo/grantAgreement/MINECO//PI15%2F00818/ES/Desarrollo de un simulador computacional de membranas para el estudio de la dinámica trans-jerárquica en la evolución de resistencia bacteriana a los antibióticos./
info:eu-repo/grantAgreement/ISCIII//PI18%2F01942/ES/Evolución de Resistomas y Resistotipos en la UVI: hacia un Análisis Particularizado de Riesgo de Emergencia e Infección por Bacterias Resistentes a Antibióticos/
info:eu-repo/grantAgreement/CIBER-BBN//CB06%2F02%2F0053/
Thanks:
F. Baquero, M. Campos, and T. M. Coque were supported by EU Joint Programming Initiative JPIAMR2016-AC16/00043 (JPIonAMR-Third call on Transmission, ST131TS project), the Health Institute Carlos III of Spain (grants ...[+]
Type: Artículo

References

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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