H. Références-bibliographiques-van-acker, P. Van-dijck, C. , and T. , Molecular mechanisms of antimicrobial tolerance and resistance in bacterial and fungal biofilms, Trends Microbiol, vol.22, pp.326-333, 2014.

M. Adam, B. Murali, N. O. Glenn, and S. S. Potter, Epigenetic inheritance based evolution of antibiotic resistance in bacteria, BMC Evolutionary Biology, vol.8, issue.1, p.52, 2008.
DOI : 10.1186/1471-2148-8-52

H. K. Alexander, S. I. Mayer, and S. Bonhoeffer, Population Heterogeneity in Mutation Rate Increases the Frequency of Higher-Order Mutants and Reduces Long-Term Mutational Load, Molecular Biology and Evolution, vol.66, pp.419-436, 2016.
DOI : 10.1099/mic.0.27230-0

K. R. Allison, M. P. Brynildsen, C. , and J. J. , Heterogeneous bacterial persisters and engineering approaches to eliminate them, Current Opinion in Microbiology, vol.14, issue.5, pp.593-598, 2011.
DOI : 10.1016/j.mib.2011.09.002

URL : http://europepmc.org/articles/pmc3196368?pdf=render

K. R. Allison, M. P. Brynildsen, C. , and J. J. , Metabolite-enabled eradication of bacterial persisters by aminoglycosides, Nature, vol.31, issue.7346, pp.216-220, 2011.
DOI : 10.1093/nar/gng015

S. D. Allison and J. B. Martiny, Resistance, resilience, and redundancy in microbial communities, Proceedings of the National Academy of Sciences, vol.88, issue.6, pp.11512-11519, 2008.
DOI : 10.1890/05-1839

URL : http://www.pnas.org/content/105/Supplement_1/11512.full.pdf

E. Alpkvist, C. Picioreanu, M. C. Van-loosdrecht, and A. Heyden, Three-dimensional biofilm model with individual cells and continuum EPS matrix, Biotechnology and Bioengineering, vol.91, issue.5, 2006.
DOI : 10.1099/00221287-147-11-2897

S. M. Amato and M. P. Brynildsen, Nutrient Transitions Are a Source of Persisters in Escherichia coli Biofilms, PLoS ONE, vol.8, issue.3, p.93110, 2014.
DOI : 10.1371/journal.pone.0093110.s015

S. M. Amato, C. H. Fazen, T. C. Henry, W. W. Mok, M. Orman et al., The role of metabolism in bacterial persistence, Frontiers in Microbiology, vol.5, p.70, 2014.
DOI : 10.3389/fmicb.2014.00070

S. M. Amato, M. A. Orman, and M. P. Brynildsen, Metabolic Control of Persister Formation in Escherichia coli, Molecular Cell, vol.50, issue.4, pp.475-87, 2013.
DOI : 10.1016/j.molcel.2013.04.002

J. N. Anderl, M. J. Franklin, and P. S. Stewart, Role of Antibiotic Penetration Limitation in Klebsiella pneumoniae Biofilm Resistance to Ampicillin and Ciprofloxacin, Antimicrobial Agents and Chemotherapy, vol.44, issue.7, pp.1818-1824, 2000.
DOI : 10.1128/AAC.44.7.1818-1824.2000

M. Arnoldini, R. Mostowy, S. Bonhoeffer, and M. Ackermann, Evolution of Stress Response in the Face of Unreliable Environmental Signals, PLoS Computational Biology, vol.8, issue.8, p.1002627, 2012.
DOI : 10.1371/journal.pcbi.1002627.s006

B. P. Ayati and I. Klapper, Models of microbial dormancy in biofilms and planktonic cultures, Communications in Mathematical Sciences, vol.10, issue.2, pp.493-511, 2012.
DOI : 10.4310/CMS.2012.v10.n2.a4

M. Ayrapetyan, T. C. Williams, and J. D. Oliver, Bridging the gap between viable but non-culturable and antibiotic persistent bacteria, Trends in Microbiology, vol.23, issue.1, pp.7-13, 2014.
DOI : 10.1016/j.tim.2014.09.004

M. Ayrapetyan, T. C. Williams, and J. D. Oliver, ABSTRACT, Applied and Environmental Microbiology, vol.80, issue.8, pp.2478-2483, 2014.
DOI : 10.1128/AEM.00080-14

D. L. Baho, H. Peter, and L. J. Tranvik, Resistance and resilience of microbial communities - temporal and spatial insurance against perturbations, Environmental Microbiology, vol.46, issue.9, pp.2283-2292, 2012.
DOI : 10.1007/s00248-003-1008-9

N. Q. Balaban, Persistence: mechanisms for triggering and enhancing phenotypic variability, Current Opinion in Genetics & Development, vol.21, issue.6, pp.768-775, 2011.
DOI : 10.1016/j.gde.2011.10.001

N. Q. Balaban, K. Gerdes, K. Lewis, and J. D. Mckinney, A problem of persistence: still more questions than answers?, Nature Reviews Microbiology, vol.467, issue.8, pp.587-591, 2013.
DOI : 10.1038/nature09333

N. Q. Balaban, J. Merrin, R. Chait, L. Kowalik, and S. Leibler, Bacterial Persistence as a Phenotypic Switch, Science, vol.305, issue.5690, pp.1622-1625, 2004.
DOI : 10.1126/science.1099390

F. Baquero, A. P. Tedim, C. , and T. M. , Antibiotic resistance shaping multi-level population biology of bacteria, Frontiers in Microbiology, vol.4, 2013.
DOI : 10.3389/fmicb.2013.00015

N. Barraud, A. Buson, W. Jarolimek, R. , and S. , Mannitol Enhances Antibiotic Sensitivity of Persister Bacteria in Pseudomonas aeruginosa Biofilms, PLoS ONE, vol.59, issue.12, pp.1-13, 2013.
DOI : 10.1371/journal.pone.0084220.t001

V. C. Barth, B. A. Rodrigues, G. D. Bonatto, S. W. Gallo, V. E. Pagnussatti et al., Heterogeneous Persister Cells Formation in Acinetobacter baumannii, PLoS ONE, vol.339, issue.12, 2013.
DOI : 10.1371/journal.pone.0084361.s001

URL : https://doi.org/10.1371/journal.pone.0084361

H. J. Beaumont, J. Gallie, C. Kost, G. C. Ferguson, and P. B. Rainey, Experimental evolution of bet hedging, Nature, vol.138, issue.7269, pp.90-93, 2009.
DOI : 10.1038/nature08504

B. Van-den-bergh, M. Fauvart, and J. Michiels, Formation, physiology, ecology, evolution and clinical importance of bacterial persisters, FEMS Microbiology Reviews, vol.56, issue.Suppl 1, pp.219-251, 2017.
DOI : 10.1128/AAC.06288-11

S. P. Bernier, D. Lebeaux, A. S. Defrancesco, A. Valomon, G. Soubigou et al., Starvation, Together with the SOS Response, Mediates High Biofilm-Specific Tolerance to the Fluoroquinolone Ofloxacin, PLoS Genetics, vol.73, issue.1, 2013.
DOI : 10.1371/journal.pgen.1003144.s008

URL : https://hal.archives-ouvertes.fr/pasteur-01385427

L. Bobay, C. C. Traverse, and H. Ochman, Impermanence of bacterial clones, Proceedings of the National Academy of Sciences, vol.133, issue.3, pp.8893-8900, 2015.
DOI : 10.1016/j.meegid.2005.02.003

B. R. Boles and P. K. Singh, Endogenous oxidative stress produces diversity and adaptability in biofilm communities, Proceedings of the National Academy of Sciences, vol.100, issue.14, pp.12503-12508, 2008.
DOI : 10.1073/pnas.1033133100

URL : http://www.pnas.org/content/105/34/12503.full.pdf

J. Bos, Q. Zhang, S. Vyawahare, E. Rogers, S. M. Rosenberg et al., Emergence of antibiotic resistance from multinucleated bacterial filaments, Proceedings of the National Academy of Sciences, vol.12, issue.5, pp.178-183, 2015.
DOI : 10.1007/978-1-4419-6199-0_1

S. Botton, M. Van-heusden, J. R. Parsons, H. Smidt, and N. Van-straalen, Resilience of Microbial Systems Towards Disturbances, Critical Reviews in Microbiology, vol.120, issue.2, pp.101-112, 2006.
DOI : 10.1086/284013

G. Brackman, P. Cos, L. Maes, H. J. Nelis, C. et al., ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.55, issue.6, pp.2655-2661, 2011.
DOI : 10.1128/AAC.00045-11

F. S. Brand and K. Jax, Focusing the Meaning(s) of Resilience: Resilience as a Descriptive Concept and a Boundary Object, Ecology and Society, vol.12, issue.1, p.23, 2007.
DOI : 10.5751/ES-02029-120123

S. S. Branda, Å. Vik, L. Friedman, and R. Kolter, Biofilms: the matrix revisited, Trends in Microbiology, vol.13, issue.1, pp.20-26, 2005.
DOI : 10.1016/j.tim.2004.11.006

A. Brauner, O. Fridman, O. Gefen, and N. Q. Balaban, Distinguishing between resistance, tolerance and persistence to antibiotic treatment, Nature Reviews Microbiology, vol.37, issue.5, pp.320-350, 2016.
DOI : 10.1007/s00284-009-9395-x

A. Brias, J. D. Mathias, and G. Deffuant, Accelerating viability kernel computation with CUDA architecture: application to bycatch fishery management, Computational Management Science, vol.23, issue.2, pp.371-391, 2016.
DOI : 10.1109/ACC.2009.5160409

A. Bridier, R. Briandet, V. Thomas, and F. Dubois-brissonnet, Resistance of bacterial biofilms to disinfectants: a review, Biofouling, vol.64, issue.9, pp.1017-1032, 2011.
DOI : 10.1046/j.1365-2958.2001.02337.x

URL : https://hal.archives-ouvertes.fr/hal-01001460

. Bridier, P. Sanchez-vizuete, M. Guilbaud, J. C. Piard, M. Naïtali et al., Biofilm-associated persistence of food-borne pathogens, Food Microbiology, vol.45, pp.167-178, 2014.
DOI : 10.1016/j.fm.2014.04.015

URL : https://hal.archives-ouvertes.fr/hal-01204463

M. Burmølle, J. S. Webb, D. Rao, L. H. Hansen, S. J. Sørensen et al., Enhanced Biofilm Formation and Increased Resistance to Antimicrobial Agents and Bacterial Invasion Are Caused by Synergistic Interactions in Multispecies Biofilms, Applied and Environmental Microbiology, vol.72, issue.6, pp.3916-3939, 2006.
DOI : 10.1128/AEM.03022-05

S. Carpenter, B. Walker, J. M. Anderies, A. , and N. , From Metaphor to Measurement: Resilience of What to What?, Ecosystems, vol.4, issue.8, pp.765-781, 2001.
DOI : 10.1007/s10021-001-0045-9

G. Carvalho, C. Guilhen, D. Balestrino, C. Forestier, M. et al., Relating switching rates between normal and persister cells to substrate and antibiotic concentrations: a mathematical modelling approach supported by experiments, Microbial Biotechnology, vol.343, issue.6, pp.1-12, 2017.
DOI : 10.1016/j.jtbi.2013.11.008

URL : https://hal.archives-ouvertes.fr/hal-01779031

J. D. Chambless, S. M. Hunt, and P. S. Stewart, A Three-Dimensional Computer Model of Four Hypothetical Mechanisms Protecting Biofilms from Antimicrobials, Applied and Environmental Microbiology, vol.72, issue.3, pp.2005-2013, 2006.
DOI : 10.1128/AEM.72.3.2005-2013.2006

J. D. Chambless and P. S. Stewart, A three-dimensional computer model analysis of three hypothetical biofilm detachment mechanisms, Biotechnology and Bioengineering, vol.91, issue.6, pp.1573-1584, 2007.
DOI : 10.2166/wst.2006.401

K. Chihara, S. Matsumoto, Y. Kagawa, and S. Tsuneda, Mathematical modeling of dormant cell formation in growing biofilm, Frontiers in Microbiology, vol.91, pp.1-8, 2015.
DOI : 10.1002/bit.20544

K. Choi and H. P. Schweizer, mini-Tn7 insertion in bacteria with single attTn7 sites: example Pseudomonas aeruginosa, Nature Protocols, vol.212, issue.1, pp.153-161, 2006.
DOI : 10.1038/nprot.2006.24

S. K. Christensen and K. Gerdes, RelE toxins from Bacteria and Archaea cleave mRNAs on translating ribosomes, which are rescued by tmRNA, Molecular Microbiology, vol.266, issue.5, pp.1389-1400, 2003.
DOI : 10.1093/emboj/18.19.5423

URL : http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2003.03512.x/pdf

D. Claessen, D. E. Rozen, O. P. Kuipers, L. Søgaard-andersen, and G. P. Van-wezel, Bacterial solutions to multicellularity: a tale of biofilms, filaments and fruiting bodies, Nature Reviews Microbiology, vol.107, issue.2, pp.115-139, 2014.
DOI : 10.1073/pnas.0911299107

J. R. Clark, S. J. Daines, T. M. Lenton, A. J. Watson, W. et al., Individual-based modelling of adaptation in marine microbial populations using genetically defined physiological parameters, Ecological Modelling, vol.222, issue.23-24, pp.3823-3837, 2011.
DOI : 10.1016/j.ecolmodel.2011.10.001

J. R. Clark, T. M. Lenton, H. T. Williams, and S. J. Daines, Environmental selection and resource allocation determine spatial patterns in picophytoplankton cell size, Limnology and Oceanography, vol.58, issue.3, pp.1008-1022, 2013.
DOI : 10.4319/lo.2013.58.3.1008

URL : http://onlinelibrary.wiley.com/doi/10.4319/lo.2013.58.3.1008/pdf

N. G. Cogan, Effects of persister formation on bacterial response to dosing, Journal of Theoretical Biology, vol.238, issue.3, pp.694-703, 2006.
DOI : 10.1016/j.jtbi.2005.06.017

N. G. Cogan, J. Brown, K. Darres, and K. Petty, ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.56, issue.9, pp.4816-4826, 2012.
DOI : 10.1128/AAC.00675-12

N. G. Cogan, B. Szomolay, and M. Dindos, Effect of Periodic Disinfection on Persisters in a One-Dimensional Biofilm Model, Bulletin of Mathematical Biology, vol.146, issue.8, pp.94-123, 2013.
DOI : 10.1099/00221287-146-3-547

N. R. Cohen, M. A. Lobritz, C. , and J. J. , Microbial Persistence and the Road to Drug Resistance, Cell Host & Microbe, vol.13, issue.6, pp.632-642, 2013.
DOI : 10.1016/j.chom.2013.05.009

B. P. Conlon, E. S. Nakayasu, L. E. Fleck, M. D. Lafleur, V. M. Isabella et al., Activated ClpP kills persisters and eradicates a chronic biofilm infection, Nature, vol.15, issue.7476, pp.365-70, 2013.
DOI : 10.1093/jac/15.suppl_A.125

URL : http://europepmc.org/articles/pmc4031760?pdf=render

A. Crombach and P. Hogeweg, Evolution of Evolvability in Gene Regulatory Networks, PLoS Computational Biology, vol.10, issue.7, p.1000112, 2008.
DOI : 10.1371/journal.pcbi.1000112.s005

S. A. Crusz, R. Popat, M. T. Rybtke, M. Cámara, M. Givskov et al., Bursting the bubble on bacterial biofilms: a flow cell methodology, Biofouling, vol.60, issue.8, pp.835-842, 2012.
DOI : 10.1016/j.mimet.2007.11.010

E. Darmon and D. R. Leach, Bacterial Genome Instability, Microbiology and Molecular Biology Reviews, vol.78, issue.1, pp.1-39, 2014.
DOI : 10.1128/MMBR.00035-13

URL : http://mmbr.asm.org/content/78/1/1.full.pdf

T. Das, S. Sehar, and M. Manefield, The roles of extracellular DNA in the structural integrity of extracellular polymeric substance and bacterial biofilm development, Environmental Microbiology Reports, vol.193, issue.6, pp.778-86, 2013.
DOI : 10.1128/JB.01131-10

C. J. Davidson and M. G. Surette, Individuality in Bacteria, Annual Review of Genetics, vol.42, issue.1, pp.253-68, 2008.
DOI : 10.1146/annurev.genet.42.110807.091601

J. Davies and D. Davies, Origins and Evolution of Antibiotic Resistance, Microbiology and Molecular Biology Reviews, vol.74, issue.3, pp.417-433, 2010.
DOI : 10.1128/MMBR.00016-10

G. Deffuant and N. Gilbert, Viability and Resilience of Complex Systems Springer, 2011.

L. Dethlefsen and D. Relman, Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation, Proceedings of the National Academy of Sciences, vol.88, issue.10, pp.4554-4561, 2011.
DOI : 10.1890/06-1736.1

T. Dörr, K. Lewis, and M. Vulic, SOS Response Induces Persistence to Fluoroquinolones in Escherichia coli, PLoS Genetics, vol.178, issue.12, 2009.
DOI : 10.1371/journal.pgen.1000760.t001

T. Dörr, M. Vuli?, L. , and K. , Ciprofloxacin Causes Persister Formation by Inducing the TisB toxin in Escherichia coli, PLoS Biology, vol.183, issue.2, pp.29-35, 2010.
DOI : 10.1371/journal.pbio.1000317.s001

B. O. Emerenini, B. A. Hense, C. Kuttler, and H. J. Eberl, A Mathematical Model of Quorum Sensing Induced Biofilm Detachment, PLOS ONE, vol.20, issue.6, pp.1-25, 2015.
DOI : 10.1371/journal.pone.0132385.s001

D. S. Esser, J. H. Leveau, M. , and K. M. , Modeling microbial growth and dynamics, Applied Microbiology and Biotechnology, vol.55, issue.21, pp.8831-8846, 2015.
DOI : 10.4315/0362-028X-55.12.973

M. G. Fagerlind, J. S. Webb, N. Barraud, D. Mcdougald, A. Jansson et al., Dynamic modelling of cell death during biofilm development, Journal of Theoretical Biology, vol.295, pp.23-36, 2012.
DOI : 10.1016/j.jtbi.2011.10.007

R. Fasani and M. Savageau, Molecular mechanisms of multiple toxin-antitoxin systems are coordinated to govern the persister phenotype, Proceedings of the National Academy of Sciences, vol.29, issue.3, pp.2528-2537, 2013.
DOI : 10.1099/00221287-29-3-421

J. Feng, D. A. Kessler, E. Ben-jacob, and H. Levine, Growth feedback as a basis for persister bistability, Proceedings of the National Academy of Sciences, vol.110, issue.27, pp.544-549, 2013.
DOI : 10.1073/pnas.1301023110

URL : http://www.pnas.org/content/111/1/544.full.pdf

T. Ferenci and R. Maharjan, Mutational heterogeneity: A key ingredient of bet-hedging and evolutionary divergence?, BioEssays, vol.39, issue.2, pp.123-130, 2015.
DOI : 10.1038/ng2051

L. Fernandez, J. M. Mercader, M. Planas-fèlix, and D. Torrents, Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities, BMC Genomics, vol.15, issue.1, p.877, 2014.
DOI : 10.1186/1471-2105-11-119

J. Ferrer, C. Prats, and D. López, Individual-based Modelling: An Essential Tool for Microbiology, Journal of Biological Physics, vol.20, issue.21, pp.19-37, 2008.
DOI : 10.1016/j.jtbi.2006.01.029

URL : http://europepmc.org/articles/pmc2577750?pdf=render

R. A. Fisher, B. Gollan, H. , and S. , Persistent bacterial infections and persister cells, Nature Reviews Microbiology, vol.14, issue.8, 2017.
DOI : 10.1038/nrmicro.2016.141

URL : http://hdl.handle.net/10044/1/53563

H. Flemming, J. Wingender, U. Szewzyk, P. Steinberg, S. A. Rice et al., Biofilms: an emergent form of bacterial life, Nature Reviews Microbiology, vol.10, issue.9, pp.563-575, 2016.
DOI : 10.1111/j.1365-2958.2005.04938.x

S. Flood and J. Schechtman, The rise of resilience: Evolution of a new concept in coastal planning in Ireland and the US, Ocean & Coastal Management, vol.102, pp.19-31, 2014.
DOI : 10.1016/j.ocecoaman.2014.08.015

C. Folke, Resilience: The emergence of a perspective for social???ecological systems analyses, Global Environmental Change, vol.16, issue.3, pp.253-267, 2006.
DOI : 10.1016/j.gloenvcha.2006.04.002

C. Folke, S. R. Carpenter, B. Walker, M. Scheffer, T. Chapin et al., Resilience Thinking: Integrating Resilience, Adaptability and Transformability, Ecology and Society, vol.15, issue.4, p.20, 2010.
DOI : 10.5751/ES-03610-150420

URL : http://www.ecologyandsociety.org/vol15/iss4/art20/ES-2010-3610.pdf

O. Fridman, A. Goldberg, I. Ronin, N. Shoresh, and N. Q. Balaban, Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations, Nature, vol.461, issue.7518, pp.418-421, 2014.
DOI : 10.1038/nature08480

R. S. Galhardo, P. J. Hastings, and S. M. Rosenberg, Mutation as a Stress Response and the Regulation of Evolvability, Critical Reviews in Biochemistry and Molecular Biology, vol.259, issue.5, pp.399-435, 2007.
DOI : 10.1126/science.7681219

G. C. Gallopín, Linkages between vulnerability, resilience, and adaptive capacity, Global Environmental Change, vol.16, issue.3, pp.293-303, 2006.
DOI : 10.1016/j.gloenvcha.2006.02.004

O. Gefen and N. Q. Balaban, The importance of being persistent: heterogeneity of bacterial populations under antibiotic stress, FEMS Microbiology Reviews, vol.43, issue.Spec No, pp.704-717, 2009.
DOI : 10.1128/AAC.34.10.1938

L. Gelens, L. Hill, A. Vandervelde, J. Danckaert, L. et al., A General Model for Toxin-Antitoxin Module Dynamics Can Explain Persister Cell Formation in E. coli, PLoS Computational Biology, vol.81, issue.8, p.1003190, 2013.
DOI : 10.1371/journal.pcbi.1003190.s009

J. Gerhart and M. Kirschner, The theory of facilitated variation, Proceedings of the National Academy of Sciences, vol.97, issue.3, pp.8582-8589, 2007.
DOI : 10.1038/sj.hdy.6800864

J. V. Gestel, N. Vlamakis, H. Kolter, and R. , Division of Labor in Biofilms: the Ecology of Cell Differentiation, Microbiology Spectrum, vol.3, issue.2, pp.1-24, 2015.
DOI : 10.1128/microbiolspec.MB-0002-2014

A. Ghanbari, J. Dehghany, T. Schwebs, M. Müsken, S. Häussler et al., Inoculation density and nutrient level determine the formation of mushroomshaped structures in Pseudomonas aeruginosa biofilms, Sci. Rep, vol.6, pp.1-12, 2016.

P. Ghosh, E. Ben-jacob, and H. Levine, Modeling cell-death patterning during biofilm formation, Physical Biology, vol.10, issue.6, p.66006, 2013.
DOI : 10.1088/1478-3975/10/6/066006

M. S. Girvan, C. D. Campbell, K. Killham, J. I. Prosser, and L. Glover, Bacterial diversity promotes community stability and functional resilience after perturbation, Environmental Microbiology, vol.143, issue.3, pp.301-313, 2005.
DOI : 10.1016/S0038-0717(97)00062-X

T. E. Gorochowski, Agent-based modelling in synthetic biology, Essays In Biochemistry, vol.60, issue.4, pp.325-336, 2016.
DOI : 10.1042/EBC20160037

URL : http://essays.biochemistry.org/content/ppebio/60/4/325.full.pdf

B. S. Griffiths and L. Philippot, Insights into the resistance and resilience of the soil microbial community, FEMS Microbiology Reviews, vol.61, issue.2, pp.112-129, 2013.
DOI : 10.1016/j.soilbio.2010.02.004

A. J. Grimbergen, J. Siebring, A. Solopova, and O. P. Kuipers, Microbial bet-hedging: the power of being different, Current Opinion in Microbiology, vol.25, pp.67-72, 2015.
DOI : 10.1016/j.mib.2015.04.008

V. Grimm and C. Wissel, Babel, or the ecological stability discussions: an inventory and analysis of terminology and a guide for avoiding confusion, Oecologia, vol.109, issue.3, pp.323-334, 1997.
DOI : 10.1007/s004420050090

C. Guilhen, A. Iltis, C. Forestier, and D. Balestrino, Genome Sequence of a Clinical Klebsiella pneumoniae Sequence Type 6 Strain, Genome Announcements, vol.34, issue.1, 2015.
DOI : 10.1093/nar/gkj406

A. M. Hall, B. Gollan, H. , and S. , Toxin???antitoxin systems: reversible toxicity, Current Opinion in Microbiology, vol.36, pp.102-110, 2017.
DOI : 10.1016/j.mib.2017.02.003

C. W. Hall and T. Mah, Molecular mechanisms of biofilm-based antibiotic resistance and tolerance in pathogenic bacteria, FEMS Microbiology Reviews, vol.46, issue.3, pp.276-301, 2017.
DOI : 10.1128/AAC.46.3.900-903.2002

M. C. Hansen, R. J. Palmer, C. Udsen, D. C. White, S. Molin et al., Assessment of GFP fluorescence in cells of Streptococcus gordonii under conditions of low pH and low oxygen concentration, Microbiology, vol.33, issue.5, pp.1383-1391, 2001.
DOI : 10.1016/0378-1119(85)90120-9

A. Harms, E. Maisonneuve, and K. Gerdes, Mechanisms of bacterial persistence 6 Références bibliographiques during stress and antibiotic exposure, Science, vol.80, issue.354, p.4268, 2016.

A. Harms, E. Maisonneuve, and K. Gerdes, Mechanisms of bacterial persistence during stress and antibiotic exposure, Science, vol.6, issue.6318, p.4268, 2016.
DOI : 10.1038/srep20519

M. Hashimoto, T. Nozoe, H. Nakaoka, R. Okura, S. Akiyoshi et al., Noise-driven growth rate gain in clonal cellular populations, Proceedings of the National Academy of Sciences, vol.5, issue.1, pp.3251-3256, 2016.
DOI : 10.1103/PhysRevLett.113.028101

V. Hauryliuk, G. C. Atkinson, K. S. Murakami, T. Tenson, and K. Gerdes, Recent functional insights into the role of (p)ppGpp in bacterial physiology, Nature Reviews Microbiology, vol.311, issue.5, pp.298-309, 2015.
DOI : 10.1126/science.1123061

S. Helaine and E. Kugelberg, Bacterial persisters: formation, eradication, and experimental systems, Trends in Microbiology, vol.22, issue.7, pp.417-424, 2014.
DOI : 10.1016/j.tim.2014.03.008

F. L. Hellweger, R. J. Clegg, J. R. Clark, C. M. Plugge, and J. Kreft, Advancing microbial sciences by individual-based modelling, Nature Reviews Microbiology, vol.48, issue.7, pp.461-471, 2016.
DOI : 10.4319/lo.2003.48.5.1732

R. Hermsen, J. B. Deris, H. , and T. , On the rapidity of antibiotic resistance evolution facilitated by a concentration gradient, Proceedings of the National Academy of Sciences, vol.330, issue.6007, pp.10775-80, 2012.
DOI : 10.1126/science.1192588

Y. Hershkovitz and A. Gasith, Resistance, resilience, and community dynamics in mediterranean-climate streams, Hydrobiologia, vol.365, issue.160, pp.59-75, 2013.
DOI : 10.1098/rstb.2010.0055

A. Heydorn, . T. Nielsen, M. Hentzer, C. Sternberg, M. Givskov et al., Quantification of biofilm structures by the novel computer program comstat, Microbiology, vol.28, issue.10, pp.2395-2407, 2000.
DOI : 10.1016/0043-1354(94)90042-6

C. S. Holling, Engineering resilience versus ecological resilience Engineering within ecological constraints, pp.31-44, 1996.

C. S. Holling, Resilience and Stability of Ecological Systems, Annual Review of Ecology and Systematics, vol.4, issue.1, pp.1-23, 1973.
DOI : 10.1146/annurev.es.04.110173.000245

S. Hosseini, K. Barker, and J. E. Ramirez-marquez, A review of definitions and measures of system resilience, Reliability Engineering & System Safety, vol.145, pp.47-61, 2016.
DOI : 10.1016/j.ress.2015.08.006

D. E. Hunt and C. S. Ward, A network-based approach to disturbance transmission through microbial interactions, Frontiers in Microbiology, vol.111, pp.1-8, 2015.
DOI : 10.1073/pnas.1324044111

M. Imran and H. L. Smith, A model of optimal dosing of antibiotic treatment in biofilm, Mathematical Biosciences and Engineering, vol.11, issue.3, pp.547-71, 2014.
DOI : 10.3934/mbe.2014.11.547

J. Iranzo, A. E. Lobkovsky, Y. I. Wolf, and E. V. Koonin, Evolutionary Dynamics of the Prokaryotic Adaptive Immunity System CRISPR-Cas in an Explicit Ecological Context, Journal of Bacteriology, vol.195, issue.17, pp.3834-3844, 2013.
DOI : 10.1128/JB.00412-13

B. Javid, F. Sorrentino, M. Toosky, W. Zheng, J. T. Pinkham et al., Mycobacterial mistranslation is necessary and sufficient for rifampicin phenotypic resistance, Proceedings of the National Academy of Sciences, vol.106, issue.44, pp.1132-1139, 2014.
DOI : 10.1073/pnas.0900589106

URL : http://www.pnas.org/content/111/3/1132.full.pdf

A. Jõers, N. Kaldalu, and T. Tenson, The Frequency of Persisters in Escherichia coli Reflects the Kinetics of Awakening from Dormancy, Journal of Bacteriology, vol.192, issue.13, pp.3379-3384, 2010.
DOI : 10.1128/JB.00056-10

A. Jolivet-gougeon and M. Bonnaure-mallet, Biofilms as a mechanism of bacterial resistance, Drug Discovery Today: Technologies, vol.11, pp.49-56, 2014.
DOI : 10.1016/j.ddtec.2014.02.003

URL : https://hal.archives-ouvertes.fr/hal-01130308

P. S. Jørgensen, D. Wernli, S. P. Carroll, R. R. Dunn, S. Harbarth et al., Use antimicrobials wisely, Nature, vol.537, issue.7619, pp.159-61, 2016.
DOI : 10.1038/537159a

H. Kahiluoto, J. Kaseva, K. Hakala, S. J. Himanen, L. Jauhiainen et al., Cultivating resilience by empirically revealing response diversity, Global Environmental Change, vol.25, pp.186-193, 2014.
DOI : 10.1016/j.gloenvcha.2014.02.002

URL : https://doi.org/10.1016/j.gloenvcha.2014.02.002

N. Kaldalu, V. Hauryliuk, and T. Tenson, Persisters???as elusive as ever, Applied Microbiology and Biotechnology, vol.8, issue.218, pp.6545-6553, 2016.
DOI : 10.1007/BF02010671

URL : https://link.springer.com/content/pdf/10.1007%2Fs00253-016-7648-8.pdf

I. Keren, N. Kaldalu, A. Spoering, Y. Wang, L. et al., Persister cells and tolerance to antimicrobials, FEMS Microbiology Letters, vol.33, issue.1, pp.13-18, 2004.
DOI : 10.1128/AAC.33.5.705

URL : https://academic.oup.com/femsle/article-pdf/230/1/13/19384487/230-1-13.pdf

C. I. Kint, N. Verstraeten, M. Fauvart, and J. Michiels, New-found fundamentals of bacterial persistence, Trends in Microbiology, vol.20, issue.12, pp.577-85, 2012.
DOI : 10.1016/j.tim.2012.08.009

M. Kirschner, Beyond Darwin: evolvability and the generation of novelty, BMC Biology, vol.11, issue.1, p.110, 2013.
DOI : 10.1016/S0022-2836(61)80072-7

H. Kitano, Towards a theory of biological robustness, Molecular Systems Biology, vol.406, p.137, 2007.
DOI : 10.1042/bj2860313

J. Klima and R. Psenner, Determination of Bacterial Cell Dry Mass by Transmission Electron Microscopy and Densitometric Image Analysis Determination of Bacterial Cell Dry Mass by Transmission Electron Microscopy and Densitometric Image Analysis, pp.688-694, 1998.

C. T. Kone, D. Sousa, G. , M. , and J. , Adaptive management of energy consumption, reliability and delay of wireless sensor node: Application to IEEE 802.15.4 wireless sensor node, PLOS ONE, vol.29, issue.2, 2017.
DOI : 10.1371/journal.pone.0172336.s001

S. König, A. Worrich, F. Centler, L. Y. Wick, A. Miltner et al., Modelling functional resilience of microbial ecosystems: Analysis of governing processes, Environmental Modelling & Software, vol.89, pp.31-39, 2016.
DOI : 10.1016/j.envsoft.2016.11.025

A. Konopka, S. Lindemann, and J. Fredrickson, Dynamics in microbial communities: unraveling mechanisms to identify principles, The ISME Journal, vol.337, issue.7, pp.1488-1495, 2015.
DOI : 10.1126/science.1224041

J. U. Kreft, G. Booth, and J. W. Wimpenny, BacSim, a simulator for individual-based modelling of bacterial colony growth, Microbiology, vol.144, issue.12, pp.3275-3287, 1998.
DOI : 10.1099/00221287-144-12-3275

J. U. Kreft, C. Picioreanu, J. W. Wimpenny, V. Loosdrecht, and M. C. , Individual-based modelling of biofilms, Microbiology, vol.28, issue.11, pp.2897-2912, 2001.
DOI : 10.1016/0043-1354(94)90043-4

L. Lardon, B. V. Merkey, S. Martins, A. Dötsch, C. Picioreanu et al., iDynoMiCS: next-generation individual-based modelling of biofilms, Environmental Microbiology, vol.177, issue.9, pp.2416-2434, 2011.
DOI : 10.1128/jb.177.12.3606-3609.1995

C. S. Laspidou, A. Kungolos, and P. Samaras, Cellular-automata and individual-based approaches for the modeling of biofilm structures: Pros and cons, Desalination, vol.250, issue.1, pp.390-394, 2010.
DOI : 10.1016/j.desal.2009.09.062

C. S. Laspidou, A. Liakopoulos, and M. G. Spiliotopoulos, A 2D Cellular Automaton Biofilm Detachment Algorithm, Lect. Notes Comput. Sci, vol.7495, pp.415-424, 2012.
DOI : 10.1007/978-3-642-33350-7_43

R. Laxminarayan, A. Duse, C. Wattal, A. K. Zaidi, H. F. Wertheim et al., Antibiotic resistance???the need for global solutions, The Lancet Infectious Diseases, vol.13, issue.12, pp.1057-1098, 2013.
DOI : 10.1016/S1473-3099(13)70318-9

S. Lechner, P. Patra, S. Klumpp, and R. Bertram, Persister Cells, Journal of Molecular Microbiology and Biotechnology, vol.95, issue.6, pp.381-391, 2012.
DOI : 10.1128/AAC.49.4.1483-1494.2005

K. W. Lee, S. Periasamy, M. Mukherjee, C. Xie, S. Kjelleberg et al., Biofilm development and enhanced stress resistance of a model, mixed-species community biofilm, The ISME Journal, vol.6, issue.4, pp.894-907, 2014.
DOI : 10.1038/ismej.2011.188

P. Leslie and J. T. Mccabe, Response Diversity and Resilience in Social-Ecological Systems, Current Anthropology, vol.54, issue.2, pp.114-143, 2013.
DOI : 10.1086/669563

I. Levin-reisman, I. Ronin, O. Gefen, I. Braniss, N. Shoresh et al., Antibiotic tolerance facilitates the evolution of resistance, Science, vol.28, issue.6327, pp.826-830, 2017.
DOI : 10.1073/pnas.1314114111

B. R. Levin and K. I. Udekwu, Population Dynamics of Antibiotic Treatment: a Mathematical Model and Hypotheses for Time-Kill and Continuous-Culture Experiments, Antimicrobial Agents and Chemotherapy, vol.54, issue.8, pp.3414-3426, 2010.
DOI : 10.1128/AAC.00381-10

S. B. Levy and B. Marshall, Antibacterial resistance worldwide: causes, challenges and responses, Nature Medicine, vol.43, issue.12s, pp.122-129, 2004.
DOI : 10.1128/AAC.48.4.1295-1299.2004

K. Lewis and Y. Shan, Why tolerance invites resistance, Science, vol.8, issue.6327, pp.796-796, 2017.
DOI : 10.1038/nature12790

L. Li, N. Mendis, H. Trigui, J. D. Oliver, and S. P. Faucher, The importance of the viable but non-culturable state in human bacterial pathogens, Frontiers in Microbiology, vol.36, issue.70, p.258, 2014.
DOI : 10.1371/journal.pone.0062388

C. Lozupone, J. I. Stombaugh, J. I. Gordon, J. K. Jansson, and R. Knight, Diversity, stability and resilience of the human gut microbiota, Nature, vol.44, issue.7415, pp.220-230
DOI : 10.1097/QCO.0b013e32834a962d

C. Lv, X. Li, F. Li, L. , and T. , Constructing the Energy Landscape for Genetic Switching System Driven by Intrinsic Noise, PLoS ONE, vol.66, issue.2, p.88167, 2014.
DOI : 10.1371/journal.pone.0088167.s003

N. Mabrouk, G. Deffuant, T. Tolker-nielsen, and C. Lobry, Bacteria can form interconnected microcolonies when a self-excreted product reduces their surface motility: evidence from individual-based model simulations, Theory in Biosciences, vol.7, issue.1, pp.1-13, 2010.
DOI : 10.1016/j.mib.2008.09.015

URL : https://hal.archives-ouvertes.fr/hal-00518088

C. N. Marques, V. C. Salisbury, J. Greenman, K. E. Bowker, N. et al., Discrepancy between viable counts and light output as viability measurements, following ciprofloxacin challenge of self-bioluminescent Pseudomonas aeruginosa biofilms, Journal of Antimicrobial Chemotherapy, vol.56, issue.4, pp.665-671, 2005.
DOI : 10.1023/A:1010615508916

S. Martin, The Cost of Restoration as a Way of Defining Resilience: a Viability Approach Applied to a Model of Lake Eutrophication, Ecology and Society, vol.9, issue.2, p.8, 2004.
DOI : 10.5751/ES-00659-090208

S. Martin, G. Deffuant, and J. M. Calabrese, Defining resilience mathematically: From attractors to viability. In, Viability and resilience of complex systems, pp.15-36, 2011.
DOI : 10.1007/978-3-642-20423-4_2

J. L. Martinez, Environmental pollution by antibiotics and by antibiotic resistance determinants, Environmental Pollution, vol.157, issue.11, pp.2893-2902, 2009.
DOI : 10.1016/j.envpol.2009.05.051

A. Martins, A. Hunyadi, and L. Amaral, Mechanisms of Resistance in Bacteria: An Evolutionary Approach, The Open Microbiology Journal, vol.7, issue.1, pp.53-61, 2013.
DOI : 10.2174/1874285801307010053

J. Mathias, J. M. Anderies, and M. A. Janssen, On our rapidly shrinking capacity to comply with the planetary boundaries on climate change, Scientific Reports, vol.60, 2017.
DOI : 10.1016/j.ecolind.2015.08.003

J. Mathias, B. Bonté, T. Cordonnier, and F. De-morogues, Using the Viability Theory to Assess the Flexibility of Forest Managers Under Ecological Intensification, Environmental Management, vol.163, issue.3, pp.1170-1183, 2015.
DOI : 10.1007/s00442-010-1581-9

J. Mathias, S. Lade, and V. Galaz, Multi-level policies and adaptive social networks ??? a conceptual modeling study for maintaining a polycentric governance system, International Journal of the Commons, vol.11, issue.1, 2017.
DOI : 10.18352/ijc.695

URL : https://hal.archives-ouvertes.fr/hal-01771014

A. Mathieu, S. Fleurier, A. Frénoy, J. Dairou, M. Bredeche et al., Discovery and Function of a General Core Hormetic Stress Response in E.??coli Induced by Sublethal Concentrations of Antibiotics, Cell Reports, vol.17, issue.1, pp.46-57, 2016.
DOI : 10.1016/j.celrep.2016.09.001

M. Meola, A. Lazzaro, and J. Zeyer, Diversity, resistance and resilience of the bacterial communities at two alpine glacier forefields after a reciprocal soil transplantation, Environmental Microbiology, vol.61, issue.203, pp.1918-1934, 2014.
DOI : 10.1016/j.soilbio.2013.02.017

J. E. Michiels, B. Van-den-bergh, N. Verstraeten, and J. Michiels, Molecular mechanisms and clinical implications of bacterial persistence, Drug Resistance Updates, vol.29, pp.76-89, 2016.
DOI : 10.1016/j.drup.2016.10.002

S. Mitri, J. B. Xavier, and K. R. Foster, Social evolution in multispecies biofilms, Proceedings of the National Academy of Sciences, vol.43, issue.7, pp.10839-10846, 2011.
DOI : 10.1128/JCM.43.7.3380-3389.2005

URL : http://www.pnas.org/content/108/Supplement_2/10839.full.pdf

N. Möker, C. R. Dean, and J. Tao, Pseudomonas aeruginosa Increases Formation of Multidrug-Tolerant Persister Cells in Response to Quorum-Sensing Signaling Molecules, Journal of Bacteriology, vol.192, issue.7, pp.1946-1955, 2010.
DOI : 10.1128/JB.01231-09

R. D. Monds, O. Toole, and G. , The developmental model of microbial biofilms: ten years of a paradigm up for review, Trends in Microbiology, vol.17, issue.2, pp.73-87, 2009.
DOI : 10.1016/j.tim.2008.11.001

A. L. Mulyukin, A. N. Kozlova, V. V. Sorokin, N. E. Suzina, T. A. Cherdyntseva et al., Surviving forms in antibiotic-treated Pseudomonas aeruginosa, Microbiology, vol.3, issue.23, pp.751-763, 2015.
DOI : 10.1038/emi.2014.3

C. D. Nadell and B. L. Bassler, A fitness trade-off between local competition and dispersal in Vibrio cholerae biofilms, Proceedings of the National Academy of Sciences, vol.24, issue.3, pp.14181-14185, 2011.
DOI : 10.1002/elps.200305584

C. D. Nadell, V. Bucci, K. Drescher, S. Levin, B. L. Bassler et al., Cutting through the complexity of cell collectives, Proceedings of the Royal Society B: Biological Sciences, vol.17, issue.5, p.20122770, 2013.
DOI : 10.1111/j.1420-9101.2004.00747.x

C. D. Nadell, K. R. Foster, X. , and J. B. , Emergence of Spatial Structure in Cell Groups and the Evolution of Cooperation, PLoS Computational Biology, vol.31, issue.3, p.1000716, 2010.
DOI : 10.1371/journal.pcbi.1000716.s006

C. D. Nadell, J. B. Xavier, S. Levin, and K. R. Foster, The Evolution of Quorum Sensing in Bacterial Biofilms, PLoS Biology, vol.32, issue.1, pp.171-0179, 2008.
DOI : 10.1371/journal.pbio.0060014.sv001

D. Nichol, M. Robertson-tessi, P. Jeavons, A. , and A. R. , Stochasticity in the Genotype-Phenotype Map: Implications for the Robustness and Persistence of Bet-Hedging, Genetics, vol.204, issue.4, pp.1523-1539, 2016.
DOI : 10.1534/genetics.116.193474

I. Olsen, Biofilm-specific antibiotic tolerance and resistance, European Journal of Clinical Microbiology & Infectious Diseases, vol.416, issue.6882, pp.877-886, 2015.
DOI : 10.1038/416740a

URL : https://link.springer.com/content/pdf/10.1007%2Fs10096-015-2323-z.pdf

M. Orman and M. P. Brynildsen, ABSTRACT, Antimicrobial Agents and Chemotherapy, vol.57, issue.7, pp.3230-3239, 2013.
DOI : 10.1128/AAC.00243-13

M. Parter, N. Kashtan, and U. And-alon, Environmental variability and modularity of bacterial metabolic networks, BMC Evolutionary Biology, vol.7, issue.1, p.169, 2007.
DOI : 10.1186/1471-2148-7-169

N. Parthuisot, P. Catala, K. Lemarchand, J. Baudart, and P. Lebaron, Evaluation of ChemChrome V6 for bacterial viability assessment in waters, Journal of Applied Microbiology, vol.83, issue.2, pp.370-380, 2000.
DOI : 10.1046/j.1365-2672.1997.00165.x

A. Penesyan, M. Gillings, and I. T. Paulsen, Antibiotic Discovery: Combatting Bacterial Resistance in Cells and in Biofilm Communities, Molecules, vol.56, issue.4, pp.5286-5298, 2015.
DOI : 10.1007/s11908-008-0006-y

C. Picioreanu, J. Kreft, M. C. Van, C. Picioreanu, J. Kreft et al., Particle-Based Multidimensional Multispecies Biofilm Model, Applied and Environmental Microbiology, vol.70, issue.5, pp.3024-3040, 2004.
DOI : 10.1128/AEM.70.5.3024-3040.2004

URL : http://aem.asm.org/content/70/5/3024.full.pdf

C. Picioreanu, M. C. Van-loosdrecht, and J. J. Heijnen, Discrete-differential modelling of biofilm structure, Water Sci. Technol, vol.39, pp.115-122, 1999.

Z. Podlesek, M. Butala, A. ?akanovi?, and D. ?gur-bertok, Antibiotic induced bacterial lysis provides a reservoir of persisters, Antonie van Leeuwenhoek, vol.56, issue.4, pp.523-528, 2016.
DOI : 10.1128/AAC.00921-12

K. Poole, Bacterial stress responses as determinants of antimicrobial resistance, Journal of Antimicrobial Chemotherapy, vol.49, issue.4, pp.2069-2089, 2012.
DOI : 10.1046/j.1365-2958.2003.03653.x

J. L. Radzikowski, S. Vedelaar, D. Siegel, A. D. Ortega, A. Schmidt et al., Bacterial persistence is an active ?S stress response to metabolic flux limitation, Mol. Syst. Biol, vol.12, 2016.
DOI : 10.15252/msb.20166998

URL : http://msb.embopress.org/content/msb/12/9/882.full.pdf

P. B. Rainey, P. B. Rainey, M. Travisano, and M. Travisano, Adaptive radiation in a heterogeneous environment, Nature, vol.394, issue.6688, pp.69-72, 1998.
DOI : 10.1038/27900

M. Richard and G. Yvert, How does evolution tune biological noise ? Front, Genet, vol.5, p.374, 2014.
DOI : 10.3389/fgene.2014.00374

URL : http://journal.frontiersin.org/article/10.3389/fgene.2014.00374/pdf

E. S. Rittershaus, S. Baek, and C. M. Sassetti, The Normalcy of Dormancy: Common Themes in Microbial Quiescence, Cell Host & Microbe, vol.13, issue.6, pp.643-51, 2013.
DOI : 10.1016/j.chom.2013.05.012

L. Robert, M. Hoffmann, N. Krell, S. Aymerich, J. Robert et al., Division in Escherichia coli is triggered by a size-sensing rather than a timing mechanism, BMC Biology, vol.12, issue.1, p.17, 2014.
DOI : 10.1088/0266-5611/25/4/045008

URL : https://hal.archives-ouvertes.fr/hal-00981312

M. E. Roberts and P. S. Stewart, Modelling protection from antimicrobial agents in biofilms through the formation of persister cells, Microbiology, vol.151, issue.1, pp.75-80, 2005.
DOI : 10.1099/mic.0.27385-0

U. Römling and C. Balsalobre, Biofilm infections, their resilience to therapy and innovative treatment strategies, Journal of Internal Medicine, vol.45, issue.6, pp.541-61, 2012.
DOI : 10.1128/mBio.00029-12

S. M. Rosenberg, C. Shee, R. L. Frisch, H. , and P. J. , : A molecular mechanism with implications for evolution and medicine, BioEssays, vol.53, issue.10, pp.885-892, 2012.
DOI : 10.1111/j.1365-2958.2004.04125.x

C. Rougé, J. Mathias, and G. Deffuant, Extending the viability theory framework of resilience to uncertain dynamics, and application to lake eutrophication, Ecological Indicators, vol.29, pp.420-433, 2013.
DOI : 10.1016/j.ecolind.2012.12.032

C. Rougé, J. Mathias, and G. Deffuant, Relevance of control theory to design and maintenance problems in time-variant reliability: The case of stochastic viability, Reliability Engineering & System Safety, vol.132, pp.250-260, 2014.
DOI : 10.1016/j.ress.2014.07.025

C. Rougé, J. Mathias, and G. Deffuant, Vulnerability: From the conceptual to the operational using a dynamical system perspective, Environmental Modelling & Software, vol.73, pp.218-230, 2015.
DOI : 10.1016/j.envsoft.2015.07.018

B. Ryall, G. Eydallin, and T. Ferenci, Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition, Microbiology and Molecular Biology Reviews, vol.76, issue.3, pp.597-625, 2012.
DOI : 10.1128/MMBR.05028-11

M. A. Sánchez-romero and J. Casadesús, Contribution of phenotypic heterogeneity to adaptive antibiotic resistance, Proceedings of the National Academy of Sciences, vol.97, issue.12, pp.355-60, 2014.
DOI : 10.1073/pnas.120163297

S. Sandoval-motta and M. Aldana, Adaptive resistance to antibiotics in bacteria: a systems biology perspective, Wiley Interdisciplinary Reviews: Systems Biology and Medicine, vol.10, issue.Pt 12, pp.253-267, 2016.
DOI : 10.1016/j.mib.2006.12.007

A. Shade and J. Gilbert, Temporal patterns of rarity provide a more complete view of microbial diversity, Trends in Microbiology, vol.23, issue.6, pp.335-340, 2015.
DOI : 10.1016/j.tim.2015.01.007

A. Shade, S. E. Jones, J. G. Caporaso, J. Handelsman, R. Knight et al., Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity, mBio, vol.5, issue.4, pp.1371-1385, 2014.
DOI : 10.1128/mBio.01371-14

A. Shade, H. Peter, S. D. Allison, D. L. Baho, M. Berga et al., Fundamentals of Microbial Community Resistance and Resilience, Frontiers in Microbiology, vol.3, p.417, 2012.
DOI : 10.3389/fmicb.2012.00417

A. Shade, J. S. Read, N. D. Youngblut, N. Fierer, R. Knight et al., Lake microbial communities are resilient after a whole-ecosystem disturbance, The ISME Journal, vol.30, issue.12, pp.2153-2167, 2012.
DOI : 10.2307/3235896

URL : http://www.nature.com/ismej/journal/v6/n12/pdf/ismej201256a.pdf

S. Skoneczny, Cellular automata-based modelling and simulation of biofilm structure on multi-core computers, Water Science and Technology, vol.72, issue.11, pp.2071-2081, 2015.
DOI : 10.2166/wst.2015.426

W. P. Smith, Y. Davit, J. M. Osborne, W. Kim, K. R. Foster et al., Cell morphology drives spatial patterning in microbial communities, Proceedings of the National Academy of Sciences, vol.11, issue.285-296, pp.280-286, 2017.
DOI : 10.1038/ncomms10508

URL : http://www.pnas.org/content/114/3/E280.full.pdf

H. S. Song, R. S. Renslow, J. K. Fredrickson, and S. R. Lindemann, Integrating, 2015.
URL : https://hal.archives-ouvertes.fr/hal-00424169

H. Suhaimi, S. Wang, and D. B. Das, Glucose diffusivity in cell culture medium, Chemical Engineering Journal, vol.269, pp.323-327, 2015.
DOI : 10.1016/j.cej.2015.01.130

S. T. Sultana, D. R. Call, H. Beyenal, H. Flemming, J. Wingender et al., Eradication of Pseudomonas aeruginosa biofilms and persister cells using an electrochemical scaffold and enhanced antibiotic susceptibility, npj Biofilms and Microbiomes, vol.1828, issue.1, 2016.
DOI : 10.1016/j.bbamem.2012.12.010

T. Szekely and K. Burrage, Stochastic simulation in systems biology, Computational and Structural Biotechnology Journal, vol.12, issue.20-21, pp.14-25, 2014.
DOI : 10.1016/j.csbj.2014.10.003

B. Szomolay and N. G. Cogan, Modelling mechanical and chemical treatment of biofilms with two phenotypic resistance mechanisms, Environmental Microbiology, vol.3, issue.6, pp.1870-1883, 2015.
DOI : 10.1038/emi.2014.3

S. Takano, B. J. Pawlowska, I. Gudelj, T. Yomo, and S. Tsuru, ABSTRACT, mBio, vol.8, issue.1, pp.2336-2352, 2017.
DOI : 10.1128/mBio.02336-16

Z. Teng, R. Gao, M. Rehim, W. , and K. , Global behaviors of Monod type chemostat model with nutrient recycling and impulsive input, Journal of Mathematical Chemistry, vol.31, issue.1, pp.276-294, 2009.
DOI : 10.1016/S1468-1218(03)00022-1

L. C. Todman, F. C. Fraser, R. Corstanje, L. K. Deeks, J. A. Harris et al., Defining and quantifying the resilience of responses to disturbance: a conceptual and modelling approach from soil science, Scientific Reports, vol.332, issue.1, pp.1-12, 2016.
DOI : 10.1126/science.1203672

L. S. Tsimring, Noise in biology, Reports on Progress in Physics, vol.77, issue.2, p.26601, 2014.
DOI : 10.1088/0034-4885/77/2/026601

A. D. Vedyaykin, A. V. Sabantsev, I. E. Vishnyakov, N. E. Morozova, and M. A. Khodorkovskii, Recovery of division process in bacterial cells after induction of SulA protein which is responsible for cytokinesis arrest during SOS-response, Cell and Tissue Biology, vol.5, issue.1, pp.89-94, 2017.
DOI : 10.1002/mbo3.336

N. M. Vega and J. Gore, Collective antibiotic resistance: mechanisms and implications, Current Opinion in Microbiology, vol.21, pp.28-34, 2014.
DOI : 10.1016/j.mib.2014.09.003

URL : http://dspace.mit.edu/bitstream/1721.1/108179/1/Collective%20antibiotic%20resistance.pdf

C. Vuotto, F. Longo, M. P. Balice, G. Donelli, and P. E. Varaldo, Antibiotic Resistance Related to Biofilm Formation in Klebsiella pneumoniae, Pathogens, vol.29, issue.3, pp.743-58, 2014.
DOI : 10.1128/AAC.00164-11

Y. Wakamoto, N. Dhar, R. Chait, K. Schneider, F. Signorino-gelo et al., Dynamic Persistence of Antibiotic-Stressed Mycobacteria, Science, vol.81, issue.8, pp.91-96, 2013.
DOI : 10.1021/j100540a008

B. Walker, C. S. Holling, S. R. Carpenter, and A. Kinzig, Resilience, Adaptability and Transformability in Social-ecological Systems, Ecology and Society, vol.9, issue.2, p.5, 2004.
DOI : 10.5751/ES-00650-090205

URL : http://doi.org/10.5751/es-00650-090205

W. Wang, J. Chen, G. Chen, X. Du, P. Cui et al., Transposon Mutagenesis Identifies Novel Genes Associated with Staphylococcus aureus Persister Formation, Frontiers in Microbiology, vol.56, 2015.
DOI : 10.1128/AAC.06288-11

URL : https://doi.org/10.3389/fmicb.2015.01437

X. Wang, Y. Kang, C. Luo, T. Zhao, L. Liu et al., Heteroresistance at the Single-Cell Level: Adapting to Antibiotic Stress through a Population-Based Strategy and Growth-Controlled Interphenotypic Coordination, mBio, vol.5, issue.1, pp.942-955, 2014.
DOI : 10.1128/mBio.00942-13

X. Wang and T. B. Wood, ABSTRACT, Applied and Environmental Microbiology, vol.77, issue.16, pp.5577-5583, 2011.
DOI : 10.1128/AEM.05068-11

URL : https://hal.archives-ouvertes.fr/hal-01351397

T. K. Wood, Combatting bacterial persister cells, Biotechnology and Bioengineering, vol.79, issue.3, pp.476-483, 2016.
DOI : 10.1128/AEM.02636-13

T. K. Wood, Combatting bacterial persister cells, Biotechnology and Bioengineering, vol.79, issue.3, pp.476-483, 2016.
DOI : 10.1128/AEM.02636-13

N. Wu, L. He, P. Cui, W. Wang, Y. Yuan et al., Ranking of persister genes in the same Escherichia coli genetic background demonstrates varying importance of individual persister genes in tolerance to different antibiotics, Frontiers in Microbiology, vol.56, issue.e3, 2015.
DOI : 10.1128/AAC.06288-11

J. B. Xavier, C. Picioreanu, V. Loosdrecht, and M. C. , A framework for multidimensional modelling of activity and structure of multispecies biofilms, Environmental Microbiology, vol.127, issue.8, pp.1085-1103, 2005.
DOI : 10.1007/978-1-4020-2792-5_9

S. Yang, I. D. Hay, D. R. Cameron, M. Speir, B. Cui et al., Antibiotic regimen based on population analysis of residing persister cells eradicates Staphylococcus epidermidis biofilms, Scientific Reports, vol.47, issue.1, p.18578, 2015.
DOI : 10.1093/jac/47.4.399

Q. Zhang, G. Lambert, D. Liao, H. Kim, K. Robin et al., Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments, Science, vol.11, issue.5, pp.1764-1767, 2011.
DOI : 10.1038/nrc3039

Y. Zhang, Persisters, persistent infections and the Yin???Yang model, Emerging Microbes & Infections, vol.3, issue.1, p.3
DOI : 10.1038/nchembio.915

URL : http://www.nature.com/emi/journal/v3/n1/pdf/emi20143a.pdf

J. Zhao, P. Seeluangsawat, W. , and Q. , Modeling antimicrobial tolerance and treatment of heterogeneous biofilms, Mathematical Biosciences, vol.282, pp.1-15, 2016.
DOI : 10.1016/j.mbs.2016.09.005

M. V. Zhurina, A. V. Gannesen, E. L. Zdorovenko, and V. K. Plakunov, Composition and functions of the extracellular polymer matrix of bacterial biofilms, Microbiology, vol.76, issue.4, pp.713-722, 2014.
DOI : 10.1128/MMBR.05028-11

K. Zrelli, O. Galy, P. Latour-lambert, L. Kirwan, J. M. Ghigo et al., Bacterial biofilm mechanical properties persist upon antibiotic treatment and survive cell death, New Journal of Physics, vol.15, issue.12, p.125026, 2013.
DOI : 10.1088/1367-2630/15/12/125026

URL : https://hal.archives-ouvertes.fr/pasteur-01378684

F. Zucca, Persistent and susceptible bacteria with individual deaths, Journal of Theoretical Biology, vol.343, pp.69-78, 2014.
DOI : 10.1016/j.jtbi.2013.11.008

URL : http://arxiv.org/pdf/1210.4074