M. Schiffman and P. E. Castle, Human Papillomavirus: Epidemiology and Public Health. Archives of Pathology & Laboratory Medicine, vol.127, pp.930-934, 2003.

D. M. Weinberger, R. Malley, and M. Lipsitch, Serotype replacement in disease after pneumococcal vaccination, The Lancet, vol.378, issue.9807, pp.62225-62233, 2011.
DOI : 10.1016/s0140-6736(10)62225-8

URL : http://europepmc.org/articles/pmc3256741?pdf=render

D. Bogaert, R. De-groot, and P. Hermans, Streptococcus pneumoniae colonisation: the key to pneumococcal disease. The Lancet Infectious Diseases, vol.4, pp.144-154, 2004.
DOI : 10.1016/s1473-3099(04)00938-7

K. E. Atkins, E. I. Lafferty, S. R. Deeny, N. G. Davies, J. V. Robotham et al., Use of mathematical modelling to assess the impact of vaccines on antibiotic resistance. The Lancet Infectious Diseases, 2017.

H. F. Chambers and F. R. Deleo, Waves of resistance: Staphylococcus aureus in the antibiotic era, Nat Rev Microbiol, vol.7, issue.9, p.19680247, 2009.

N. G. Reich, S. Shrestha, A. A. King, P. Rohani, J. Lessler et al., Interactions between serotypes of dengue highlight epidemiological impact of cross-immunity, J R Soc Interface, vol.10, issue.86, p.23825116, 2013.

T. Cohen, C. Colijn, and M. Murray, Modeling the effects of strain diversity and mechanisms of strain competition on the potential performance of new tuberculosis vaccines, Proc Natl Acad Sci U S A, vol.105, issue.42, p.18849476, 2008.

A. H. Melnyk, A. Wong, and R. Kassen, The fitness costs of antibiotic resistance mutations, Evol Appl, vol.8, issue.3, p.25861385, 2015.

L. Opatowski, E. Varon, C. Dupont, L. Temime, S. Van-der-werf et al., Assessing pneumococcal meningitis association with viral respiratory infections and antibiotics: insights from statistical and mathematical models, Proceedings Biological Sciences, vol.280, p.23782877, 1764.
DOI : 10.1098/rspb.2013.0519

URL : http://rspb.royalsocietypublishing.org/content/280/1764/20130519.full.pdf

H. W. Boucher and G. R. Corey, Epidemiology of Methicillin-Resistant Staphylococcus aureus, Clin Infect Dis, vol.46, p.18462089, 2008.

S. Cobey and M. Lipsitch, Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes, Science, vol.335, issue.6074, p.22383809, 2012.

C. L. Murall, C. T. Bauch, and T. Day, Could the human papillomavirus vaccines drive virulence evolution?, Proc R Soc B, vol.282, p.25429011, 1798.
DOI : 10.1098/rspb.2014.1069

URL : http://rspb.royalsocietypublishing.org/content/282/1798/20141069.full.pdf

D. M. Aanensen, E. J. Feil, M. Holden, J. Dordel, C. A. Yeats et al., Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in, Europe. mBio, vol.7, issue.3, p.27150362, 2016.

P. Lemey, A. Rambaut, T. Bedford, N. Faria, F. Bielejec et al., Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2, PLoS Pathog, vol.10, issue.2, p.24586153, 2014.

T. Donker, S. Reuter, J. Scriberras, R. Reynolds, N. M. Brown et al., Population genetic structuring of methicillin-resistant Staphylococcus aureus clone EMRSA-15 within UK reflects patient referral patterns, Microbial Genomics, vol.3, issue.7, p.29026654, 2017.
DOI : 10.1099/mgen.0.000113

URL : https://mgen.microbiologyresearch.org/deliver/fulltext/mgen/3/7/mgen000113.pdf?itemId=/content/journal/mgen/10.1099/mgen.0.000113&mimeType=pdf&isFastTrackArticle=

T. Obadia, R. Silhol, L. Opatowski, L. Temime, J. Legrand et al., Detailed Contact Data and the Dissemination of Staphylococcus aureus in Hospitals, PLOS Computational Biology, vol.11, issue.3, p.25789632, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01134050

N. Nekkab, P. Astagneau, L. Temime, and P. Crépey, Spread of hospital-acquired infections: A comparison of healthcare networks, PLOS Computational Biology, vol.13, issue.8, p.28837555, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01578692

C. Fraser, W. P. Hanage, and B. G. Spratt, Neutral microepidemic evolution of bacterial pathogens, Proceedings of the National Academy of Sciences of the United States of America, vol.102, issue.6, p.15684071, 2005.
DOI : 10.1073/pnas.0406993102

URL : http://www.pnas.org/content/102/6/1968.full.pdf

K. Robinson, N. Fyson, T. Cohen, C. Fraser, and C. Colijn, How the Dynamics and Structure of Sexual Contact Networks Shape Pathogen Phylogenies, PLOS Computational Biology, vol.9, issue.6, p.23818840, 2013.

J. Matt and P. R. Keeling, Modeling Infectious Diseases in Humans and Animals, 2008.

A. Wesolowski, N. Eagle, A. J. Tatem, D. L. Smith, A. M. Noor et al., Quantifying the impact of human mobility on malaria, Science, vol.338, issue.6104, pp.267-270, 2012.

D. Balcan, V. Colizza, B. Gonçalves, H. Hu, J. J. Ramasco et al., Multiscale mobility networks and the spatial spreading of infectious diseases, Proceedings of the National Academy of Sciences of the United States of America, vol.106, issue.51, pp.21484-21489, 2009.

T. Louail, M. Lenormand, M. Picornell, O. G. Cantú, R. Herranz et al., Uncovering the spatial structure of mobility networks, Nature Communications, vol.6, p.25607690, 2015.
URL : https://hal.archives-ouvertes.fr/cea-01118965

L. Rocha, F. Liljeros, and P. Holme, Information dynamics shape the sexual networks of Internet-mediated prostitution, Proceedings of the National Academy of Sciences, vol.107, issue.13, pp.5706-5711, 2010.

R. Mastrandrea, J. Fournet, and A. Barrat, Contact Patterns in a High School: A Comparison between Data Collected Using Wearable Sensors, Contact Diaries and Friendship Surveys, PLOS ONE, vol.10, issue.9, p.26325289, 2015.
DOI : 10.1371/journal.pone.0136497

URL : https://hal.archives-ouvertes.fr/hal-01238308

M. Salathé, M. Kazandjieva, J. W. Lee, P. Levis, M. W. Feldman et al., A high-resolution human contact network for infectious disease transmission, Proceedings of the National Academy of Sciences, vol.107, issue.51, pp.22020-22025, 2010.

M. Génois, C. L. Vestergaard, J. Fournet, A. Panisson, I. Bonmarin et al., Data on face-to-face contacts in an office building suggest a low-cost vaccination strategy based on community linkers, Network Science, vol.3, issue.3, pp.326-347, 2015.

A. Duval, T. Obadia, L. Martinet, P. Y. Boë-lle, E. Fleury et al., Measuring dynamic social contacts in a rehabilitation hospital: effect of wards, patient and staff characteristics, Scientific Reports, vol.8, issue.1, p.29374222, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01696186

P. Vanhems, A. Barrat, C. Cattuto, J. F. Pinton, N. Khanafer et al., Estimating Potential Infection Transmission Routes in Hospital Wards Using Wearable Proximity Sensors, PLOS ONE, vol.8, issue.9, p.24040129, 2013.
DOI : 10.1371/journal.pone.0073970

URL : https://hal.archives-ouvertes.fr/hal-00862591

N. Voirin, C. Payet, A. Barrat, C. Cattuto, N. Khanafer et al., Combining High-Resolution Contact Data with Virological Data to Investigate Influenza Transmission in a Tertiary Care Hospital, Infection Control & Hospital Epidemiology, vol.36, issue.3, pp.254-260, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01123961

R. Assab, N. Nekkab, P. Cré-pey, P. Astagneau, D. Guillemot et al., Mathematical models of infection transmission in healthcare settings: recent advances from the use of network structured data. Current Opinion in Infectious Diseases, vol.30, p.28570284, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01548909

P. Holme and . Saramä, , 2013.

R. Pastor-satorras, C. Castellano, P. Van-mieghem, and A. Vespignani, Epidemic processes in complex networks, Reviews of Modern Physics, vol.87, issue.3, pp.925-979, 2015.
DOI : 10.1103/revmodphys.87.925

URL : https://link.aps.org/accepted/10.1103/RevModPhys.87.925

N. Perra, B. Gonçalves, R. Pastor-satorras, and A. Vespignani, Activity driven modeling of time varying networks, Scientific Reports, vol.2, p.22741058, 2012.
DOI : 10.1038/srep00469

URL : https://www.nature.com/articles/srep00469.pdf

M. Barthé-lemy, A. Barrat, R. Pastor-satorras, and A. Vespignani, Dynamical patterns of epidemic outbreaks in complex heterogeneous networks, Journal of Theoretical Biology, vol.235, issue.2, p.15862595, 2005.

M. Salathé and J. H. Jones, Dynamics and Control of Diseases in Networks with Community Structure, PLOS Computational Biology, vol.6, issue.4, p.20386735, 2010.

P. Sah, S. T. Leu, P. C. Cross, P. J. Hudson, and S. Bansal, Unraveling the disease consequences and mechanisms of modular structure in animal social networks, Proceedings of the National Academy of Sciences, vol.114, issue.16, pp.4165-4170, 2017.

P. Holme and F. Liljeros, Birth and death of links control disease spreading in empirical contact networks, Scientific Reports, vol.4, p.24851942, 2014.

D. Sahneh, F. Scoglio, and C. , Competitive epidemic spreading over arbitrary multilayer networks, Physical Review E, vol.89, issue.6, p.62817, 2014.

C. Poletto, S. Meloni, A. Van-metre, V. Colizza, Y. Moreno et al., Characterising two-pathogen competition in spatially structured environments, Scientific Reports, vol.5, p.25600088, 2015.
DOI : 10.1038/srep07895

URL : https://hal.archives-ouvertes.fr/hal-01116381

C. Poletto, S. Meloni, V. Colizza, Y. Moreno, and A. Vespignani, Host Mobility Drives Pathogen Competition in Spatially Structured Populations, PLOS Computational Biology, vol.9, issue.8, p.23966843, 2013.
DOI : 10.1371/journal.pcbi.1003169

URL : https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003169&type=printable

J. Sanz, C. Y. Xia, S. Meloni, and Y. Moreno, Dynamics of Interacting Diseases, Phys Rev X, vol.4, issue.4, p.41005, 2014.
DOI : 10.1103/physrevx.4.041005

URL : https://doi.org/10.1103/physrevx.4.041005

B. Karrer and M. Newman, Competing epidemics on complex networks, Phys Rev E, vol.84, issue.3, p.36106, 2011.
DOI : 10.1103/physreve.84.036106

URL : https://link.aps.org/accepted/10.1103/PhysRevE.84.036106

W. Cai, L. Chen, F. Ghanbarnejad, and P. Grassberger, Avalanche outbreaks emerging in cooperative contagions, Nature Physics, vol.11, issue.11, pp.936-940, 2015.
DOI : 10.1038/nphys3457

L. Hébert-dufresne and B. M. Althouse, Complex dynamics of synergistic coinfections on realistically clustered networks, Proceedings of the National Academy of Sciences, vol.112, issue.33, pp.10551-10556, 2015.

G. E. Leventhal, A. L. Hill, M. A. Nowak, and S. Bonhoeffer, Evolution and emergence of infectious diseases in theoretical and real-world networks, Nature Communications, vol.6, p.25592476, 2015.

K. Eames and M. J. Keeling, Coexistence and Specialization of Pathogen Strains on Contact Networks, The American Naturalist, vol.168, issue.2, p.16874632, 2006.

B. Wmv and M. C. Boerlijst, Emergent trade-offs and selection for outbreak frequency in spatial epidemics, Proceedings of the National Academy of Sciences, vol.101, issue.52, pp.18246-18250, 2004.

S. Lion and S. Gandon, Spatial evolutionary epidemiology of spreading epidemics, Proceedings Biological Sciences, vol.283, p.27798295, 1841.
DOI : 10.1098/rspb.2016.1170

URL : https://hal.archives-ouvertes.fr/hal-02122259

C. O. Buckee, K. Koelle, M. J. Mustard, and S. Gupta, The effects of host contact network structure on pathogen diversity and strain structure, PNAS, vol.101, issue.29, p.15247422, 2004.

C. Buckee, L. Danon, and S. Gupta, Host community structure and the maintenance of pathogen diversity, Proceedings of the Royal Society of London B: Biological Sciences, vol.274, pp.1715-1721, 1619.

E. K. Morris, T. Caruso, F. Buscot, M. Fischer, C. Hancock et al., Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories, Ecol Evol, vol.4, issue.18, p.25478144, 2014.
DOI : 10.1002/ece3.1155

URL : https://doi.org/10.1002/ece3.1155

S. Azaele, S. Suweis, J. Grilli, I. Volkov, J. R. Banavar et al., Statistical mechanics of ecological systems: Neutral theory and beyond, Rev Mod Phys, vol.88, issue.3, p.35003, 2016.
DOI : 10.1103/revmodphys.88.035003

URL : http://eprints.whiterose.ac.uk/94121/1/RU10023_Azaele_et_al_2015_lastversion.pdf

P. A. Debenedictis, On the Correlations between Certain Diversity Indices, The American Naturalist, vol.107, issue.954, pp.295-302, 1973.

R. Pastor-satorras and C. Castellano, Distinct types of eigenvector localization in networks, Scientific Reports, vol.6, p.18847, 2016.

S. Suweis, E. Bertuzzo, L. Mari, I. Rodriguez-iturbe, A. Maritan et al., On species persistence-time distributions, Journal of Theoretical Biology, vol.303, p.22763130, 2012.
DOI : 10.1016/j.jtbi.2012.02.022

URL : http://arxiv.org/pdf/1203.4482

E. Van-kleef, J. V. Robotham, M. Jit, S. R. Deeny, and W. J. Edmunds, Modelling the transmission of healthcare associated infections: a systematic review, BMC Infect Dis, vol.13, p.23809195, 2013.

L. Martinet, C. Crespelle, E. Fleury, P. Y. Boëlle, and D. Guillemot, The Link Stream of Contacts in a Whole Hospital, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01969491

R. Kouyos, E. Klein, and B. Grenfell, Hospital-Community Interactions Foster Coexistence between Methicillin-Resistant Strains of Staphylococcus aureus, PLOS Pathogens, vol.9, issue.2, p.23468619, 2013.

M. J. Bonten, D. J. Austin, and M. Lipsitch, Understanding the spread of antibiotic resistant pathogens in hospitals: mathematical models as tools for control, vol.33, pp.1739-1746, 2001.

E. Margolis, A. Yates, and B. R. Levin, The ecology of nasal colonization of Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus: the role of competition and interactions with host's immune response, BMC Microbiol, vol.10, p.20178591, 2010.

M. Dall'antonia, P. G. Coen, M. Wilks, A. Whiley, and M. Millar, Competition between methicillin-sensitive and -resistant Staphylococcus aureus in the anterior nares, J Hosp Infect, vol.61, issue.1, p.15893854, 2005.

Q. Chang, M. Lipsitch, and W. P. Hanage, Impact of Host Heterogeneity on the Efficacy of Interventions to Reduce Staphylococcus aureus Carriage, Infect Control Hosp Epidemiol, vol.37, issue.2, p.26598029, 2016.

S. Cobey, E. B. Baskerville, C. Colijn, W. Hanage, C. Fraser et al., Host population structure and treatment frequency maintain balancing selection on drug resistance, Journal of The Royal Society Interface, vol.14, issue.133, 2017.
DOI : 10.1098/rsif.2017.0295

URL : https://royalsocietypublishing.org/doi/pdf/10.1098/rsif.2017.0295

E. Van-duijkeren, R. Ikawaty, M. J. Broekhuizen-stins, M. D. Jansen, E. C. Spalburg et al., Transmission of methicillin-resistant Staphylococcus aureus strains between different kinds of pig farms, Veterinary Microbiology, vol.126, issue.4, p.17765409, 2008.

E. Gjini, C. Valente, R. Sá--leão, and M. Gomes, How direct competition shapes coexistence and vaccine effects in multi-strain pathogen systems, Journal of Theoretical Biology, vol.388, p.26471070, 2016.

M. Lipsitch, C. Colijn, T. Cohen, W. P. Hanage, and C. Fraser, No coexistence for free: Neutral null models for multistrain pathogens, Epidemics, vol.1, issue.1, p.21352747, 2009.

V. Buendía, M. A. Muñoz, and S. Manrubia, Limited role of spatial self-structuring in emergent trade-offs during pathogen evolution, 2018.

M. T. Sofonea, S. Alizon, and Y. Michalakis, Exposing the diversity of multiple infection patterns, Journal of Theoretical Biology, vol.419, p.28193485, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01567902

M. Li, V. D. Rao, T. Gernat, and H. Dankowicz, Lifetime-preserving reference models for characterizing spreading dynamics on temporal networks, Scientific Reports, vol.8, issue.1, p.709, 2018.

A. Stanoev, D. Trpevski, and L. Kocarev, Modeling the Spread of Multiple Concurrent Contagions on Networks, PLOS ONE, vol.9, issue.6, p.24922541, 2014.

T. Lauderdale, J. T. Wang, W. S. Lee, J. H. Huang, L. C. Mcdonald et al., Carriage rates of methicillin-resistant Staphylococcus aureus (MRSA) depend on anatomic location, the number of sites cultured, culture methods, and the distribution of clonotypes, Eur J Clin Microbiol Infect Dis, vol.29, issue.12, p.20820833, 2010.

C. Gardiner, Stochastic Methods: A Handbook for the Natural and Social Sciences, 2009.