Human Papillomavirus: Epidemiology and Public Health. Archives of Pathology & Laboratory Medicine, vol.127, pp.930-934, 2003. ,
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
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
Use of mathematical modelling to assess the impact of vaccines on antibiotic resistance. The Lancet Infectious Diseases, 2017. ,
Waves of resistance: Staphylococcus aureus in the antibiotic era, Nat Rev Microbiol, vol.7, issue.9, p.19680247, 2009. ,
Interactions between serotypes of dengue highlight epidemiological impact of cross-immunity, J R Soc Interface, vol.10, issue.86, p.23825116, 2013. ,
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. ,
The fitness costs of antibiotic resistance mutations, Evol Appl, vol.8, issue.3, p.25861385, 2015. ,
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
Epidemiology of Methicillin-Resistant Staphylococcus aureus, Clin Infect Dis, vol.46, p.18462089, 2008. ,
Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes, Science, vol.335, issue.6074, p.22383809, 2012. ,
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
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. ,
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. ,
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=
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
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
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
How the Dynamics and Structure of Sexual Contact Networks Shape Pathogen Phylogenies, PLOS Computational Biology, vol.9, issue.6, p.23818840, 2013. ,
, Modeling Infectious Diseases in Humans and Animals, 2008.
Quantifying the impact of human mobility on malaria, Science, vol.338, issue.6104, pp.267-270, 2012. ,
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. ,
Uncovering the spatial structure of mobility networks, Nature Communications, vol.6, p.25607690, 2015. ,
URL : https://hal.archives-ouvertes.fr/cea-01118965
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. ,
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
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. ,
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. ,
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
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
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
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
, , 2013.
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
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
Dynamical patterns of epidemic outbreaks in complex heterogeneous networks, Journal of Theoretical Biology, vol.235, issue.2, p.15862595, 2005. ,
Dynamics and Control of Diseases in Networks with Community Structure, PLOS Computational Biology, vol.6, issue.4, p.20386735, 2010. ,
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. ,
Birth and death of links control disease spreading in empirical contact networks, Scientific Reports, vol.4, p.24851942, 2014. ,
Competitive epidemic spreading over arbitrary multilayer networks, Physical Review E, vol.89, issue.6, p.62817, 2014. ,
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
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
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
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
Avalanche outbreaks emerging in cooperative contagions, Nature Physics, vol.11, issue.11, pp.936-940, 2015. ,
DOI : 10.1038/nphys3457
Complex dynamics of synergistic coinfections on realistically clustered networks, Proceedings of the National Academy of Sciences, vol.112, issue.33, pp.10551-10556, 2015. ,
Evolution and emergence of infectious diseases in theoretical and real-world networks, Nature Communications, vol.6, p.25592476, 2015. ,
Coexistence and Specialization of Pathogen Strains on Contact Networks, The American Naturalist, vol.168, issue.2, p.16874632, 2006. ,
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. ,
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
The effects of host contact network structure on pathogen diversity and strain structure, PNAS, vol.101, issue.29, p.15247422, 2004. ,
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. ,
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
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
On the Correlations between Certain Diversity Indices, The American Naturalist, vol.107, issue.954, pp.295-302, 1973. ,
Distinct types of eigenvector localization in networks, Scientific Reports, vol.6, p.18847, 2016. ,
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
Modelling the transmission of healthcare associated infections: a systematic review, BMC Infect Dis, vol.13, p.23809195, 2013. ,
The Link Stream of Contacts in a Whole Hospital, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01969491
Hospital-Community Interactions Foster Coexistence between Methicillin-Resistant Strains of Staphylococcus aureus, PLOS Pathogens, vol.9, issue.2, p.23468619, 2013. ,
Understanding the spread of antibiotic resistant pathogens in hospitals: mathematical models as tools for control, vol.33, pp.1739-1746, 2001. ,
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. ,
Competition between methicillin-sensitive and -resistant Staphylococcus aureus in the anterior nares, J Hosp Infect, vol.61, issue.1, p.15893854, 2005. ,
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. ,
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
Transmission of methicillin-resistant Staphylococcus aureus strains between different kinds of pig farms, Veterinary Microbiology, vol.126, issue.4, p.17765409, 2008. ,
How direct competition shapes coexistence and vaccine effects in multi-strain pathogen systems, Journal of Theoretical Biology, vol.388, p.26471070, 2016. ,
No coexistence for free: Neutral null models for multistrain pathogens, Epidemics, vol.1, issue.1, p.21352747, 2009. ,
Limited role of spatial self-structuring in emergent trade-offs during pathogen evolution, 2018. ,
Exposing the diversity of multiple infection patterns, Journal of Theoretical Biology, vol.419, p.28193485, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01567902
Lifetime-preserving reference models for characterizing spreading dynamics on temporal networks, Scientific Reports, vol.8, issue.1, p.709, 2018. ,
Modeling the Spread of Multiple Concurrent Contagions on Networks, PLOS ONE, vol.9, issue.6, p.24922541, 2014. ,
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. ,
, Stochastic Methods: A Handbook for the Natural and Social Sciences, 2009.