How direct competition shapes coexistence and vaccine effects in multi-strain pathogen systems.

[1]  M. Lipsitch,et al.  Carriage burden, multiple colonization and antibiotic pressure promote emergence of resistant vaccine escape pneumococci , 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.

[2]  Carmen Lía Murall,et al.  Revising ecological assumptions about Human papillomavirus interactions and type replacement. , 2014, Journal of theoretical biology.

[3]  Samuel Alizon,et al.  Co-infection and super-infection models in evolutionary epidemiology , 2013, Interface Focus.

[4]  V. Isham,et al.  A mathematical model of serotype replacement in pneumococcal carriage following vaccination , 2013, Journal of The Royal Society Interface.

[5]  Gunnar Rätsch,et al.  Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota , 2013, PLoS Comput. Biol..

[6]  W. Edmunds,et al.  The impact of specific and non-specific immunity on the ecology of Streptococcus pneumoniae and the implications for vaccination , 2013, Proceedings of the Royal Society B: Biological Sciences.

[7]  D. Cummings,et al.  Breaking the symmetry: immune enhancement increases persistence of dengue viruses in the presence of asymmetric transmission rates. , 2013, Journal of theoretical biology.

[8]  Mats Gyllenberg,et al.  Estimating the Transmission Dynamics of Streptococcus pneumoniae from Strain Prevalence Data , 2013, Biometrics.

[9]  K. O'Brien,et al.  Competition Between Streptococcus Pneumoniae Strains: Implications for Vaccine-Induced Replacement in Colonization and Disease , 2013, Epidemiology.

[10]  I. Hung,et al.  Regional epidemiology of invasive pneumococcal disease in Asian adults: epidemiology, disease burden, serotype distribution, and antimicrobial resistance patterns and prevention. , 2013, International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases.

[11]  M. Lipsitch,et al.  Population genomics of post-vaccine changes in pneumococcal epidemiology , 2013, Nature Genetics.

[12]  K. Auranen,et al.  Comparative analysis of Streptococcus pneumoniae transmission in Portuguese and Finnish day-care centres , 2013, BMC Infectious Diseases.

[13]  K. Auranen,et al.  Pneumococcal Transmission and Disease In Silico: A Microsimulation Model of the Indirect Effects of Vaccination , 2013, PloS one.

[14]  M. Halloran,et al.  Estimating Strain‐Specific and Overall Efficacy of Polyvalent Vaccines Against Recurrent Pathogens From a Cross‐Sectional Study , 2013, Biometrics.

[15]  B. Grenfell,et al.  Hospital-Community Interactions Foster Coexistence between Methicillin-Resistant Strains of Staphylococcus aureus , 2013, PLoS pathogens.

[16]  E. Sanders,et al.  Viral and Bacterial Interactions in the Upper Respiratory Tract , 2013, PLoS pathogens.

[17]  K. Edwards,et al.  Density Interactions Among Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus in the Nasopharynx of Young Peruvian Children , 2013, The Pediatric infectious disease journal.

[18]  R. Heyderman,et al.  Regulation of Naturally Acquired Mucosal Immunity to Streptococcus pneumoniae in Healthy Malawian Adults and Children , 2012, PloS one.

[19]  A. D'Amour,et al.  Estimating Rates of Carriage Acquisition and Clearance and Competitive Ability for Pneumococcal Serotypes in Kenya With a Markov Transition Model , 2012, Epidemiology.

[20]  S Ballesteros,et al.  Dynamic noise, chaos and parameter estimation in population biology , 2012, Interface Focus.

[21]  S. Hubbell,et al.  The case for ecological neutral theory. , 2012, Trends in Ecology & Evolution.

[22]  J. Marimón,et al.  Dynamics of pneumococcal nasopharyngeal carriage in healthy children attending a day care center in northern Spain. influence of detection techniques on the results , 2012, BMC Infectious Diseases.

[23]  M. Lipsitch,et al.  Niche and Neutral Effects of Acquired Immunity Permit Coexistence of Pneumococcal Serotypes , 2012, Science.

[24]  Aras Kadioglu,et al.  Capsule Type of Streptococcus pneumoniae Determines Growth Phenotype , 2012, PLoS pathogens.

[25]  J. Hinds,et al.  Decrease in Pneumococcal Co-Colonization following Vaccination with the Seven-Valent Pneumococcal Conjugate Vaccine , 2012, PloS one.

[26]  M. Lipsitch,et al.  Serotype replacement in disease after pneumococcal vaccination , 2011, The Lancet.

[27]  T. Day,et al.  BRIDGING SCALES IN THE EVOLUTION OF INFECTIOUS DISEASE LIFE HISTORIES: THEORY , 2011, Evolution; international journal of organic evolution.

[28]  T. Day,et al.  BRIDGING SCALES IN THE EVOLUTION OF INFECTIOUS DISEASE LIFE HISTORIES: APPLICATION , 2011, Evolution; international journal of organic evolution.

[29]  Pejman Rohani,et al.  Statistical Inference for Multi-Pathogen Systems , 2011, PLoS Comput. Biol..

[30]  H. de Lencastre,et al.  Clonal Evolution Leading to Maintenance of Antibiotic Resistance Rates among Colonizing Pneumococci in the PCV7 Era in Portugal , 2011, Journal of Clinical Microbiology.

[31]  Susan M. Huse,et al.  Variability and Diversity of Nasopharyngeal Microbiota in Children: A Metagenomic Analysis , 2011, PloS one.

[32]  M. Ramirez,et al.  Prophage Spontaneous Activation Promotes DNA Release Enhancing Biofilm Formation in Streptococcus pneumoniae , 2010, PloS one.

[33]  S. Wood Statistical inference for noisy nonlinear ecological dynamic systems , 2010, Nature.

[34]  Ryan A Chisholm,et al.  Niche and neutral models predict asymptotically equivalent species abundance distributions in high-diversity ecological communities , 2010, Proceedings of the National Academy of Sciences.

[35]  Jason Hinds,et al.  Multiple Colonization with S. pneumoniae before and after Introduction of the Seven-Valent Conjugated Pneumococcal Polysaccharide Vaccine , 2010, PloS one.

[36]  M. P. van der Linden,et al.  Regional differences in serotype distribution, pneumococcal vaccine coverage, and antimicrobial resistance of invasive pneumococcal disease among German federal states. , 2010, International journal of medical microbiology : IJMM.

[37]  B. Levin,et al.  The ecology of nasal colonization of Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus: the role of competition and interactions with host's immune response , 2010, BMC Microbiology.

[38]  Marc Lipsitch,et al.  What is the mechanism for persistent coexistence of drug-susceptible and drug-resistant strains of Streptococcus pneumoniae? , 2009, Journal of The Royal Society Interface.

[39]  Kari Auranen,et al.  Bmc Infectious Diseases Outbreaks of Streptococcus Pneumoniae Carriage in Day Care Cohorts in Finland – Implications for Elimination of Transmission , 2022 .

[40]  K. Auranen,et al.  Estimation of vaccine efficacy against acquisition of pneumococcal carriage. , 2009, Vaccine.

[41]  J. Galagan,et al.  Pneumococcal Capsular Polysaccharide Structure Predicts Serotype Prevalence , 2009, PLoS pathogens.

[42]  D. Bogaert,et al.  Multiplex PCR reveals a high rate of nasopharyngeal pneumococcal 7-valent conjugate vaccine serotypes co-colonizing indigenous Warao children in Venezuela. , 2009, Journal of medical microbiology.

[43]  K. Mühlemann,et al.  Detection of Streptococcus pneumoniae Strain Cocolonization in the Nasopharynx , 2009, Journal of Clinical Microbiology.

[44]  M. Moore Rethinking replacement and resistance. , 2009, The Journal of infectious diseases.

[45]  Marc Lipsitch,et al.  No coexistence for free: neutral null models for multistrain pathogens. , 2009, Epidemics.

[46]  Benjamin M. Bolker,et al.  Ecological Models and Data in R , 2008 .

[47]  Sylvain Gandon,et al.  Evidences of parasite evolution after vaccination. , 2008, Vaccine.

[48]  M. Lipsitch,et al.  Epidemiologic evidence for serotype-specific acquired immunity to pneumococcal carriage. , 2008, The Journal of infectious diseases.

[49]  Jeffrey N. Weiser,et al.  The role of Streptococcus pneumoniae virulence factors in host respiratory colonization and disease , 2008, Nature Reviews Microbiology.

[50]  C. Whitney,et al.  Emergence of nonvaccine serotypes following introduction of pneumococcal conjugate vaccine: cause and effect? , 2008, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[51]  João André Carriço,et al.  High Rates of Transmission of and Colonization by Streptococcus pneumoniae and Haemophilus influenzae within a Day Care Center Revealed in a Longitudinal Study , 2007, Journal of Clinical Microbiology.

[52]  Marc Lipsitch,et al.  Patterns of antigenic diversity and the mechanisms that maintain them , 2007, Journal of The Royal Society Interface.

[53]  M. Moorhouse,et al.  Nasopharyngeal co-colonization with Staphylococcus aureus and Streptococcus pneumoniae in children is bacterial genotype independent. , 2007, Microbiology.

[54]  Heikki Haario,et al.  DRAM: Efficient adaptive MCMC , 2006, Stat. Comput..

[55]  A. Nelson,et al.  Capsule Enhances Pneumococcal Colonization by Limiting Mucus-Mediated Clearance , 2006, Infection and Immunity.

[56]  J. Weiser,et al.  The blp Bacteriocins of Streptococcus pneumoniae Mediate Intraspecies Competition both In Vitro and In Vivo , 2006, Infection and Immunity.

[57]  Stephen P Hubbell,et al.  Neutral theory and the evolution of ecological equivalence. , 2006, Ecology.

[58]  Julian Parkhill,et al.  Genetic Analysis of the Capsular Biosynthetic Locus from All 90 Pneumococcal Serotypes , 2006, PLoS genetics.

[59]  João André Carriço,et al.  Natural history of drug-resistant clones of Streptococcus pneumoniae colonizing healthy children in Portugal. , 2005, Microbial drug resistance.

[60]  M. Begon,et al.  Ecology: From Individuals to Ecosystems , 2005 .

[61]  Sébastien Guiral,et al.  Competence-programmed predation of noncompetent cells in the human pathogen Streptococcus pneumoniae: genetic requirements. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[62]  Christophe Fraser,et al.  Neutral microepidemic evolution of bacterial pathogens. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[63]  Lucia H. Lee,et al.  Mucosal Immunity Induced by Pneumococcal Glycoconjugate , 2005, Critical reviews in microbiology.

[64]  K. Auranen,et al.  The influence of competition and vaccination on the coexistence of two pneumococcal serotypes , 2004, Epidemiology and Infection.

[65]  David Tilman,et al.  Niche tradeoffs, neutrality, and community structure: a stochastic theory of resource competition, invasion, and community assembly. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[66]  Jérôme Chave,et al.  Neutral theory and community ecology , 2004 .

[67]  Bradley P. Carlin,et al.  Bayesian measures of model complexity and fit , 2002 .

[68]  M. Golubitsky,et al.  The Symmetry Perspective: From Equilibrium to Chaos in Phase Space and Physical Space , 2002 .

[69]  T. Jukes,et al.  The neutral theory of molecular evolution. , 2000, Genetics.

[70]  A. R. Gallant,et al.  Noise and Nonlinearity in Measles Epidemics: Combining Mechanistic and Statistical Approaches to Population Modeling , 1998, The American Naturalist.

[71]  M. Lipsitch,et al.  Vaccination against colonizing bacteria with multiple serotypes. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[72]  Maurice W. Sabelis,et al.  The Dynamics of Multiple Infection and the Evolution of Virulence , 1995, The American Naturalist.

[73]  T. Fagerström,et al.  Competition and coexistence in plant communities. , 1994, Trends in ecology & evolution.

[74]  R. Anderson,et al.  Theoretical studies of the effects of heterogeneity in the parasite population on the transmission dynamics of malaria , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[75]  Martin A. Nowak,et al.  Superinfection and the evolution of parasite virulence , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[76]  S. Levin The problem of pattern and scale in ecology , 1992 .

[77]  H J Bremermann,et al.  A competitive exclusion principle for pathogen virulence , 1989, Journal of mathematical biology.

[78]  D. Tilman The Importance of the Mechanisms of Interspecific Competition , 1987, The American Naturalist.

[79]  R M May,et al.  Epidemiology and genetics in the coevolution of parasites and hosts , 1983, Proceedings of the Royal Society of London. Series B. Biological Sciences.

[80]  S. Levin,et al.  Selection of Intermediate Rates of Increase in Parasite-Host Systems , 1981, The American Naturalist.

[81]  K Dietz,et al.  Epidemiologic interference of virus populations , 1979, Journal of mathematical biology.

[82]  I. Eshel On the founder effect and the evolution of altruistic traits: an ecogenetical approach. , 1977, Theoretical population biology.

[83]  I. Eshel,et al.  On the founder effect and the evolution of altruistic traits. , 1976, Theoretical population biology.

[84]  Darlington Pj Competition, competitive repulsion, and coexistence. , 1972 .

[85]  G. Hooft Breaking the Symmetry , 2005 .

[86]  A. Hastings Transients: the key to long-term ecological understanding? , 2004, Trends in ecology & evolution.

[87]  G. F. Gause The struggle for existence , 1971 .

[88]  A. Tanskanen,et al.  American Journal of Epidemiology Practice of Epidemiology Between-strain Competition in Acquisition and Clearance of Pneumococcal Carriage—epidemiologic Evidence from a Longitudinal Study of Day-care Children , 2022 .