title: How direct competition shapes coexistence and vaccine effects in multi-strain pathogen systems.
abstract: We describe an integrated modeling framework for understanding strain coexistence in polymorphic pathogen systems. Previous studies have debated the utility of neutral formulations and focused on cross-immunity between strains as a major stabilizing mechanism. Here we convey that direct competition for colonization mediates stable coexistence only when competitive abilities amongst pathogen clones satisfy certain pairwise asymmetries. We illustrate our ideas with nested SIS models of single and dual colonization, applied to polymorphic pneumococcal bacteria. By fitting the models to cross-sectional prevalence data from Portugal (before and after the introduction of a seven-valent pneumococcal conjugate vaccine), we are able to not only statistically compare neutral and non-neutral epidemiological formulations, but also estimate vaccine efficacy, transmission and competition parameters simultaneously. Our study highlights that the response of polymorphic pathogen populations to interventions holds crucial information about strain interactions, which can be extracted by suitable nested modeling.
authors.affiliation: Instituto Gulbenkian de Ciência, Apartado 14, 2781-901 Oeiras, Portugal. Electronic address: egjini@igc.gulbenkian.pt.
authors.forename: Erida
authors.initials: E
authors.lastname: Gjini
authors.affiliation: Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
authors.forename: Carina
authors.initials: C
authors.lastname: Valente
authors.affiliation: Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
authors.forename: Raquel
authors.initials: R
authors.lastname: Sá-Leão
authors.affiliation: CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade de Porto, Portugal; Instituto de Matemática e Estatística, Universidade de São Paulo, Brazil; Liverpool School of Tropical Medicine, Liverpool, United Kingdom.
authors.forename: M Gabriela M
authors.initials: MG
authors.lastname: Gomes
mesh_terms: D000465:Algorithms; D002648:Child; D015169:Colony Count, Microbial; D000069443:Heptavalent Pneumococcal Conjugate Vaccine / Q000276:immunology / Q000627:therapeutic use; D054884:Host-Pathogen Interactions / Q000187:drug effects / Q000276:immunology; D006801:Humans; D008954:Models, Biological; D011008:Pneumococcal Infections / Q000276:immunology* / Q000382:microbiology / Q000517:prevention & control; D022242:Pneumococcal Vaccines / Q000276:immunology* / Q000627:therapeutic use; D012703:Serotyping; D013045:Species Specificity; D013296:Streptococcus pneumoniae / Q000145:classification / Q000276:immunology* / Q000502:physiology; D016896:Treatment Outcome; D014611:Vaccination / Q000379:methods
chemical_list: D000069443:Heptavalent Pneumococcal Conjugate Vaccine; D022242:Pneumococcal Vaccines
keywords: Bayesian inference; Co-infection; Ecology; Neutral model; PCV7; Pneumococcus