Host contact dynamics shapes richness and dominance of pathogen strains

Francesco Pinotti 1 Éric Fleury 2 Didier Guillemot 3 Pierre-Yves Böelle 1 Chiara Poletto 1, *
* Corresponding author
1 iPLESP - Institut Pierre Louis d'Epidémiologie et de Santé Publique
2 DANTE - Dynamic Networks : Temporal and Structural Capture Approach
Inria Grenoble - Rhône-Alpes, LIP - Laboratoire de l'Informatique du Parallélisme, IXXI - Institut Rhône-Alpin des systèmes complexes
3 B2PHI - Biostatistique, Biomathématique, Pharmacoépidémiologie et Maladies Infectieuses
Abstract : The interaction among multiple microbial strains affects the spread of infectious diseases and the efficacy of interventions. Genomic tools have made it increasingly easy to observe pathogenic strains diversity, but the best interpretation of such diversity has remained difficult because of relationships with host and environmental factors. Here, we focus on host-to-host contact behavior and study how it changes populations of pathogens in a minimal model of multi-strain interaction. We simulated a population of identical strains competing by mutual exclusion and spreading on a dynamical network of hosts according to a stochastic susceptible-infectious-susceptible model. We computed ecological indicators of diversity and dominance in strain populations for a collection of networks illustrating various properties found in real-world examples. Heterogeneities in the number of contacts among hosts were found to reduce diversity and increase dominance by making the repartition of strains among infected hosts more uneven, while strong community structure among hosts increased strain diversity. We found that the introduction of strains associated with hosts entering and leaving the system led to the highest pathogenic richness at intermediate turnover levels. These results were finally illustrated using the spread of Staphylococcus aureus in a long-term health-care facility where close proximity interactions and strain carriage were collected simultaneously. We found that network structural and temporal properties could account for a large part of the variability observed in strain diversity. These results show how stochasticity and network structure affect the population ecology of pathogens and warn against interpreting observations as unambiguous evidence of epidemiological differences between strains.
Document type :
Journal articles
Complete list of metadatas

Cited literature [73 references]  Display  Hide  Download
https://www.hal.inserm.fr/inserm-02153754
Contributor : Myriam Bodescot <>
Submitted on : Wednesday, June 12, 2019 - 2:33:10 PM
Last modification on : Tuesday, November 19, 2019 - 12:59:36 PM

File

journal.pcbi.1006530.pdf
Publication funded by an institution

Identifiers

Collections

UVSQ | IPLESP | INRIA | SORBONNE-UNIVERSITE | B2PHI | SU-MEDECINE | UNIV-PARIS-SACLAY | UNIV-LYON3 | ENS-LYON | CNRS | UNIV-LYON1 | INSA-LYON | LIP | UNIV-LYON2 | INSA-GROUPE | UGA

Citation

Francesco Pinotti, Éric Fleury, Didier Guillemot, Pierre-Yves Böelle, Chiara Poletto. Host contact dynamics shapes richness and dominance of pathogen strains. PLoS Computational Biology, Public Library of Science, 2019, 15 (5), pp.e1006530. ⟨10.1371/journal.pcbi.1006530⟩. ⟨inserm-02153754⟩

Export

BibTeX TEI DC DCterms EndNote

Share

Metrics

Record views

86

Files downloads

54

Contact

CCSD