Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Host contact dynamics shapes richness and dominance of pathogen strains

Francesco Pinotti, Éric Fleury, Didier Guillemot, View ORCID ProfilePierre-Yves Böelle, View ORCID ProfileChiara Poletto
doi: https://doi.org/10.1101/428185
Francesco Pinotti
1Sorbonne Université, INSERM, Institut Pierre Louis d’ Épidémiologie et de Santé Publique, Paris, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Éric Fleury
2INRIA, Paris, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Didier Guillemot
3Inserm, UVSQ, Institut Pasteur, Université Paris-Saclay, Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases (B2PHI), Paris, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Pierre-Yves Böelle
1Sorbonne Université, INSERM, Institut Pierre Louis d’ Épidémiologie et de Santé Publique, Paris, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Pierre-Yves Böelle
Chiara Poletto
1Sorbonne Université, INSERM, Institut Pierre Louis d’ Épidémiologie et de Santé Publique, Paris, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Chiara Poletto
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

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 warns against interpreting observations as unambiguous evidence of epidemiological differences between strains.

Author summary Pathogens are structured in multiple strains that interact and co-circulate on the same host population. This ecological diversity affects, in many cases, the spread dynamics and the efficacy of vaccination and antibiotic treatment. Thus understanding its biological and host-behavioral drivers is crucial for outbreak assessment and for explaining trends of new-strain emergence. We used stochastic modeling and network theory to quantify the role of host contact behavior on strain richness and dominance. We systematically compared multi-strain spread on different network models displaying properties observed in real-world contact patterns. We then analyzed the real-case example of Staphylococcus aureus spread in a hospital, leveraging on a combined dataset of carriage and close proximity interactions. We found that contact dynamics has a profound impact on a strain population. Contact heterogeneity, for instance, reduces strain diversity by reducing the number of circulating strains and leading few strains to dominate over the others. These results have important implications in disease ecology and in the epidemiological interpretation of biological data.

Footnotes

  • ↵* chiara.poletto{at}inserm.fr

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted September 26, 2018.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Host contact dynamics shapes richness and dominance of pathogen strains
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Host contact dynamics shapes richness and dominance of pathogen strains
Francesco Pinotti, Éric Fleury, Didier Guillemot, Pierre-Yves Böelle, Chiara Poletto
bioRxiv 428185; doi: https://doi.org/10.1101/428185
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
Host contact dynamics shapes richness and dominance of pathogen strains
Francesco Pinotti, Éric Fleury, Didier Guillemot, Pierre-Yves Böelle, Chiara Poletto
bioRxiv 428185; doi: https://doi.org/10.1101/428185

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Epidemiology
Subject Areas
All Articles
  • Animal Behavior and Cognition (2430)
  • Biochemistry (4787)
  • Bioengineering (3330)
  • Bioinformatics (14671)
  • Biophysics (6634)
  • Cancer Biology (5167)
  • Cell Biology (7423)
  • Clinical Trials (138)
  • Developmental Biology (4362)
  • Ecology (6873)
  • Epidemiology (2057)
  • Evolutionary Biology (9913)
  • Genetics (7344)
  • Genomics (9522)
  • Immunology (4550)
  • Microbiology (12673)
  • Molecular Biology (4942)
  • Neuroscience (28313)
  • Paleontology (199)
  • Pathology (808)
  • Pharmacology and Toxicology (1391)
  • Physiology (2024)
  • Plant Biology (4492)
  • Scientific Communication and Education (977)
  • Synthetic Biology (1299)
  • Systems Biology (3912)
  • Zoology (725)