Epidemiological and ecological modelling reveal diversity in microbial population structures from a cross-sectional community swabbing study

Respiratory tract infections (RTI) are responsible for over 4 million deaths per year worldwide with pathobiont carriage a required precursor to infection. Through a cross-sectional community-based nasal self-swabbing study we sought to determine carriage epidemiology for respiratory pathogens among...

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Bibliographic Details
Published in:bioRxiv 2017-01
Main Authors: Coughtrie, Abigail L, Morris, Denise E, Anderson, Rebecca, Begum, Nelupha, Cleary, David W, Faust, Saul N, Jefferies, Johanna M, Kraaijeveld, Alex R, Moore, Michael V, Mullee, Mark A, Roderick, Paul J, Tuck, Andrew, Whittaker, Robert N, Ho, Ming Yuen, Doncaster, C Patrick, Clarke, Stuart C
Format: Article
Language:English
Subjects:
Community composition
Coronaviruses
Epidemiology
Influenza
Mathematical models
Niches
Parainfluenza
Respiratory diseases
Respiratory tract diseases
Rhinovirus
Species
Streptococcus infections
Viruses
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Summary:Respiratory tract infections (RTI) are responsible for over 4 million deaths per year worldwide with pathobiont carriage a required precursor to infection. Through a cross-sectional community-based nasal self-swabbing study we sought to determine carriage epidemiology for respiratory pathogens amongst bacteria (Streptococcus pneumoniae, Haemophilus influenza, Moraxella catarrhalis, Staphylococcus aureus, Pseudomonas aeruginosa and Neisseria meningitidis) and viruses (RSV, Influenza viruses A and B, Rhinovirus/Enterovirus, Coronavirus, Parainfluenza viruses 1-3 and Adenovirus (ADV)). Carriage of bacterial and viral species was shown to vary with participant age, recent RTI and the presence of other species. The spatial structure of microbial respiratory communities was less nested (more disordered) in the young (0-4 years) and those with recent RTI. Species frequency distributions were flatter than random expectation in young individuals ( 2 = 20.42, p = 0.002), indicating spatial clumping of species consistent with facilitative relationships amongst them. Deviations from a neutral model of ecological niches were observed for samples collected in the summer and from older individuals (those aged 5-17, 18-64 and 65 years) but not in samples collected from winter, younger individuals (those aged 0-4 years), individuals with recent RTI and individuals without recent RTI, demonstrating the importance of both neutral and niche processes in respiratory community assembly. The application of epidemiological methods and ecological theory to sets of respiratory tract samples has yielded novel insights into the factors that drive microbial community composition, such as seasonality and age, as well as species patterns and interactions within the nose.
DOI:10.1101/099069