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

Abigail L. Coughtrie; Denise E. Morris; Rebecca Anderson; Nelupha Begum; David W. Cleary; Saul N. Faust; Johanna M. Jefferies; Alex R. Kraaijeveld; Michael V. Moore; Mark A. Mullee; Paul J. Roderick; Andrew Tuck; Robert N. Whittaker; Ho Ming Yuen; C. Patrick Doncaster; Stuart C. Clarke

Understanding the prevalence and community distribution of bacterial and viral pathogens, particularly where carriage is a prerequisite for progression to disease, is a key undertaking in the on-going development of interventional responses to changing epidemiology. Here we set out to determine the distribution of pathobiont bacterial and viral species commonly associated with respiratory tract infections using culture-independent approaches and ecological models of community assemblage as well as co-occurrence. Using multivariate analysis of microbial prevalence, we demonstrated that age affects carriage for a number of The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/099069 doi: bioRxiv preprint this set of isolates, which is indicative of the effectiveness of current PCV-13 and Hib vaccines in targeting specific serotypes as well as the effect of herd immunity in protecting individuals within age groups unlikely to have received these vaccines (41, 42) . The high proportion of non-vaccine type (NVT) S. pneumoniae reflects the process of serotype replacement as a result of vaccination, although it is not thought to lead to future large increases in the incidence of invasive disease caused by NVTs (43) . The identification of increasingly common NVT serotypes 6C, 11A/D and 23B and non-typeable H. influenzae provides important information for the epidemiological assessment of vaccines and for the development of future vaccines.