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

The interactions and interplay between bacterial and viral species within the respiratory tract is thought to affect the shift from asymptomatic carriage to serious invasive illness (4) . Such interactions will be driven by species presence and diversity of the resident communities of the respiratory tract. Here diversity in species richness and abundance is thought to offer protection from invading pathogens and overgrowth of a single species (5, 6) . It is likely that the dynamics of community structure may impact on infection risk. Species diversity can be measured in the presence of different species within the respiratory tract (inter-species diversity) or the presence of different bacterial strains and types of a single species (intraspecies). The former can be assessed using conventional culture methods or molecular techniques such as real-time polymerase chain reaction (PCR) and 16S rRNA gene sequencing (7, 8) . Intra-species analysis gives insight into the distribution of different types of a species that may display differential capacity for disease. It requires techniques such as serotyping and multi-locus sequence typing (MLST) (9) (10) (11) (12) , or expansions of the MLST methodology such as whole-genome MLST (wgMLST) (13) and ribosomal MLST (rMLST) (14) .