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

Nose swab samples were collected as part of a large population-based cross-sectional carriage study undertaken with two separate time-points, May to August 2012 (late spring/summer) and February to April 2013 (winter/early spring), following protocols described in reference (22) . Briefly this involved the collection of nose swabs from the two time-points were collected from different individuals from twenty general practitioners (GP) practices from the South East hub of the Wessex Primary Care Research Network. Figure 1 depicts the structure of the study. Swabs were immersed into skimmed milk, tryptone, The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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 Variables assessed for inclusion by univariate analyses included age (in years), recent RTI (self-reported, RTI within a month prior to swabbing), geographical location (practices were grouped into six geographical areas, recent use of antibiotics (self-reported, antibiotics taken within a month prior to swabbing), immunisation status (self-reported, immunisations in-line with the national schedule), season (winter or summer swabbing) and presence of other microbial species within the same sample. (27, 28) ) and genes associated with virulence (Pathogenic Bacteria Database (VFBD) (29, 30) ). Antigens that are or have been considered as vaccine candidates were of particular interest. S. pneumoniae vaccine candidates included piaA, pspA, pspC/cbpA, psaA, nanA, lytA and ply (31) (32) (33) (34) . H. influenzae vaccine candidates included hpd, ompP2, ompP5, tbpA/B, hmw1/2 and Hia (35, 36) . iPCRess was also used to identify penicillin binding protein genes pbp1a, pbp2x and pbp2b genes within S. pneumoniae isolates (37) and the H. influenzae protein D (hdp) gene (38) .