Modulation of nasopharyngeal innate defenses by viral coinfection predisposes individuals to experimental pneumococcal carriage

Glennie, S; Gritzfeld, J F; Pennington, S H; Garner-Jones, M; Coombes, N; Hopkins, M J; Vadesilho, C F; Miyaji, E N; Wang, D; Wright, A D; Collins, A M; Gordon, S B; Ferreira, D M

Statistical analysis. Fisher's exact test was used to compare the proportion of carriers that were virus positive and virus negative. Pearson's correlation coefficient was used to compare log-transformed FH levels and pneumococcal carriage density. Flow cytometry data were analyzed using Flow Jo v7.6.1 (Tree Star, Ashland, OR). To account for possible correlation among the repeated measurements in carriage status and density, GEE model was employed for the data analysis. For the GEE analysis of carriage presence (yes or no), binomial distribution and logit link function were used. For the GEE analysis of carriage density, log-transformed density was used as the dependent variable and normal distribution and identity link function were used. Three GEE models were estimated to assess the effects of FH levels and virus status on carriage status and density, separately and jointly. Model 1 has virus status (positive and negative) and day (days 2, 7, and 14) as predictors; model 2 has FH levels in log scale and day as predictors; model 3 has FH levels and virus status, day, and interaction between FH levels and virus as predictors.