Computational protocol: Rapid replacement by non-vaccine pneumococcal serotypes may mitigate the impact of the pneumococcal conjugate vaccine on nasopharyngeal bacterial ecology

Similar protocols

Protocol publication

[…] Differences in baseline characteristics of the study participants recruited into the three study groups were tested using the Chi square test, Fisher’s exact test or Kruskal-Wallis test where appropriate. A mixed effects model was used to compare richness and Shannon α diversity across the study groups. Richness was positively skewed and was square root transformed for statistical analysis. Time-invariant risk factors (gender, place of birth, number of siblings, maternal age) and time-variant risk factors (age, vaccination period, season, breast feeding, travelling, antibiotic usage and nutritional status based on weight for height) were used as explanatory variables. Age and vaccination group were the main exposure risk factors and the remaining explanatory risk factors were considered as potential confounders. A random-intercept model was used to handle these two types of explanatory risk factors. All explanatory risk factors mentioned above were included in the fixed effects component of the model as well as pairwise and triple interaction terms between time, group and period. A backward model selection approach using the Wald test was adopted. Explanatory risk factors with a non-significant effect at the 5% significance level were discarded. Model residuals and random effects were checked for reliability. Kaplan Meier survival curves were used to compare the rates to first acquisition of pneumococcus and PCV7 serotypes in the three study groups. Statistical analyses were performed using STATA/SE 14.1, USA. Microbial community composition, structure and ecology analyses were performed using the Phyloseq package with R version 3.2.1. To reduce noise, low-occurrence, poorly represented OTUs were filtered out i.e. OTUs that did not appear more than once in 10% of the samples. To evaluate the effect of PCV7 vaccination group on overall microbial composition, the phylogenetic dis(similarities) among communities from the three groups were evaluated by metric multidimensional scaling (MDS)/ Principle component analysis (PCoA) on weighted UniFrac distance. Differential abundance of individual OTUs across the vaccination groups was explored using the DESeq package-extensions in the Phyloseq package. […]

Pipeline specifications

Software tools phyloseq, DESeq
Application Phylogenetics
Diseases Pulmonary Fibrosis