Genome-wide association study of Streptococcus pneumoniae identifies disease-associated genetic variation

This study employed multiple GWAS analyses to compare genomic differences between infection and carriage isolates so as to determine whether genetic variation is unevenly enriched in the infection isolates. Briefly, a two-stage analysis process was employed to reveal the infection-associated k-mers by comprehensive GWAS analyses. First, a univariate LMM was fitted to initially screen infection-associated k-mers by the Pyseer (v1.3.10) Second, we used multiple methods (Scoary, LASSO and VSURF) to minimize false-positive associations and identify consensus infection-associated k-mers.The importance of k-mers was ranked by the mean decrease in impurity (Mean Decrease Gini, MDG), which is a measure of the predictor’s contribution to the correct sample classification.