Functional enrichment analysis

Functional roles and pathways were assigned using KEGG designations [36] and TIGRfams [37] for each non-synonymous SNV and non-neutral IS event, and the number of genes within each category was determined for ACICU. To identify statistically significant enrichment in functional classes of genes, hypergeometric probability tests were conducted. In the calculation, the population size was the number of all genes in the PanOCT shared clusters for the 136 genomes (553,343 genes); the population successes value was calculated as the number of genes in each functional role or pathway category based on its abundance in ACICU multiplied by each genes’ occurrence in the PanOCT shared clusters; sample size was the number of SNV or IS events for isolate-specific (IS), patient-restricted (PR), or patient-specific (PS) categories, respectively; and the number of sample successes was the number of hit genes in each category.