Table 2.
Staphylococcus aureus Genes under Positive Selection during Chronic Cystic Fibrosis Respiratory Infection
| Gene | Function | dN/dS Mutation Counts (Ratio) | dN/dS Proportion P Value | Proportion of Disruptive Mutations* (%) |
|---|---|---|---|---|
| rpoB | DNA-directed RNA polymerase, β subunit | 37/3 (12.3) | 10−7.2 | 0.0 |
| fmtB | LPXTG-motif cell wall anchor domain | 40/7 (5.7) | 10−5.4 | 11.1 |
| agrA | Accessory gene regulator A | 18/0 (∞) | 10−5.2 | 22.2 |
| rpsJ | 30S ribosomal protein S10 | 18/0 (∞) | 10−5.2 | 0.0 |
| rsbU | Sigma factor B regulator protein | 18/0 (∞) | 10−5.2 | 11.1 |
| thyA | Thymidylate synthase | 21/1 (21) | 10−5 | 42.9 |
| set9 | Superantigen-like protein | 17/0 (∞) | 10−4.9 | 0.0 |
| walK | Two-component sensor histidine kinase | 20/1 (20) | 10−4.7 | 0.0 |
| ebh | Surface protein, ECM binding protein–like protein A | 73/26 (2.8) | 10−4.5 | 11.6 |
Definition of abbreviations: ECM = extracellular matrix; dN = nonsynonymous; dS = synonymous.
*
The proportion of “disruptive” mutations equals the number of stop-gain, frameshift, or large (affecting more than one codon) indels divided by the total number of nonsynonymous mutations observed in the gene.