Table 2.
Comparison of DEGs of PaeAG1 at 2.5 and 5 h after treatment with ciprofloxacin, and specific phages or categories of virulence factors, including shared genes (intersection) and total genes at both times (union), the regulation and the type of elements.
| Determinants | Sets of DEGs | ||||||
|---|---|---|---|---|---|---|---|
| Type | Specific elements | Total genes (in PaeAG1 genome) | 2.5 h | 5 h | 2.5 h ∩ 5 h | 2.5 h ∪ 5 h | Regulation* and observations |
| Antibiotic resistance | Total | 56 | 3 | 2 | 2 | 3 | Down, lactamases |
| Phages | PPpW | 12 | 0 | 0 | 0 | 0 | No DEGs |
| phiCTX | 25 | 2 | 3 | 2 | 3 | Up | |
| F10 | 62 | 1 | 9 | 0 | 10 | Up | |
| JBD44 | 105 | 34 | 65 | 34 | 65 | Up | |
| JDO24 | 59 | 4 | 7 | 4 | 7 | Up | |
| phi3 | 45 | 0 | 0 | 0 | 0 | No DEGs | |
| Total | 308 | 41 | 84 | 40 | 85 | – | |
| Virulence factors | Adherence | 96 | 11 | 19 | 11 | 19 | Down |
| Antimicrobial activity | 17 | 1 | 6 | 1 | 6 | Up, phenazines | |
| Antiphagocytosis | 25 | 0 | 0 | 0 | 0 | No DEGs | |
| Phospholipases | 3 | 0 | 0 | 0 | 0 | No DEGs | |
| Biosurfactant | 3 | 0 | 0 | 0 | 0 | No DEGs | |
| Iron uptake | 28 | 0 | 1 | 0 | 1 | Up, Pyochelin | |
| Protease | 4 | 1 | 2 | 1 | 2 | Up, elastases | |
| Quorum sensing | 5 | 0 | 1 | 0 | 1 | Up, RhlR | |
| Regulation GacS/GacA system | 2 | 0 | 0 | 0 | 0 | No DEGs | |
| Secretion system | 63 | 0 | 2 | 0 | 2 | Down, T3SS | |
| Toxins | 4 | 0 | 1 | 0 | 1 | Up, hydrogen cyanide | |
| Total | 250 | 13 | 32 | 13 | 32 | – | |
*Based in logFC of genes for both times 2.5 and 5 h. Type of elements is also shown.