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 | – | |
