Table 2. The distribution of pathogen-specific and common VFs in each functional category according to the VFDB classification.
| VFDB classification | Pathogen-specific VFs |
Common VFs |
P valueb | ||
|---|---|---|---|---|---|
| # | %a | # | %a | ||
| Functional categories with a higher percentage of pathogen-specific VFs | |||||
| Exotoxin | 73 | 11.77 | 37 | 2.70 | 1.49e−14* |
| Type IV secretion system (T4SS) | 76 | 12.26 | 56 | 4.09 | 4.01e−10* |
| Unclassified protein (T3SS)c | 90 | 14.52 | 99 | 7.24 | 9.84e−06* |
| Effector protein (T3SS) | 31 | 5.00 | 18 | 1.32 | 1.41e−05* |
| Pathogenicity islandd | 171 | 27.58 | 267 | 19.52 | 3.34e−04* |
| Antiphagocytosis-associated protein | 4 | 0.65 | 1 | 0.07 | 1.24e−01 |
| Chaperone(T3SS) | 8 | 1.29 | 7 | 0.51 | 2.58e−01 |
| Protease | 7 | 1.13 | 7 | 0.51 | 3.85e−01 |
| Type VII secretion system | 14 | 2.26 | 18 | 1.32 | 4.30e−01 |
| Plasminogen activator | 2 | 0.32 | 1 | 0.07 | 4.92e−01 |
| Translocation protein (T3SS) | 5 | 0.81 | 5 | 0.37 | 6.16e−01 |
| Anti-proteolysis | 1 | 0.16 | 0 | 0.00 | 6.11e−01 |
| Afimbrial adhesin | 28 | 4.52 | 49 | 3.58 | 6.68e−01 |
| Actin-based motility | 1 | 0.16 | 1 | 0.07 | 8.60e−01 |
| Proinflammatory effect | 1 | 0.16 | 1 | 0.07 | 8.32e−01 |
| Exoenzyme | 12 | 1.94 | 22 | 1.61 | 1 |
| Secretion apparatus protein(T3SS) | 12 | 1.94 | 25 | 1.83 | 1 |
| Categories with a higher percentage of common VFs | |||||
| Flagella | 1 | 0.16 | 146 | 10.67 | 1.08e−14* |
| Capsule | 11 | 1.77 | 122 | 8.92 | 7.70e−08* |
| Endotoxin or lipopolysaccharide(LPS) | 4 | 0.65 | 70 | 5.12 | 5.50e−07* |
| Iron uptake | 9 | 1.45 | 88 | 6.43 | 1.90e−05* |
| Regulation | 0 | 0.00 | 33 | 2.41 | 2.62e−05* |
| Type VI secretion system(T6SS) | 1 | 0.16 | 37 | 2.70 | 1.01e−04* |
| Type II secretion system(T2SS) | 2 | 0.32 | 30 | 2.19 | 6.24e−03* |
| Stress protein | 0 | 0.00 | 12 | 0.88 | 8.71e−02 |
| Cell metabolism | 0 | 0.00 | 9 | 0.66 | 2.11e−01 |
| Unclassified | 6 | 0.97 | 30 | 2.19 | 2.64e−01 |
| Urease | 0 | 0.00 | 7 | 0.51 | 2.90e−01 |
| Immune evasion | 1 | 0.16 | 10 | 0.73 | 4.42e−01 |
| Cell wall | 1 | 0.16 | 10 | 0.73 | 4.22e−01 |
| Biofilm formation | 0 | 0.00 | 4 | 0.29 | 5.97e−01 |
| Intracellular survival | 0 | 0.00 | 4 | 0.29 | 5.75e−01 |
| Invasion | 3 | 0.48 | 13 | 0.95 | 7.05e−01 |
| Magnesium uptake | 0 | 0.00 | 3 | 0.22 | 8.52e−01 |
| IgA1 protease | 0 | 0.00 | 3 | 0.22 | 8.26e−01 |
| Serum resistance | 0 | 0.00 | 3 | 0.22 | 8.02e−01 |
| Fimbriae | 44 | 7.10 | 103 | 7.53 | 1 |
| Molecular mimicry | 1 | 0.16 | 3 | 0.22 | 1 |
| Manganese uptake | 0 | 0.00 | 1 | 0.07 | 1 |
| Complement protease | 0 | 0.00 | 2 | 0.15 | 1 |
| Nutrient acquisition | 0 | 0.00 | 1 | 0.07 | 1 |
| Biosurfacant | 0 | 0.00 | 2 | 0.15 | 1 |
| Peptidase | 0 | 0.00 | 1 | 0.07 | 1 |
| Enzyme | 0 | 0.00 | 1 | 0.07 | 1 |
| Heat-shock protein | 0 | 0.00 | 1 | 0.07 | 1 |
| Pigment | 0 | 0.00 | 2 | 0.15 | 1 |
| Bile resistance | 0 | 0.00 | 1 | 0.07 | 1 |
| Complement resistance | 0 | 0.00 | 1 | 0.07 | 1 |
| Resistance to antimicrobial peptides | 0 | 0.00 | 1 | 0.07 | 1 |
| SUM | 620 | 1368 | |||
a The percentage of pathogen-specific or common VFs in a given functional category. bPearson Chi-square test with Yates continuity correction (see Materials and Methods). Asterisks indicate statistical significance (P value < 0.05). cThe number of the genes involved with T3SS, except for the number of effector proteins, chaperones, translocation apparatus proteins and secretion apparatus proteins included in the T3SS. dThe number of the genes involved in PAIs, not including the number of the virulence factors included in other functional categories, e.g., the number of the genes encoding T3SS or T4SS in PAIs.