Table 2.
Prevalence rates of genes associated with DNA metabolism, lysogeny, virulence, and antimicrobial resistance among S. aureus phages in the subdividing clusters. NA, not applicable.
| Function | Proteins | Number (%) of Positive Bacteriophages | p-Value | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Lineage I (n = 20) | Clade IIa (n = 8) | Clade IIb (n = 2) | Clade IIc (n = 45) | Clade IIIa (n = 29) | Clade IIIb (n = 16) | Clade IIIc (n = 11) | Clade IIId (n = 22) | Clade IIIe (n = 28) | Singletons (n = 7) | Total (n = 188) |
|||
| DNA metabolism | DNA synthesis | 4(20.0) | 4(50.0) | 1(50.0) | 17(37.8) | 7(24.1) | 2(12.5) | 3(27.3) | 6(27.3) | 6(21.4) | 1(14.3) | 51(27.1) | NA |
| DNA binding | 15(75.0) | 4(50.0) | 1(50.0) | 16(35.6) | 10(34.5) | 5(31.3) | 6(54.5) | 9(40.9) | 13(46.4) | 3(42.9) | 82(43.6) | NA | |
| DNA polymerase | 10(50.0) | 6(75.0) | 1(50.0) | 19(42.2) | 19(65.5) | 8(50.0) | 4(36.4) | 4(18.2) | 9(32.1) | 6(85.7) | 86(45.7) | 0.020 | |
| DNA primase/helicase | 4(20.0) | 5(62.5) | 1(50.0) | 22(48.9) | 9(31.0) | 3(18.8) | 3(27.3) | 7(31.8) | 7(25.0) | 2(28.6) | 63(33.5) | NA | |
| DNA helicase | 4(20.0) | 5(62.5) | 2(1.0) | 26(57.8) | 9(31.0) | 4(25.0) | 3(27.3) | 12(54.5) | 9(32.1) | 3(42.9) | 77(41.0) | NA | |
| DNA primase | 4(20.0) | 5(62.5) | 1(50.0) | 21(46.7) | 9(31.0) | 3(18.8) | 3(27.3) | 7(31.8) | 7(25.0) | 2(28.6) | 62(33.0) | NA | |
| DNA modification | 0(0) | 0(0) | 0(0) | 1(2.2) | 0(0) | 0(0) | 0(0) | 0(0) | 0(0) | 0(0) | 1(0.5) | NA | |
| DNA methylase | 0(0) | 1(12.5) | 0(0) | 0(0) | 0(0) | 1(6.3) | 0(0) | 0(0) | 0(0) | 0(0) | 2(1.1) | NA | |
| DNA repair | 3(15.0) | 2(25.0) | 0(0) | 4(8.9) | 1(3.4) | 1(6.3) | 0(0) | 2(9.1) | 3(10.7) | 0(0) | 16(8.5) | NA | |
| DNA sliding clump inhibitor | 2(10.0) | 3(37.5) | 1(50.0) | 18(40.0) | 8(27.6) | 2(12.5) | 3(27.3) | 5(22.7) | 6(21.4) | 2(28.6) | 50(26.6) | NA | |
| RNA ligase | 2(10.0) | 3(37.5) | 0(0) | 10(22.2) | 6(20.7) | 1(6.3) | 1(9.1) | 1(4.5) | 4(14.3) | 1(14.3) | 29(15.4) | NA | |
| RNA polymerase | 4(20.0) | 5(62.5) | 1(50.0) | 21(46.7) | 9(31.0) | 3(18.8) | 3(27.3) | 7(31.8) | 7(25.0) | 2(28.6) | 62(33.0) | NA | |
| Type III restriction enzyme | 5(25.0) | 5(62.5) | 1(50.0) | 22(48.9) | 9(31.0) | 3(18.8) | 3(27.3) | 7(31.8) | 7(25.0) | 2(28.6) | 64(34.0) | NA | |
| Lysogeny | Recombinase | 0(0) | 0(0) | 2(1.0) | 45(1.0) | 0(0) | 0(0) | 0(0) | 0(0) | 0(0) | 1(14.3) | 48(25.5) | <0.001 |
| Transposase | 0(0) | 7(87.5) | 0(0) | 1(2.2) | 0(0) | 0(0) | 0(0) | 0(0) | 0(0) | 1(14.3) | 9(4.8) | <0.001 | |
| Integrase | 0(0) | 0(0) | 0(0) | 0(0) | 11(37.9) | 9(56.3) | 6(54.5) | 5(22.7) | 8(28.6) | 5(71.4) | 44(23.4) | <0.001 | |
| Repressor | 0(0) | 0(0) | 0(0) | 0(0) | 4(13.8) | 3(18.8) | 5(45.5) | 10(45.5) | 3(10.7) | 1(14.3) | 26(13.8) | <0.001 | |
| Anti-repressor | 0(0) | 0(0) | 0(0) | 0(0) | 2(6.9) | 13(81.3) | 10(90.9) | 21(95.5) | 17(60.7) | 1(14.3) | 64(34.0) | <0.001 | |
| Clp protease | 0(0) | 0(0) | 0(0) | 0(0) | 29(1.0) | 13(81.3) | 0(0) | 0(0) | 0(0) | 1(14.3) | 43(22.9) | NA | |
| Virulence | Virulence E family protein | 4(20.0) | 6(75.0) | 1(50.0) | 25(55.6) | 15(51.7) | 8(50.0) | 5(45.5) | 10(45.5) | 9(32.1) | 4(57.1) | 87(46.3) | NA |
| Panton-Valentine leukocidin | 2(10.0) | 2(25.0) | 1(50.0) | 15(33.3) | 10(34.4) | 11(68.8) | 7(63.4) | 11(50.0) | 11(39.3) | 5(71.4) | 75(39.9) | 0.005 | |
| dUTP pyrophosphatase | 0(0) | 1(12.5) | 1(50.0) | 9(20.0) | 7(24.1) | 2(12.5) | 4(36.4) | 8(36.4) | 8(28.6) | 2(28.6) | 43(22.9) | 0.025 | |
| Complement inhibitor sciderin | 0(0) | 0(0) | 0(0) | 2(4.4) | 1(3.4) | 1(6.3) | 3(27.3) | 0(0) | 3(10.7) | 2(28.6) | 12(6.4) | 0.079 | |
| Staphylokinase | 0(0) | 0(0) | 0(0) | 2(4.4) | 1(3.4) | 1(6.3) | 3(27.3) | 1(4.5) | 1(3.6) | 1(14.3) | 10(5.3) | NA | |
| beta hemolysin | 0(0) | 0(0) | 0(0) | 0(0) | 0(0) | 0(0) | 1(9.1) | 0(0) | 1(3.6) | 0(0) | 2(1.1) | NA | |
| gamma hemolysin | 0(0) | 0(0) | 0(0) | 0(0) | 1(3.4) | 1(6.3) | 0(0) | 0(0) | 0(0) | 0(0) | 2(1.1) | NA | |
| ARG | beta-lactamase | 1(5.0) | 1(12.5) | 0(0) | 2(4.4) | 0(0) | 1(6.3) | 4(36.4) | 1(4.5) | 4(14.3) | 2(28.6) | 13(8.5) | NA |