Table 2 Comparison of amplification of virulence genes between PCR on bacterial cultures and direct PCR on biopsy material
PCR on Biopsy | ||||||
|---|---|---|---|---|---|---|
Culture | cagA + | cag PAI empty site | cagA + cag PAI empty site | No amplification with primer | % Agreement (95% CI) | Kappa (95% CI) |
CagA+ | 31(52) | 0(0) | 3(5) | 3(5) | Â | Â |
cag PAI empty site | 0(0) | 12(20) | 0(0) | 2(3) | Â | Â |
cagA+ cag PAI empty | 4(7) | 1(2) | 2(3) | 2(3) | 84.9(75.3,94.5) | 0.70(0.50,0.91) |
| Â | s1 | s2 | s1&s2 | Missing | Â | Â |
s1 | 31(52) | 4(7) | 0(0) | 5(8) | Â | Â |
s2 | 5(8) | 9(15) | 0(0) | 1(2) | Â | Â |
s1&s2 | 3(5) | 1(2) | 0(0) | 1(2) | 75.5(63.9,87.1) | 0.45(0.21,0.68) |
| Â | m1 | m2 | m1&m2 | Missing | Â | Â |
m1 | 18(30) | 1(2) | 1(2) | 6(10) | Â | Â |
m2 | 1(2) | 17(28) | 0(0) | 2(3) | Â | Â |
m1&m2 | 4(7) | 5(8) | 3(5) | 2(3) | 76.0(64.2,87.8) | 0.62(0.42,0.82) |
| Â | iceA1 | iceA2 | icA1&2 | Missing | Â | Â |
iceA1 | 5(8) | 0(0) | 1(2) | 3(5) | Â | Â |
iceA2 | 1(2) | 11(18) | 29(48) | 7(12) | Â | Â |
iceA1&2 | 0(0) | 3(5) | 0(0) | 0(0) | 32.0(19.1,44.9) | 0.06(-0.05,0.16) |