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Table 2 Comparison of amplification of virulence genes between PCR on bacterial cultures and direct PCR on biopsy material

From: PCR-based genotyping of Helicobacter pylori of Gambian children and adults directly from biopsy specimens and bacterial cultures

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)   
cag PAI
empty site
0(0) 12(20) 0(0) 2(3)   
cagA+ cag
PAI empty
4(7) 1(2) 2(3) 2(3) 84.9(75.3,94.5) 0.70(0.50,0.91)
  s1 s2 s1&s2 Missing   
s1 31(52) 4(7) 0(0) 5(8)   
s2 5(8) 9(15) 0(0) 1(2)   
s1&s2 3(5) 1(2) 0(0) 1(2) 75.5(63.9,87.1) 0.45(0.21,0.68)
  m1 m2 m1&m2 Missing   
m1 18(30) 1(2) 1(2) 6(10)   
m2 1(2) 17(28) 0(0) 2(3)   
m1&m2 4(7) 5(8) 3(5) 2(3) 76.0(64.2,87.8) 0.62(0.42,0.82)
  iceA1 iceA2 icA1&2 Missing   
iceA1 5(8) 0(0) 1(2) 3(5)   
iceA2 1(2) 11(18) 29(48) 7(12)   
iceA1&2 0(0) 3(5) 0(0) 0(0) 32.0(19.1,44.9) 0.06(-0.05,0.16)