Comparison of three PCR methods for detection of Helicobacter pylori DNA and detection of cagA gene in gastric biopsy specimens

Table 1 Conditions for four different PCR methods

Target (reference), nucleotide	Primer names and sequences	PCR conditions
(nt) positions amplified, and size
of PCR products
26-kDa SSA gene (5),	Primer 3, 5’-TGGCGTGTCTATTGACAGCGAGC-3’	98°C, 10 min (1cycle);
nt 474-776, 303 bp	Primer 4, 5’-CCTGCTGGGCATACTTCACCAG-3’	92°C, 30 s; 68°C, 1 min (37cycles); 92°C,
		30 s 68°C, 1 min; 72°C, 2 min (6 cycles)
Urease A gene (4),	HPU1, 5’-GCCAATGGTAAATTAGTT-3’	94°C, 1 min; 45°C, 1 min
nt 304-714, 411 bp	HPU2, 5’-CTCCTTAATTGTTTTTAC-3’	72°C, 1 min (35 cycles)
glmM gene (3)	Forward primer, 5’-AAGCTTTTAGGGGTGTTAGGGGTTT-3’	93°C, 1 min; 55°C, 1 min;
nt 784-1077, 294 bp	Reverse primer, 5’-AAGCTTACTTTCTAACACTAACGC-3’	72°C, 1 min (35 cycles)
CagA gene	Primer 1, 5’-CCATGAATTTTTGATCCGTTCGG-3’	94°C, 1 min, 58°C, 1 min; 72°C,
		1 min (40 cycles)
nt 394 bp	Primer 2, 5’-GATAACAGGCAAGCTTTTGAGGGA-3’

Table 2 Results of three PCR methods and cagA gene for the detection of H pylori from gastric biopsy

Biopsy(n = 63)	ureA	glmM	26-kDa	Cag A +	Culture	CLO
22	+	+	+	15	9+, 13-	18+, 4-
11	+	-	-	-	11-	3+, 8-
5	-	+	-	-	5-	3+, 2-
2	-	-	+	-	2-	2-
4	+	+	-	-	4-	2-, 2+
2	+	-	+	-	1+, 1-	2+
2	-	+	+	-	1+, 1-	2+
15	-	-	-	-	15-	15-

-: negative, +: positive.

Table 3 Positive and negative predictive values of three dif-ferent PCR methods

Value	Results [(%, No. of samples with value/total No.)] for PCR method
	ureA gene	glmM gene	26-kDa gene
Positive predictive1	91 (10/11)	91 (10/11)	100 (11/11)
Negative predictive2	44 (23/52)	56 (29/52)	67 (35/52)

¹Compared with 11 culture- positive samples,

²Compared with 52 culture- negative samples.