The study was aimed at comparing PCR methods of direct detection from biopsy using the boiling method and one other method with two known gold standards (histology and CLO test) for the diagnosis of H. pylori in Nigeria. A total of 168 biopsies (three from antrum and one from corpus each) were taken from 42 patients presenting with various gastroduodenal symptons after informed consent was obtained from them.The biopsies were analysed using the CLO test kit and histology, while the boiling method as described by Holmes and Quigley (1981) was used to obtain DNA and then PCR using the 16S rRNA gene, glmM gene and cagA gene. With CLO test 15/42 (35.71%) were positive, histology 13/42 (30.95%) were positive, 16S rRNA 22/42 (52.38%) were positive, glmM 19/42 (45.24%) were positive, cagA 19/42 (45.24%) were positive. The sensitivity and specificity of the PCR tests with CLO as the gold standard showed that the tests were 100% sensitive and varied between 74.1% to 84.1% in specificity. The PPV and NPV showed that the NPV was almost 100%, while the PPV was between 68.2% and 75%. Using the histology as the gold standard, the sensitivity was almost 100% while the specificity, the PPV were reduced in comparison to the CLO test. The PCR test using the glmM gene appears to be the most reliable test for diagnosis of H. pylori in Nigeria most especially where culture is difficult due to the power outages.
Keywords: CLO test; PCR; biopsies; histology.