Direct detection and analysis of vacA genotypes and cagA gene of Helicobacter pylori from gastric biopsies by a novel multiplex polymerase chain reaction assay

Several tests/methods for the infection, detection, and genotyping of Helicobacter pylori have been developed in the past; all these differ in specificity and sensitivity and thereby could not be routinely used in clinical study especially in resource-poor developing countries. In the present study, a novel method based on multiplex polymerase chain reaction (PCR) assay was developed to detect H. pylori in patients suffering from gastrointestinal diseases. This method does not require steps of sonication, boiling, or centrifugation for obtaining DNA from biopsy samples, which are otherwise prerequisite in detecting H. pylori by PCR assay. Two hundred seventy-six patients were examined, of which 182 cases (excluding 36 patients having multiple H. pylori strain infection and 8 showing amplification of 16S rDNA only) were H. pylori positive. The dominant vacA genotype was s1 and m1 being present in 168 (92.3%) and 106 (58.2%) patients, respectively, followed by m2 (41.7%), and the lowest being s2 (7.7%). Detection of H. pylori by this method seems rapid, simpler, and suitable for both types 1 and 2 bacteria. Furthermore, genotyping of vacA and cagA genes could also be routinely performed in a large number of patients for diagnostic purposes.