Detecting the Helicobacter pylori 16S rRNA Gene in Dyspepsia Patients Using Real-Time PCR

Rike Syahniar, Mardiastuti H Wahid, Ari Fahrial Syam, Andi Yasmon


Background: early detection of H. pylori is essential to prevent the development of infections into gastric malignancies. The coccoid form of H. pylori is difficult to detect either by culture or histopathology; however, it can be detected using molecular methods, such as real-time PCR. The study was expected to provide new information on the development of H. pylori detection. Methods: a cross-sectional study was conducted at the Gastrointestinal Endoscopy Center of Cipto Mangunkusumo Hospital between October 2016 and August 2017. The sampling method used was consecutive sampling. Biopsy from gastric antrum and corpus were performed in 64 patients. We collected 2 specimens from each site to be examined using real-time PCR and histopathology. Initially, we conducted real-time PCR optimization followed by application of clinical samples from gastric biopsy. Data analysis using McNemar’s χ2 and Kappa tests. Results: the real-time PCR showed 25% positivity, while the positive proportion of histopathological examination was 14%. Real-time PCR has a sensitivity and specificity 88.9% dan 85.5%, respectively. The McNemar’s χ2 test showed that there is significantly different (p=0.039) between the two tests; kappa value (p=0.561).  Conclusion: the real-time PCR examination is more sensitive than histopathology. This technique can improve diagnosis by 11% compared to histopathological examination.


H. pylori; histopathology; real-time PCR


Correa P, Piazuelo MB. Helicobacter pylori infection and gastric adenocarcinoma. US Gastroenterol Hepatol Rev. 2011;7(1):59–64.

International Agency for Research on Cancer. Schistosomes, liver flukes and Helicobacter pylori. Vol 61. Lyon, France: IARC Press; 1994. IARC Monographs on the evaluation of carcinogenic risks to humans; p. 177-240

Syam AF, Miftahussurur M, Maknun D, et al. Risk factors and prevalence of Helicobacter pylori in five largest islands of Indonesia: A preliminary study. J Plos One. 2015;10(11):e0140186.

Abdullah M, Ohtsuka H, Rani AA, et al. Helicobacter pylori infection and gastropathy: A comparison between Indonesian and Japanese patients. World J Gastroenterol. 2009;15(39):4928-41.

Syam AF, Fauzi A, Abdullah M, et al. Demographical distribution on the incidence of Helicobacter pylori infection in Jakarta: Obtaining samples from 5 municipalities. J Gastroenterol, Hepatol Digestive Endosc. 2014;15(2):73-7.

Wang YK, Kuo FC, Liu CJ, et al. Diagnosis of Helicobacter pylori infection: Current options and developments. World J Gastroenterol. 2015;21(40): 11221–35.

Lee JY, Nayoung K. Diagnosis of Helicobacter pylori by invasive test: histology. Ann Transl Med. 2015;3(1):10.

Dunn BE, Cohen H, Blaser MJ. Helicobacter pylori. Clin Microbiol Rev. 1997;10:720-41.

Lee CH, Huang TC, Lin CL, et al. Performance of routine Helicobacter pylori invasive tests in patients with dyspepsia. Gastroenterol Res Pract. 2013.

Johannessen R, Jianu C, Kleveland PM, et al. Polymerase chain reaction versus culture in the diagnosis of Helicobacter pylori infection. J Gastroenterol. 2013;(e1)5:1-6.

Triana N, Unita M, Fantoni J, et al. Pemeriksaan Helicobacter pylori dengan PCR dari lambung penderita gastritis kronis. 2010;19(1):6-12.

Shukla SK, Prasad KN, Tripathi A, et al. Quantitation of Helicobacter pylori ureC gene and its comparison with different diagnostic techniques and gastric histopathology. J Microbiol Methods. 2011;86:231–7.

Sugimoto M, Wu JY, Abudayyeh S, et al. Unreliability of results of PCR detection of Helicobacter pylori in clinical or environmental samples. J Clinical Microb. 2009;47(3):738–42.

Peek RM, Miller GG, Tham KT, et al. Detection of Helicobacter pylori gene expression in human gastric mucosa. J Clin Microbiol.1995;33(1):28-32.

Ciesielska U, Dzięgiel P, Jagoda E, et al. The detection of Helicobacter pylori in paraffin sections using the PCR technique and various primers as compared to histological techniques. Folia Morphol (Warsz). 2004;63(2):229-31.

Shahamat M, Alavi M, Watts JEM, et al. Development of two PCR-based techniques for detecting helical and coccoid forms of Helicobacter pylori. J Clin Microbiol. 2004;42(8):3613–9.

Saez J, Belda S, SantibáñezM, et al. Real-time PCR for diagnosing Helicobacter pylori infection in patients with upper gastrointestinal bleeding: Comparison with other classical diagnostic methods. J Clin Microbiol. 2012;50(10):3233–7.

Ottiwet O, Chomvarin C, ChaicumparK, et al. Nested polymerase chain reaction for detection of Helicobacter pylori in gastric biopsy specimens. J Trop Med Public Health. 2010;41(6):1423-31.

Tankovic J, Plankaert MCT, DeforgesL, et al. Routine use real-time PCR for detection of Helicobacter pylori and of clarithromycin resistence. Gastroenterol Clin Biol. 2007;31:792-5.

Lee HC,Wang CK, Huang TC, et al. Performance of routine Helicobacter pylori invasive tests in patients with dyspepsia. Hindawi Publishing Corp. 2013;2013:1-5.

Kobayashi D, Eishi Y, OhkusaT, et al. Gastric mucosal density of Helicobacter pylori estimated by real-time PCR compared with results of urea breath test and histological grading. J Med Microbiol. 2002;51:305-11.

Ribeiro ML, Ecclissato CC, Mattos RG, et al. Quantitative real-time PCR for the clinical detection of Helicobacter pylori. Genetics Mol Biol. 2007;30(2):431-4.

Kalali B, Formichella L. Gerhard M. Diagnosis of Helicobacter pylori: Changes towards the future. MDPI J. 2015;3:122-35.

Lazaro MJR, Lario S, Casalots A, et al. Real-time PCR improves Helicobacter pylori detection in patients with peptic ulcer bleeding. Plos One J. 2010;6(5): e20009.

Full Text: PDF


  • There are currently no refbacks.