PCR-based Diagnosis of Helicobacter pylori

  • November 5, 2023
  • Posted by: OptimizeIAS Team
  • Category: DPN Topics
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PCR-based Diagnosis of Helicobacter pylori

Subject: Science and technology

Section: Biotechnology

In the news-

The team of researchers from the National Institute of Cholera and Enteric Diseases (ICMR-NICED) Kolkata, developed a two-step PCR-based assay to detect Helicobacter pylori (H. pylori) infection and to identify the clarithromycin-resistant bacteria.

Helicobacter pylori (H. pylori)

  • Helicobacter pylori is a gram-negative spiral-shaped bacteria that colonies the gastric mucosa.
  • The bacteria adapts to survive in the acidic environment of the stomach and with the help of various adhesins/receptor molecules, it attaches to the host cells.
  • Most of the infections by pylori are asymptomatic and approximately 10-15% of them develop peptic ulcers.

  • H. pylori colonization in gastric epithelial cells is more prominent in developing countries mostly due to contaminated food, water, and poor hygiene. In India, 60-70% of the population is affected with the H. pylori infection, which is often acquired during childhood and remains in the stomach throughout life.

Diagnosis of H. pylori infection

The diagnosis is mainly done in two ways-

  1. Non-Invasive tests: The non-invasive diagnostic tests are done without performing endoscopy. The urea breath test (UBT), stool antigen test (SAT), serological tests, and tests using molecular methods are all non-invasive tests
  2. Invasive tests: The invasive diagnostic available methods are endoscopic imaging, histology determination, rapid urease testing, and tests using culture and molecular methods.

Limitations of previously used diagnosis

  1. The tests are not specific and sensitive to H. pylori.
  2. The tests are expensive.
  3. The culture of H. pylori is slow-growing, hence the diagnosis takes several days (sometimes even more than a week).
  4. Not effective in identifying the drug-resistant strains.

Dr. Ashish Kumar Mukhopadhyay’s (NICED) research: The team from NICED identified that the drug resistance in the bacteria is due to a point mutation (A to G mutation at 2143 position) in the 23S ribosomal RNA (rRNA) gene.

Bioinformatics study revealed that drug-resistant and drug-sensitive strains had very different binding affinities for the drug – “the drug’s binding affinity to mutant was weaker compared with the drug-sensitive bacteria”.

The team developed a two-step PCR-based assay to first detect H. pylori and then to differentiate resistant isolates from biopsy samples.

Ist step: 617 base pair segment containing the point mutation was amplified using DNA from biopsy samples.

2nd step: 183 base pairs amplified by the first PCR step are used as a template and two allele-specific primers are used for amplification.

Benefits of the PCR-based assay:

  1. It is a rapid and reliable diagnostic tool.
  2. 100% specificity and sensitivity in detecting pylori infection.
  3. The assay can distinguish between drug resistance and drug-sensitive bacteria.

Conclusion

The progressive increase in antibiotic resistance represents a real and serious health problem. The improvement and development of diagnostic methods, such as PCR-based molecular techniques, are promising tools to detect antibiotic resistance at an individual level and, thus, can offer targeted antibiotic treatment.

PCR-based Diagnosis of Helicobacter pylori Science and tech