Molecular Characterization of cagA and vacA Virulence Genes in Helicobacter pylori Isolates From Patients With Gastroduodenal Diseases: A Cross-Sectional Study

Background Helicobacter pylori is an important gastric pathogen linked to several upper gastrointestinal (UGI) conditions, including gastritis, peptic ulcer disease, and gastric cancers. Its ability to cause disease is largely driven by major virulence factors, such as the cytotoxin-associated gene A (cagA) and the vacuolating cytotoxin gene (vacA). This study aimed to determine the prevalence of H. pylori among patients presenting with UGI symptoms using both phenotypic and molecular methods, and to identify the presence of cagA and vacA genes in the isolates. Materials and methods Patients with symptomatic GI complaints who underwent UGI endoscopy were enrolled. Four gastric biopsy specimens were collected from each patient in brain-heart infusion medium and sent from the medical gastroenterology division for microbiological and molecular testing. Identification of H. pylori was performed using standard culture techniques with Skirrow Campylobacter medium and growth supplements. Molecular detection was carried out using polymerase chain reaction (PCR). DNA was extracted using Amp Ready reagent and stored at -20°C until analysis. Data were collected using a structured proforma and analyzed with Epi Info version 7.3.2 (Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA). Categorical variables were summarized as percentages with 95% confidence intervals (CI). Associations were assessed using the chi-square test or Fisher’s exact test, with p ≤ 0.05 considered statistically significant. Results Among the 250 gastric biopsy samples processed, H. pylori grew on culture in 38 samples (15.2%). PCR targeting the ureB gene detected H. pylori DNA in 36 samples (14.4%). Of these PCR-positive isolates, 30 (83.3%) carried both the cagA and vacA virulence genes. Genotyping showed that the vacA s1 and m1 alleles frequently coexisted, with the s1m1 genotype being the most common and associated with higher virulence. Conclusion PCR-based testing proved more sensitive and efficient for detecting H. pylori and its key virulence markers compared to conventional culture methods. Incorporating molecular techniques into routine diagnostic workflows may facilitate earlier and more accurate identification of high-risk strains.