BackgroundThe most prevalent stomach infection in the world is caused byHelicobacter pylori(H. pylori). Several pathogenicity genes, includingcagA, vacA, babA2, dupA, iceA,andoipA, are associated with an increased risk of gastrointestinal disease such as peptic ulcer and stomach cancer. This research aims to determine the prevalence of differentH. pylorigenotypes and correlate their risk in the development of gastrointestinal diseases in the Ecuadorian population.MethodsA cross-sectional research of 225 patients at the Calderón Hospital in Quito, Ecuador, was conducted. End point PCRs were run to determine the presence of16S rRNA, cagA, vacA (m1), vacA (s1), babA2, dupA, iceA1, and oipAvirulence genes. Chi-square test, odds ratios (OR) and 95% confidence intervals (CI) were utilized for the statistical analysis.ResultsH. pyloriinfection was present in 62.7% of people. Peptic ulcers were seen in 22.2% and malignant lesions in 3.6% of patients. GenesoipA(93.6%),vacA (s1)(70.9%), andbabA2(70.2%) were the most prevalent.cagA/vacA (s1m1)andcagA/oipA (s1m1)combinations were found in 31.2% and 22.7% of the cases, respectively. Acute inflammation has a significant correlation with the genescagA(OR = 4.96 95% CI: 1.1–22.41),babA2(OR = 2.78 95% CI: 1.06–7.3), and thecagA/oipAcombination (OR = 4.78, 95% CI: 1.06–21.62). Follicular hyperplasia was associated withiceA1(OR = 3.13; 95% CI: 1.2–8.16),babA2(OR = 2.56; 95% CI: 1.14–5.77),cagA(OR = 2.19; 95% CI: 1.06–4.52), and thecagA/oipAcombination (OR = 2.32, 95% CI: 1.12–4.84). ThevacA (m1)andvacA (s1m1)genes were associated with gastric intestinal metaplasia (OR = 2.71 95% CI: 1.17–6.29) (OR = 2.33 95% CI: 1.03–5.24). Finally, we showed thatcagA/vacA (s1m1)gene combination increased the risk of duodenal ulcer development (OR = 2.89, 95% CI 1.10–7.58).ConclusionThis study makes a significant contribution by offering genotypic information regardingH. pyloriinfection. The presence of severalH. pylorigenes was associated with the onset of gastrointestinal illness in the Ecuadorian population.