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To study the epidemiology and pathogenicity of mixed infection of Helicobacter pylori (H. pylori) strains with multiple vacA m-region subtypes and/or iceA mixed genotype among the Bai, Naxi, and Han populations in Yunnan province.Gastric mucous membrane were obtained by gastroscopy from 444 patients with digestive ulcer or chronic gastritis, 165 of Han nationality, 117 of Bai nationality, and 162 of Naxi nationality. H. pylori was isolated from 109 patients and cultured. RT-PCR was used to detect the Helicobacter pylori strains vacA gene subtype and iceA genes.The overall rates of vacA gene s1 type and vacA gene s2 type were 98.2% (107/109) and 1.8% (2/109) respectively. The overall rates of vacA gene m2 type, vacA gene m1a type, vacA gene m1b type, and mixed types were 45.9% (50/109), 0.9% (1.109), 23.9% (26/109), and 11% (12/109) respectively; and m region was not identified in 18.3% (20/109) of the strains. The overall rates of iceA1 and iceA2 genes were 67.0% (73/109) and 41.3% (45/109) respectively. In the specimens from the patients of Bai nationality, as regards the s region, only s1 type was identified in all specimens; the rates of vacA gene m2 type, vacA gene m1a type, vacA gene m1b type, and mixed type were 45.2% (14/31), 3.2% (1/31), 12.9% (4/31), and 16.2% (5/31) respectively, and m region was not identified in 22.6% of the strains; and the rates of iceA1 and iceA2 were 87.1% (27/31) and 61.3% (19/31) respectively. In the specimens from the patients of Naxi nationally, The rates of vacA gene s1 type and s2 type were 95.6% (43/45) and 4.4% (2/45), the rates of vacA gene m2 type, vacA gene m1b type, and mixed m-type were 33.3% (15/45), 37.8% (17/45), and 6.7% (3/45) respectively, no m1a type was found, and m region was not identified in 22.2% of the strains; the rates of iceA1 and iceA2 were 48.9% (22/45) and 31.1% (14/45) respectively. In the specimens of the patients of Han nationality, as regards the s region, all specimens were s1 type; the rates of vacA gene m2 type, vacA gene m1b type, and mixed type were 63.6% (21/33), 15.2% (5/33), and 12.1% (4/33) respectively, and m region was not identified in 9.1% (3/33) of the strains; the rates of iceA1 and iceA2 were 72.7% (24/33) and 36.4% (12/33) respectively. 34 of the 109 patients (31.2%) suffered from mixed infection of vacA gene m mixed subtype and/or iceA mixed genotype, 64.7% of which (22/34) suffering iceA1 + iceA2 infection, 23.5% of which (8/34) being iceA + vacA mixed infection, and 11.8% of which (4/34) being vacA subtype mixed infection, with the former incidence of the former group significantly higher than those of the 2 latter groups (both P0.001). The mixed infection rate of the Bai nationality (67.7%, 21/31) was significantly higher than those of the Naxi nationality (20.0%, 9/45, P0.001) and Han nationality (12.1%, 4/33, P0.001) without a significant difference between the Naxi and Han nationalities (P0.05). The mixed infection rate of iceA1 + iceA2 of the Bai nationality (61.3%, 19/31) was significantly higher than those of the Naxi nationality (17.8%, 8/45, P0.001) and Han nationality (9.1%, 3/33, P0.001) without a significant difference between the Naxi and Han nationalities (P0.05). The mixed rate of the patients with digestive ulcer was 30.2% (16/53), not significantly different from that of the patients with chronic gastritis (32.1%, 18/56, P0.05). 16 of the 34 cases of mixed infection were patients of digestive ulcer; and 8 of the 34 cases were patients with chronic gastritis. 8 of the 34 cases (23.5%) of mixed infection were cases of infection of vacA gene m mixed subtypes and iceA mixed genotype; among which 7 were patients with digestive ulcer and 1 case was patient of chronic gastritis. Thus the rate of vacA gene m mixed subtypes and iceA mixed genotype was 43.8% (7/16) in the patients with digestive ulcer, significantly higher than in the patient with chronic gastritis (5.6%, 1/18, P = 0.014). 22 of the 34 cases of mixed infection (64.7%) suffered from infection of iceA mixed gene subtypes. Among these 22 cases 15 were patients with chronic gastritis and 7 were patients with digestive ulcer. Thus the rate of iceA mixed subtypes infection was 43.8% (7/16) in the patients with digestive ulcer, significantly lower than in the patient with chronic gastritis (83.3%, 15/18, P = 0.016). In the 21 mixed infection patients of Bai nationality, the rate of vacA gene mixed sybtype + iceA gene mixed subtypes infection was 100% in the patients with digestive ulcer (100%, 5/5), significantly higher than that of single vacA gene subtype + iceA gene mixed subtypes (37.5%, 6/16, P = 0.0258). The mixed infection rate of H. pylori strains was 32.1%.The mixed infection rate of the Bai nationality is higher than those of the Han and Naxi nationalities. Detection of mixed infection by vacA genotypes is more sensitive in Han populations. Detection of multiple infections by iceA gene mixed subtypes is more sensitive in Bai and Naxi populations.