Geographical variation in the frequency of various gastroduodenal pathologies was shown to be related to the geographical diversity of H. pylori CagA Glu-Pro-Ile-Tyr-Ala (EPIYA) patterns. We examined the EPIYA patterns of H. pylori and the association of EPIYA patterns with gastric cancer (GC) for the first time, to the best of our knowledge, in Turkey. The patient group (PG) contained 60 patients [38 GC and 22 duodenal ulcer (DU) patients]. The control group (CG) was 110 individuals [94 gastritis patients and 16 persons with a normal gastrointestinal system (NGIS)]. Specific primers were used for the detection of cagA including empty-site-positive and EPIYA-A, -B, -C, -D PCR. Bands of EPIYA-A, -B, -C were confirmed by DNA sequencing. One hundred and forty-two (83.5 %) strains [60 in the PG (38 GC, 22 DU), 82 in the CG (72 gastritis, 10 NGIS)] were positive for the cagA gene. EPIYA-C with multiple repeats was detected in 34 (23.9 %) strains, and 22 (64.7 %) were from GC patients. EPIYA-C with one repeat was detected in 89 (62.7 %) strains, and 54 (60.7 %) were from gastritis patients. EPIYT was detected in 10 strains, and EPIYA-D was not detected. The number of EPIYA-C with multiple repeats was significantly higher for the PG than for the CG (P,0.0001). In GC patients, the number of EPIYA-C with multiple repeats was significantly higher than one repeat (P,0.0001). In conclusion, our study showed that multiple EPIYA-C repeats increases the GC risk by 30.6-fold and the DU risk by 8.9-fold versus the CG. This indicates that Western-type H. pylori strains in Turkey have similar EPIYA motifs to those of neighbouring countries and Western populations. INTRODUCTIONHelicobacter pylori is the principal cause of gastritis and gastric or duodenal ulcer (DU) diseases and is involved in the development of gastric cancer (GC) and mucosaassociated lymphoid tissue lymphoma (Atherton, 2006).H. pylori is a class 1 carcinogen identified by the International Agency for Research on Cancer for chronic and persistent infections. It is resistant to antibacterial agents in spite of innate and adaptive immunity (International Agency for Research on Cancer, 1994). Depending on virulence factors such as cytotoxin-associated gene A (CagA), blood group antigen-binding adhesion (BabA2) and vacuolating cytotoxin gene A (VacA), different genotypes cause different pathological and clinical outcomes and geographical regional differences (Atherton et al., 1995;Basso et al., 2008). Recently, the Glu-Pro-Ile-Tyr-Ala (EPIYA)Abbreviations: cagPAI, cag pathogenicity island; CG, control group; CI, confidence interval; DU, duodenal ulcer; EPIYA, Glu-Pro-Ile-Tyr-Ala; CagA, cytotoxin-associated gene A; GC, gastric cancer; NGIS, normal gastrointestinal system; PG, patient group; OR, odds ratio. pattern of CagA was suggested to be involved in the pathogenesis of GC, as this pattern manifests important variations depending on the region (Argent et al., 2004(Argent et al., , 2005.The CagA protein is injected into host epithelial cells with its peptidoglycan b...

RT-qPCR targeting the 85B gene of M. tuberculosis seems to be a more useful and rapid technique than DNA-based methods for detecting live M. tuberculosis bacilli from sputum specimens.

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Background/Aims: Helicobacter pylori (H. pylori) is a microaerophilic bacterium related with peptic ulcer and gastric cancer. Its virulence factors include cytotoxin-associated gene A (CagA) and vacuolating cytotoxin gene A (VacA) proteins. Cytokine release inducted by H. pylori colonization has an important role in pathogenesis of H. pylori. The severity of gastric pathologies depends on the H. pylori genotypes found in different geographical regions. We aimed to determine the relationship between different H. pylori genotypes and their effects on the cytokine release levels. Materials and Methods: ureC, cagA, vacAs1/s2, vacAm1/m2, and blood group antigen-binding adhesion protein A2 (babA2) virulence related genes were investigated in 21 H. pylori strains. Genotyping of 21 strains were made due to the presence of cagA, vacAs1/s2, vacAm1/m2, and babA2 genes. The H. pylori strains were cultured together with THP-1 and neutrophil-differentiated Human promyelocytic leukemia cells (HL-60) cells. The levels of cytokines interleukin (IL)-1β, IL-6, IL-8, IL-12, tumor necrosis factor-alpha (TNF-α), and IL-10 in these cells were measured after co-culturing with H. pylori strains. Results: The following five different genotypes were detected: Genotype1: cagA and vacAs1m2; Genotype2: cagA and vacAs1m1; Genotype3: cagA, vacAs1m2, and babA2; Genotype4: vacAs2m2; and Genotype5: cagA and vacAs2m2. All these genotypes significantly induced the levels of IL-1β, IL-6, IL-8, IL 10, and TNF-α in THP-1 cells. Genotype 5 caused higher amounts of IL-1β, IL-6, TNF-α, and IL-10, whereas genotype 1 induced the highest levels of IL-8. In neutrophil-differentiated HL-60 cells, genotype 4 increased IL-6 levels and genotype 3 and 4 elevated IL-8 levels significantly. Conclusion: These results suggested that cytokine response of the host varies depending on the specific immune response of the host against different H. pylori strains.

Opportunistic infections such as cryptosporidiosis and cyclosporiasis are commonly encountered in patients with acquired immunodeficiency syndrome (AIDS). We investigated the existence of opportunistic protozoans that significantly affect the quality of life in HIV-1 infected patients using conventional and molecular methods. The study group comprised 115 HIV-1 positive patients. In the identification of Cyclospora cayetanensis and Cryptosporidium, the formol-ether precipitation method was used and smears were evaluated in optical microscope by staining modified Ziehl-Neelsen (ZN). The primers and probes used for PCR were Heat shock protein 70 for C. cayetanensis and the oocysts wall protein for Cryptosporidium spp.. Cyclospora and Cryptosporidium spp. oocysts were detected in one and two patients, respectively, by staining, whereas we detected C. cayetanensis in three patients out of 115 (2.6%) by PCR, and Cryptosporidium spp. in a further three patients (2.6%). C. cayetensis was detected in patients with CD4 counts of 64 cells/μm, 182 cells/μm and 287 cells/μm, respectively. Cryptosporidium spp. was detected in patients with CD4 counts of 176 cells/μm, 241 cells/μm and 669 cells/μm. As conclusion, PCR method is faster and more sensitive than microscopic methods and to screen intestinal pathogens routinely in patients infected with HIV should not be neglected in developing countries like Turkey.