The Role of Akkermansia muciniphila and Faecalibacterium prausnitzii in the Pathogenesis of Ulcerative Colitis and Crohn's Disease.

BACKGROUND: Crohn's disease (CD) and ulcerative colitis (UC) are inflammatory bowel diseases with uncertain etiology. We aimed to determine the amounts of Akkermansia muciniphila and Faecalibacterium prausnitzii in the intestinal microbiota of these patients and to correlate their amounts with blood IL-8, IL-10, and IL-12 cytokine levels. METHODS: Thirty UC, 30 CDs, and 46 healthy controls were included. IL-8, IL-10, and IL-12 levels of blood samples were analyzed by ELISA. The amounts of Akkermansia muciniphila and Faecalibacterium prausnitzii were determined by the LightCycler 480 qPCR system. RESULTS: F. prausnitzii, A. muciniphila, IL-10, and IL-12 decreased in patient groups, while IL-8 decreased in UC but increased in CD. A significant difference was detected between the patient and control groups in terms of F. prausnitzii, A. muciniphila, and IL-8, but not for others. The amount of F. prausnitzii was correlated with IL-8 and IL-10 in UC and with IL-10 in CD patients. CONCLUSIONS: The decrease in the amount of F. prausnitzii was associated with the increase in UC disease severity. A. muciniphila and F. prausnitzii were detected in lower amounts in both diseases. F. prausnitzii decreased more with the severity of UC, suggesting that these bacteria may have complex roles in their etiopathogenesis.

The Relationship between Gastroduodenal Pathologies and Helicobacter pylori cagL (Cytotoxin-Associated Gene L) Polymorphism.

BACKGROUND: The polymorphisms in the region between 58 and 62 amino acids of the 194-amino acid CagL protein (CagL hypervariable motif) affect the binding affinity of CagL to integrin α5ß1 (ITGA5B1) receptor in host epithelial cells and have an effect on the development of various gastrointestinal diseases. We aimed to evaluate the associations of gastroduodenal pathologies, with the polymorphisms of cagL gene of Helicobacter pylori (H. pylori) and also associations between vacA genotypes and cagL polymorphisms. METHODS: A total of 19 gastric cancer, 16 duodenal ulcer, and 26 non-ulcer dyspepsia patients were included in this case-control study. All cases had H. pylori. A fragment of 651 bp from gene cagL (hp0539) and cagA, vacA genes was amplified by polymerase chain reaction. Purified polymerase chain reaction products were sequenced by Sanger sequencing, and nucleotide sequences were translated into amino acid sequences. RESULTS: All of the H. pylori strains had cagL and cagA genes. In the 16 (84%) gastric cancer cases, the D58 amino acid polymorphism was significant than the 4 (15.4%) duodenal ulcer cases (P = .029), and the D58/K59 amino acid polymorphism was significant in 12 (63.1%) of the gastric cancer cases than 1 (3.85%) duodenal ulcer case (P = .008). D58/K59 and DKIGQ (n = 10; 52.63%) were the most common polymorphisms in the gastric cancer and were associated with the vacA genotype s1/m2, respectively (P = .022 and P = .008). The D58/K59 amino acid polymorphism was found to have a significant Odds Ratio (OR) value of 8.9 (P = .0017) in multivariate logistic regression analysis. CONCLUSIONS: The risk of gastric cancer development is 8.9 times higher with D58/K59 polymorphism.

Investigation of Obesity-Related HAdV-36 in NAFLD Patients: a Case-Control Study.

BACKGROUND: HAdV-36 leads to adipocyte proliferation of adipose tissue through E4orf1 gene, leading to the development of obesity and related diseases. We aimed to investigate the presence and any association of HAdV-36 in non-alcoholic fatty liver disease (NAFLD) patients Methods: The patient group was composed of 116 patients; 30 obese patients with NAFLD (BMI > 30 kg/m2), 30 patients with Diabetes Mellitus (DM)+NAFLD (BMI > 30 kg/m2), 16 patients with NAFLD (BMI < 30 kg/m2), and operated obese group with NAFLD (BMI > 30 kg/m2). The control group comprised 81 non-obese healthy adults. Liver adipose tissue samples were obtained in 30 operated NAFLD patients. HAdV-36-DNA, HAdV-36 neutralizing antibodies, serum lipid, and adipokine levels were analyzed. RESULTS: HAdV-36 neutralizing antibodies (HAdV-36 Ab-positive) were detected in 10/116 and 2/81 participants in the study and control groups, respectively; the difference was statistically significant (p < 0.005). LDL, total cholesterol but not adipokine levels were found to be significantly higher in HadV-36 Ab-positive patients (p < 0.05). While HAdV-36 was identified as a risk factor with OR = 4.11 in univariate analyses, there was no significant difference in binary logistic regression analysis. HAdV-36-DNA was detected in the adipose tissue samples of two patients. CONCLUSIONS: We suggest that the presence of HAdV-36 may lead to the development of obesity with the increase in adipose tissue, and diseases such as hyperlipidemia, NAFLD, DM, and metabolic syndrome may develop on the basis of chronic inflammation caused by obesity. Thus, HAdV-36 may be a plausible risk factor for the development of NAFLD.

Humoral and Cellular Immunity to Severe Acute Respiratory Syndrome Coronavirus-2 Vaccination in Patients with Sarcoidosis

Background: The coronavirus disease 2019 vaccine induces both antibody and T-cell immune responses and has been proven to be effective in preventing coronavirus disease 2019, including its severe disease form, in healthy individuals. However, the details of severe acute respiratory syndrome coronavirus-2 immunoglobulin-G antibody responses and severe acute respiratory syndrome coronavirus-2 specific T-cell responses in patients with sarcoidosis are unknown. Aim: To measure and compare antibody responses and T cell responses using enzyme-linked immunosorbent assays and interferon-gamma release assay in sarcoidosis patients infected with coronavirus disease 2019 and vaccinated with CoronaVac. Study Design: A prospective cohort study. Methods: A total of 28 coronavirus disease 2019 polymerase chain reaction test-positive sarcoidosis patients who were infected with severe acute respiratory syndrome coronavirus-2 in the past 6 months and did not have coronavirus disease 2019 vaccination and 28 sarcoidosis patients who were administered with 2 doses of CoronaVac and never had coronavirus disease 2019 were included in this study. The immune response levels of patients were determined by measuring the severe acute respiratory syndrome coronavirus-2 immunglobulinG and interferon-gamma levels in the blood of the patients by the enzyme-linked immunosorbent assays method and interferon-gamma release assay tests, respectively. Results: The mean age of the patients in the COVID-infected group was 48.1 ± 11.3, while the mean age of the patients in the vaccinated group was 55.6 ± 9.32. The mean time elapsed after infection was 97.32 ± 42.1 days, while 61.3 ± 28.7 days had passed since the second vaccination dose. In the COVID-infected group, immunoglobulin-G and interferon-gamma release tests were positive in 64.3% and 89.3% of the patients, respectively. In the vaccinated group, immunoglobulin-G was positive in 10.7% of the patients, and interferon-gamma release test was positive in 14.3%. Conclusion: Innate immune responses are better than adaptive immune responses in patients with sarcoidosis. The coronaVac vaccine is insufficient to generate humoral and cellular immunities in patients with sarcoidosis.

The Role of Adenovirus-36 in Adults with Obesity-Induced Type 2 Diabetes.

BACKGROUND: Obesity may also develop due to a viral infection caused by adenovirus 36. We aimed to detect the presence of neutralizing antibodies against Ad-36 in adult patients who developed type 2 diabetes due to obesity (BMI ≥ 30 kg/m2). METHODS: The patient group (PG) was composed of 80 obese people with type 2 diabetes, the patient control group (PCG) was composed of 40 non-obese people with type 2 diabetes, and the healthy control group (HCG) was com-posed of 40 non-obese people without type 1 or type 2 diabetes in this case-control study. The presence of Ad-36 neutralizing antibodies was studied by serum neutralization assay. RESULTS: A significant difference was found between the PG and HCG in terms of Ad-36 antibody positivity (p < 0.0001) but no significant difference was detected between the PG and the PCG (p > 0.05). BMI, serum leptin, adiponectin, and triglyceride levels were significantly higher in the PG (p < 0.05). Conversely, TNF-α and IL-6 levels were significantly lower in the PG (p < 0.0001). When the two groups were compared, the mean levels of total cho-lesterol and LDL in the PG were found to be high, although not significant (p > 0.05). In type 2 diabetes patients (n = 120), age, BMI, HDL, LDL, triglyceride, total cholesterol, Ad-36 presence, leptin, adiponectin, TNF-α, and IL-6 parameters were taken as independent variables for logistic regression. While BMIs was found to be significant (odds ration [OR] = 2.358; p = 0.0001, 95% Cl 1.507 - 3.690, Ad-36 presence was found to be a significant (OR = 27.352; p = 0.003, 95% Cl 3.157 - 236.961). Our study showed that BMI and Ad-36 increase type 2 diabetes risk by 2.3 and 27.3-fold in the PG and PCG (type 2 diabetes patients) versus the HCG. There was also a significant difference between PCG and HCG. CONCLUSIONS: We suggest that Ad-36 seropositivity is also a risk factor for the development of type 2 diabetes independent of being obese.

Comparison of SARS-CoV-2 Antibody Levels after a Third Heterologous and Homologous BNT162b2 Booster Dose.

This study aimed to determine the anti-S (receptor binding protein) RBD IgG antibody titers formed against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) and the neutralizing antibody inhibition percentages (nAb IH%) in blood samples taken after two doses of inactive or mRNA-based vaccine and a booster dose. Volunteers with two doses of inactivated CoronaVac (heterologous group; n = 75) and BioNTech (BNT)162b2 mRNA vaccine (homologous group; n = 75) were included in this study. All participants preferred the BNT162b2 vaccine as a booster dose. First, peripheral blood samples were taken 3 months after the second vaccine dose. Second, peripheral blood samples were taken 1 month after the booster dose. Anti-S-RBD IgG titers were determined by CMIA (SARS-CoV-2 IgG II Quant). Neutralizing antibodies were detected by a surrogate neutralization assay (SARS-CoV-2 NeutraLISA, Euroimmun, Lübeck, Germany). The median age of the volunteers was 40 (IQR 29-47) years old. After the heterologous booster dose, anti-S-RBD IgG levels and neutralizing antibodies increased approximately 50-fold and 9-fold, respectively. Anti-S-RBD IgG titers increased by 9 and 57 times, respectively, while nAb IH% increased by 1.5 and 16 times, respectively, among those with heterologous reminder doses and those with and without a prior history of coronavirus disease (COVID-19). This study showed that after the administration of a heterologous booster dose with BNT162b2 to those whose primary vaccination was with inactivated CoronaVac, the binding and neutralizing antibody levels were similar to those who received a homologous BNT162b2 booster dose. It was observed that the administration of heterologous and homologous booster doses resulted in the development of similar levels of neutralizing antibodies, independently from a prior history of COVID-19.

Association of SARS-CoV-2 IgG Antibody Levels with Clinical/Laboratory Characteristics in COVID-19 Patients: Data from a Turkish Study.

BACKGROUND: COVID-19 causes clinical manifestations ranging from asymptomatic infection to multi-organ failure. It is reported that those with severe disease have higher anti-SARS-CoV-2 antibody titers compared to asymptomatic or mild cases. We evaluated the correlation of antibody responses with laboratory and clinical indicators in COVID-19 patients. METHODS: Seventy-nine male and 66 female patients (mean age: 39) with at least one positive SARS-CoV-2 RT-PCR test and SARS-CoV-2 IgG antibody result after acute infection were included. RESULTS: Seventy-six (52%), 45 (31%), and 24 (17%) patients had mild, moderate, and severe clinical findings, respectively. Patients with high body mass index and advanced age had significantly more severe disease (p < 0.001). A significant correlation was found between the increase in lymphopenia, C-reactive protein, ferritin, D-dimer, and lactate dehydrogenase and the severity of clinical findings (p = 0.0001). SARS-CoV-2 IgG antibody test was positive in 128 (88.3%) patients. A significant correlation was found between disease severity and antibody levels in the comparison of all groups (p < 0.001). CONCLUSIONS: Long-term monitoring of immune responses will be required to determine the appropriate time for the administration of new vaccines.

Anti-SARS-CoV-2 IgG and Neutralizing Antibody Levels in Patients with Past COVID-19 Infection: A Longitudinal Study

Background: Monitoring the longevity of immunoglobulin G (IgG) responses following severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections is vital to understanding the role of antibodies in preventing infection. Aims: To determine the quantitative IgG responses specific to the Spike-S1 (S1) receptor-binding domain (S1/RBD) region of the virus in serum samples taken between 4 weeks and 7 months after polymerase chain reaction (PCR) positivity in patients who are diagnosed with coronavirus disease-2019 (COVID-19). Study Design: A longitudinal study. Methods: This study included 113 patients with a clinical and molecular diagnosis of COVID-19. The first and second serum samples were taken 1 and 7 months, respectively, after the PCR positivity. S1/RBD-specific IgG antibody response was assayed using anti-SARS-CoV- 2 QuantiVac ELISA (IgG) kit (Euroimmun, Lübeck, Germany). The neutralizing antibodies were investigated in 57 patients whose IgG test results were above the cut-off value. Results: In 57 patients with SARS-CoV-2 IgG, the anti-SARS-CoV-2 IgG quantitative antibody levels significantly decreased after 7 months (Z = −2.197, p = 0.028). A correlation was detected between the anti-SARS-CoV-2 IgG and nAb percent inhibition (IH%) levels detected in 1 month (rs = 0.496, p < 0.001), but without significant correlation in serum samples taken on 7 months. The nAb IH% levels of the first and second were compared for COVID-19 severity and revealed no statistical difference (p = 0.256). In the second serum sample, the nAb IH%s of patients with moderate COVID-19 showed a statistically significant difference from patients with mild COVID-19 (p = 0.018), but without significant differences between severe and moderate or mild COVID-19. Conclusion: SARS-CoV-2 quantitative IgG antibody titers are significantly reduced at long-term follow-up (> 6 months). Due to the limited information on seroconversion, comprehensive studies should be conducted for long-term follow-up of the immune response against SARS-CoV-2.

Epstein-Barr Virus and Helicobacter pylori co-infection in patients with gastric cancer and duodenale ulcer.

We aimed to detect EBV/Hp (Epstein-Barr Virus/Helicobacter pylori) co-infection by determining the number of copies of EBV/EBER-1 in the gastric biopsy samples of the Hp (+) GC, peptic ulcer (PU), and non-ulcer dyspepsia (NUD) cases. The patient group (PG), with 34 patients (34 GC and 30 PU patients) and a control group with 40 NUD cases were included. All patients and controls were Hp positive. EBV/EBNA-1 IgG were measured by the Anti-EBNA-1 ELISA IgG kit. Determination and quantification of EBV/EBER-1 gene region was performed by qPCR. EBV/EBER-1 positivity was 35.29% (12/34), 6.6% (2/30) and 2.5% (1/40) in GC, PU and 40 NUD cases, respectively. A significant difference was found between the GC and NUD cases (p=0.001). A significant difference was found between the groups for mean EBV/EBER-1 copy numbers (p=0.019). No significant difference was found between GC and the NUD cases (p=0.1455) for EBV/EBNA-1 IgG antibody positivity. EBV/EBER-1 positivity (OR=3.319), and age ≥55 years old (OR=2.331) were found to be a significant in multivariate logistic regression. In conclusion, our data suggest that the GC risk by EBVand Hp co-infection increased 3.3 times.

Point Mutations at gyrA and gyrB Genes of Levofloxacin Resistant Helicobacter pylori Strains and Dual Resistance with Clarithromycin.

BACKGROUND: Spontaneous point mutations in genes encoding gyrA/B subunits of DNA gyrase are responsible for fluoroquinolone resistance. We aimed to determine the clarithromycin and levofloxacin resistance phenotypically in H. pylori strains and to investigate the mutations responsible for levofloxacin resistance and the effects of these mutations on dual antibiotic resistance. METHODS: A total of 65 H. pylori isolates were included. The E-test method was used for the clarithromycin and le-vofloxacin antimicrobial susceptibility test. Real-time PCR was used to detect the point mutations. RESULTS: Twenty-four (36.9%) of 65 H. pylori strains were phenotypically resistant to clarithromycin and 14 (21.5%) to levofloxacin. The phenotypic levofloxacin resistance rate of strains with Asn87Lys and Asp91Asn mutations were significantly higher (gyrA gene) (p < 0.05). The phenotypic levofloxacin resistance rate of strains with Arg484Lys and Asp481Glu mutations were significantly higher (gyrB gene) (p < 0.05). The Asn87Lys mutation increased the risk of phenotypes being resistant to levofloxacin 70.156 times and Asp91Asn mutation increased 125,427 times higher. Seven (10.8%) of 65 H. pylori strains showed dual resistance to both levofloxacin and clarithromycin. The rate of being dual resistant with A2143G mutation (clarithromycin resistance) was found to be significantly higher (p < 0.05). CONCLUSIONS: The Asn87Lys and Asp91Asn mutations in the gyrA gene had a phenotypically enhancing effect on levofloxacin resistance, while the presence of Asp481Glu and Arg484Lys mutations in the gyrB gene did not. The existence of dual resistance was developed with the increase in clarithromycin and levofloxacin resistance rates.

Association between human leukocyte antigen gene polymorphisms and multiple EPIYA-C repeats in gastrointestinal disorders.

BACKGROUND: Polymorphisms of human leukocyte antigen (HLA) genes are suggested to increase the risk of gastric cancer (GC). AIM: To investigate the HLA allele frequencies of patients with GC relative to a control group in terms of CagA+ multiple (≥ 2) EPIYA-C repeats. METHODS: The patient group comprised 94 patients [44 GC and 50 duodenal ulcer (DU) patients], and the control group comprised 86 individuals [(50 non-ulcer dyspepsia patients and 36 people with asymptomatic Helicobacter pylori (H. pylori)]. Polymerase chain reaction was performed for the amplification of the H. pylori cagA gene and typing of EPIYA motifs. HLA sequence-specific oligonucleotide (SSO) typing was performed using Lifecodes SSO typing kits (HLA-A, HLA-B HLA-C, HLA-DRB1, and HLA-DQA1-B1 kits). RESULTS: The comparison of GC cases in terms of CagA+ multiple (≥ 2) EPIYA-C repeats showed that only the HLA-DQB1*06 allele [odds ratio (OR): 0.37, P = 0.036] was significantly lower, but significance was lost after correction (Pc = 0.1845). The HLA-DQA1*01 allele had a high ratio in GC cases with multiple EPIYA-C repeats, but this was not significant in the univariate analysis. We compared allele frequencies in the DU cases alone and in GC and DU cases together using the same criterion, and none of the HLA alleles were significantly associated with GC or DU. Also, none of the alleles were detected as independent risk factors after the multivariate analysis. On the other hand, in a multivariate logistic regression with no discriminative criterion, HLA-DQA1*01 (OR = 1.848), HLA-DQB1*06 (OR = 1.821) and HLA-A*02 (OR = 1.579) alleles were detected as independent risk factors for GC and DU. CONCLUSION: None of the HLA alleles were detected as independent risk factors in terms of CagA+ multiple EPIYA-C repeats. However, HLA-DQA1*01, HLA-DQB1*0601, and HLA-A*2 were independent risk factors with no criterion in the multivariate analysis. We suggest that the association of these alleles with gastric malignancies is not specifically related to cagA and multiple EPIYA C repeats.

Evaluating the effectiveness of anti-tuberculosis treatment by detecting Mycobacterium tuberculosis 85B messenger RNA expression in sputum.

BACKGROUND: The antigen 85 complex (85B) is secreted in large quantities from growing mycobacteria and the presence of bacterial mRNA is an indicator of cell viability. The quantitative detection of 85B mRNA expression levels can be used to assess the success of anti-tuberculosis treatment outcomes to detect viable mycobacteria cells. Therefore, we evaluated the levels of 85B mRNA of Mycobacterium tuberculosis strains in patients with pulmonary tuberculosis. METHODS: Thirty patients with primary tuberculosis were included in this study. The sputum specimens of patients were collected on days 0, 15, and 30 days and were cultured and evaluated by 85B mRNA-based RT-qPCR. RESULTS: Overall, 23 of the studied tuberculosis strains were susceptible to the primary anti-tuberculosis antibiotics used in this study, 7 were resistant. By the 30th day of treatment, 85B mRNA was detected in only one of the susceptible strains, but in all 7 of the resistant strains, though the relative gene expression varied between the strains. This difference between the susceptible and resistant strains at day 30 was statistically significant (p < 0.05). CONCLUSION: 85B mRNA expression levels could be used to follow up on primary tuberculosis cases. 85B mRNA seems to be a good diagnostic marker for monitoring anti-tuberculosis treatment outcomes.

The Prevalence of Periodontal Pathogenic Bacteria in Atherosclerotic Cardiovascular Disease.

BACKGROUND: A possible link between periodontal pathogenic bacteria and atherosclerosis may exist based on the inflammatory mechanisms initiated by bacteria found in periodontal lesions. Our aim was to investigate the presence of DNA originating from T. denticola, C. rectus, T. forsythia, and P. gingivalis in the vascular tissue specimens obtained from patients who underwent surgery for arteriosclerotic vascular disease in this study. METHODS: A total of 96 patients diagnosed with valvular heart disease due to atherosclerosis and 85 patients with advanced aortic valve stenosis due to rheumatic fever and had undergone aortic valve replacement were included as the study (PG) and the control groups (CG), respectively. Atheroma plaques and vascular tissue specimens were collected from PG and CG during cardiovascular surgical procedures. Revitalization of the lyophilized T. denticola, ATCC 35405; C. rectus, ATCC 33238; P. gingivalis, ATCC 33277 and T. forsythia, ATCC 43037 strains was performed according to the manufacturer's instructions. C. rectus, T. forsythia, and T. denticola DNA samples were analyzed using the one-step in-house PCR method. RESULTS: In one (1.04%) and three (3.13%) out of 96 atherosclerotic PG tissue specimens, P. gingivalis and T. for-sythia DNA were detected, respectively. No T. denticola or C. rectus DNA was found in the study specimens. Periodontal pathogenic bacteria were not observed in 85 CG tissue specimens. There was no statistically significant difference between PG and CG for the presence of P. gingivalis and T. forsythia DNA using Fischer's Exact test (p > 0.05). CONCLUSIONS: In conclusion, with the case-control studies on a small scale such as in our study, it is not possible to determine a causality relationship between periodontal pathogenic bacteria and formation of atherosclerosis. Periodontal pathogenic bacteria may not be the only factor that causes inflammatory diseases associated with atherosclerosis. Host response and inflammatory mechanisms may be affected by other factors such as ethnicity, dietary habits, nutritional availability, and lifestyle. Taken together, it is difficult to conclude a causal link between periodontal pathogenic bacteria and formation of atherosclerosis.

Association between polymorphisms in HLA-A, HLA-B, HLA-DR, and DQ genes from gastric cancer and duodenal ulcer patients and cagL among cagA-positive Helicobacter pylori strains: The first study in a Turkish population.

Colonization of the human gastric mucosa by H. pylori may cause peptic and duodenal ulcers (DUs), gastric lymphomas, and gastric cancers. The cagL gene is a component of cag T4SS and is involved in cagA translocation into host. An association between the risk of gastric cancer and the type of HLA class II (DR and/or DQ) was suggested in different populations. The aim of this study was to investigate, the clinical association of the cagL gene with host HLA alleles in H. pylori strains that were isolated from patients with gastric cancer, DU, and non-ulcer dyspepsia (NUD) and to determine the HLA allele that confers susceptibility or resistance for the risk of gastric cancer and DU development in Turkish patients. A total of 94 patients (44 gastric cancer and 50 DU patients; 58 male, 36 female; mean age, 49.6 years), and 86 individuals (50 NUD patients and 36 persons with normal gastrointestinal system [NGIS]; 30 male, 56 female; mean age, 47.3 years) were included as the patient and the control groups, respectively. CagA and cagL were determined by PCR method. DNA from peripheral blood samples was obtained by EZ-DNA extraction kit. For HLA SSO typing, LIFECODES SSO Typing kits (HLA-A, HLA-B HLA-C, HLA-DRB1 and HLA-DQA1/B1 kits) were used. The CagL/CagA positivity distribution in the groups were as follows: 42 (95.4%) gastric cancer, 46 (92%) DU and, 34 (68%) NUD and no NGIS cases. The HLA-DQA1*01 (OR: 3.82) allele was significantly different, suggesting that these individuals with H. pylori strains harbouring the CagL/CagA positivity are susceptible to the risk of gastric cancer and DU, and the HLA-DQA1*05 (OR, 0.318) allele was suggested as a protective allele for the risk of gastric cancer and DU using univariate analyses. HLA-DQA1*01 (OR, 2.21), HLA-DQB1*06 (OR, 2.67), sex (male, OR, 2.27), and CagL/CagA/(<2) EPIYA C repeats (OR, 5.72) were detected independent risk factors that increased the risk of gastric cancer and DU using multivariate analyses. However, the HLA-DRB1*04 (OR, 0.28) allele was shown to be a protective allele, which decreased the risk of gastric cancer and DU. Gastric pathologies result from an interaction between bacterial virulence factors, host epigenetic and environmental factors, and H. pylori strain heterogeneity, such as genotypic variation among strains and variations in H. pylori populations within an individual host.

Evaluation of the possible involvement of Ad-36-induced adipogenesis and coronary artery disease development in mediastinal adipose tissue samples.

Mediastinal fat has been suggested to be associated with cardiovascular diseases such as carotid stiffness, atherosclerosis and coronary artery calcification. We investigated the possible role of Ad-36-induced obesity in the pathogenesis of the coronary artery disease (CAD). Ad-36 DNA was investigated in the anterior mediastinal fat tissue samples of obese adults with CAD. Seventy-five obese adults with left main coronary artery (LMCA) disease, 28 non-obese adults with valvular heart diseases, and 48 healthy individuals without cardiovascular problems were included as the obese patient group (OPG), non-obese patient group (NOG) and healthy control group (HCG), respectively. We also simultaneously investigated Ad-36 antibodies by serum neutralization test (SNA), and measured leptin and adinopectin levels. Ad-36 antibodies were detected only in 10 patients (13.3%) within the 75 OPG. A statistically significant difference was detected between OPG, NOG and HCG in terms of Ad-36 antibody positivity (p>0.05). Ad-36 DNA was not detected in mediastinal tissue samples of OPG and NOP without PCR inhibitors. We suggest that Ad-36 may not have an affinity for mediastinal adipose tissue in obese patients with left main CAD and valvular heart diseases. Ad-36 antibody positivity results are not sufficient to reach a causal relationship.

Helicobacter pylori-miRNA interaction in gastric cancer tissues: First prospective study from Turkey.

Helicobacter pylori (H. pylori) is involved in the etiology of gastric cancer (GC). miRNAs are short RNAs that regulate gene expression by marking mRNAs for degradation. miRNAs are involved in tumorigenesis, metastasis, and cell proliferation. We aimed to investigate the miRNA expression profiles of tissues from H. pylori (+) and (-) GC patients. Forty GC patients, 20 H. pylori (+) and 20 H. pylori (-), and a healthy control group were included. The miRNA expression levels were investigated by microarrays and quantitative RT-PCR. We detected 9 upregulated and 4 downregulated miRNAs by microarray. We selected 5 upregulated and 5 downregulated miRNAs for the quantitative RT-PCR assay. The relative fold changes of miRNAs in the cancerous tissue and non-tumor mucosa specimens of H. pylori (+) GC patients for hsa-miR-194 were 4.24- and 3.83-fold higher, respectively, whereas the hsa-miR-145 expression levels were downregulated 0.33-fold and 0.43-fold, respectively, in the same group. The presence of H. pylori significantly upregulated hsa-miR-194 and downregulated hsa-miR-145 expression levels in H. pylori (+) GC cases, compared to H. pylori (-) GC cases. Regional differences in the virulence of H. pylori strains may also be involved in the up- or downregulation of miRNA expression levels.

Comparison of new and classical point mutations associated with clarithromycin resistance in Helicobacter pylori strains isolated from dyspeptic patients and their effects on phenotypic clarithromycin resistance.

PURPOSE: We aimed to investigate the presence of three recently identified point mutations (A2115G, G2141A and A2144T) of the 23 S rRNA gene and compare them with the three most frequently encountered point mutations (A2142G, A2142C and A2143G) in Helicobacter pylori strains in Turkey. METHODOLOGY: A total of 63 patients (mean 47.08±12.27) were included. The E-test method (for clarithromycin) was used for the clarithromycin antimicrobial susceptibility test of isolated H. pylori strains. Real-time PCR was used to detect the point mutations. RESULTS: A total of 24 out of 63 H. pylori strains (38.1%) were detected as clarithromycin resistant (>0.5 mg l-1 ). The new A2115G (n:6, 25%), A2144T (n:7, 29.1%) and G2141A, 8 (n:8, 33.3%) mutations and the classical A2142G (n:8, 33.3%) and A2143G (n:11, 45.8%) point mutations were detected in the 24 clarithromycin-resistant strains. The A2144T point mutation had the highest median MIC value (3 mg l-1 ) amongst the new mutations, but the classical mutations (A2142G and A2143G) had the highest median MIC values (256 mg l-1 ) overall. The presence of the A2115G (OR:31.66), A2144T (OR:36.92) or G2141A (OR:28.16) mutations increased the likelihood of clarithromycin resistance in H. pylori strains by 31.66-, 36.92- and 28.16-fold (ORs), respectively, according to the binary logistic regression analysis. CONCLUSION: We concluded that classical mutations of the 23 S rRNA gene resulted in higher clarithromycin MIC values than new mutations. These new point mutations caused moderate elevations in the MIC values of clarithromycin-resistant H. pylori strains.

A Retrospective Analysis of Anaerobic Bacteria Isolated in 236 Cases of Pleural Empyema and their Prevalance of Antimicrobial Resistance in Turkey.

BACKGROUND: Parapneumonic effusions usually occur secondary to an infection and produce pus (empyema) that accumulates in the pleural space. We aimed to evaluate the prevalence of anerobes in patients with empyema and to assess their resistance patterns for seven antimicrobials. METHODS: Pleural fluid specimens from 236 patients were inoculated on Schaedler agar. Anaerobic bacteria were identified via API 20 A. Susceptibility testing for penicillin, ampicillin + sulbactam, amoxicillin + clavulanate, cefoxitin, clindamycin, metronidazole, and imipenem were performed with the E-test. RESULTS: There were 118 anaerobic bacterial strains detected in 66 (27.9%) of the 236 specimens. Gram-positive anaerobic cocci were detected in 54.23% and the predominant cocci were 41 Peptostreptococcus spp, (34.75%) followed by 17 P. acnes (14.41%) and 6 C. tertium (5.08%). The Gram-negative anaerobes were B. fragilis (28, 23.73%), P. melaninogenica (8, 6.78%), P. intermedia (4, 3.39%), F. nucleatum (6, 5.08%), F. mortiferum (5, 4.24%), and P. asaccharolytica (3, 2.54%). All anaerobic strains were susceptible to ampicillin + sulbactam, amoxicillin + clavulanate, and imipenem. The highest MIC was found to be > 256 µg/mL for penicillin in B. fragilis strains, 128 µg/mL for cefoxitin in P. melaninogenica strains, 32 µg/mL for clindamycin and 64 µg/mL for metronidazole in P. acnes strains. Clindamycin resistance was detected in 46.6% B. fragilis, and 17.6% for P. acnes. Thirty-eight (32.2%) strains produced beta-lactamase. CONCLUSIONS: The use of antimicrobial agents for thoracic empyema should be based on the isolated pathogens and their resistance profiles. Clinicians should be aware of the wide diversity of anaerobic genera and species in cases of pleural empyema.

Diagnostic performance of the RT-qPCR method targeting 85B mRNA in the diagnosis of pulmonary Mycobacterium tuberculosis infection.

BACKGROUND: Several nucleic acid amplification techniques (IS6110, 16S rRNA, and 85B mRNA) were developed for the rapid, direct detection of Mycobacterium tuberculosis. We aimed to assess the diagnostic performance of 85B mRNA-based RT-qPCR by comparing with the real-time PCR COBAS TaqMan MTB Kit while using the BACTEC MGIT 960 method as the gold standard. METHODS: 60 patients with confirmed pulmonary TB and 60 individuals without TB were included as the study and control groups, respectively. Sputum specimens were cultured using LJ and BACTEC MGIT 960 systems. Extracted DNA was used for COBAS PCR in a CONAS TaqMan 48 analyzer. 85B mRNA detection was performed by RT-qPCR. RESULTS: The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of COBAS TaqMan MTB Test were detected as 93.3%, 83.3%, 84.8%, 92.6%, and 88.3%, respectively. The same diagnostic parameters of RT-qPCR were: 98.3%, 95.0%, 95.2%, 98.3%, and 96.7%, respectively. According to the binary logistic regression analysis, RT-qPCR (OR: 19,924, p<0.001) was identified as the more optimal test. CONCLUSION: 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.

Problems encountered in conventional HIV 1/2 Algorithms: lack of necessity for immunoblot assays to confirm repeated ELISA reactive results.

BACKGROUND: The use of conventional (serologically based) HIV 1/2 diagnostic algorithms has become controversial in recent years. OBJECTIVES: Sera from patients who underwent verification tests were evaluated because repeated ELISA-reactive results demonstrated a HIV1+HIV2 positive band pattern. METHODS: The line immunoassay (LIA) test was used for repeated HIV enzyme immunoassays (EIA)-reactive sera in patients at three centers. The Bio-Rad Geenius™ HIV 1/2 and the HIV-1 RNA tests were used. HIV-1 and RNA HIV-2 were investigated using PCR. RESULTS: LIA was used to evaluate 3,224 out of 10,591 samples with repeated ELISA reactivity (30%). We found that 32 (1%) of the sera, along with HIV1 bands and HIV2 gp36 bands, were positive. Only 28 of the 32 verified serum samples with gp36 bands were repeated, and no gp36 band positivity was detected using the Bio-Rad Geenius™ HIV-1/2 confirmatory assay in these serum samples. The HIV-2 proviral DNAs were also negative. Therefore, we excluded the possibility of HIV1+2 co-infection. All samples from the 32 patients were positive for HIV-1 RNA. CONCLUSION: Our findings highlight the need to exclude confirmatory tests like the LIA test from the current diagnostic HIV algorithm and replace it with rapid HIV-1 and HIV-2 confirmatory immunochromotographic tests.