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 α5β1 (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.

Similar bacterial signatures in the gut microbiota of type 1 and type 2 diabetes patients and its association with G protein-coupled receptor 41 and 43 gene expression.

Purpose: There are conflicting reports regarding the abundance of short-chain fatty acids producing bacteria in the gut microbiota in patients with type 1 and type 2 diabetes. We aimed to determine the amount of , and in the gut microbiota in patients with type1 and type2 diabetes, compared with the healthy controls and analyze the correlation between the gene expression levels of two hort-chain fatty acids receptors and

Methods: Forty type 1, 40 type 2 stool and blood samples of diabetes patients, and 40 healthy control samples were studied. DNA and RNA were extracted, and bacteria were detected using a Microbial DNA qPCR Assay kit.

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.

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 ()].

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.

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.

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.

Presence of biofilm and adhesin genes in Staphylococcus aureus strains taken from chronic wound infections and their genotypic and phenotypic antimicrobial sensitivity patterns.

The purpose of this research was to examine biofilm (icaA, icaD and bap) and adhesin (clfA, fnbA, cna) genes, and also assess the genotypic and phenotypic antimicrobial resistance patterns of Staphylococcus aureus strains taken from wound specimens in Mardin, Turkey. A total of 220 wound specimens were investigated. The biofilm forming ability and resistance pattern for eleven antimicrobial agents were investigated by conventional and multiplex PCR methods.

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.

Role of Alvarado score and biological indicators of C-reactive protein, procalicitonin and neopterin in diagnosis of acute appendicitis.

Background: The determination of a definitive preoperative diagnosis of acute appendicitis (AA) remains a challenge; however, delays in diagnosis increase complication rates. The aim of this study was to investigate the contribution of the Alvarado score (AS) alone and the AS combined with the use of the biological indicators of C-reactive protein (CRP), procalcitonin (PCT) and neopterin (NP) in the diagnosis.

Methods: Serum was collected from 100 patients who were admitted to the general surgery clinic of Istanbul University, Cerrahpasa Medical Faculty between March 4, 2014 and July 29, 2015 with the pre-diagnosis of AA and who agreed to take part in the study.

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.

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.

Pneumococcal Nasopharyngeal Carriage in Young Healthy Children After Pneumococcal Conjugate Vaccine in Turkey.

Aims: To determine the prevalence of nasopharyngeal carriage of Streptococcus pneumoniae in healthy children aged 0-6 years who were vaccinated with pneumococcal conjugate vaccine.

Methods: This cross-sectional study was conducted on 150 healthy Turkish children between 1 month and 6 years of age. Serotyping was performed and risk factors of carriage were evaluated.

The relationship of Chlamydophila pneumoniae with schizophrenia: The role of brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3) in this relationship.

Several pathogens have been suspected of playing a role in the pathogenesis of schizophrenia. Chronic inflammation has been proposed to occur as a result of persistent infection caused by Chlamydophila pneumoniae cells that reside in brain endothelial cells for many years. It was recently hypothesized that brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3) may play prominent roles in the development of schizophrenia.

Travel-associated infections caused by unusual serogroups of Legionella pneumophila identified using Legionella BIOCHIP slides in Turkey and Iraq.

Background: Although Legionella pneumophila serogroup 1 is the common disease causing serogroup, rare serogroups can also may cause legionellosis. A 54-year-old male patient (index case) reported that he had been on a religious trip (for visiting, tomb of Ali, which is important for Shias) to Iraq with a large group (50 shia pilgrims from Kars city of Turkey) two weeks prior to admission. Due to civil war, the hotel where the patient stayed in Iraq lacked proper hygiene.

Prevalence of Primary Antimicrobial Resistance of H. pylori in Turkey: A Systematic Review.

Background: The prevalence of clarithromycin resistance has increased to the 20% or more in different regions of the world. Clarithromycin resistance is known to be responsible for most of the treatment failures in Helicobacter pylori (H. pylori) infection.

Hemophilus Influenzae Infections with Abscess Formation in Adults: a Retrospective Study Covering an Eleven-Year Period.

Background: The aim of this study was to investigate the presence of Haemophilus influenzae in abscesses in adults and to determine their antibiotic resistance patterns.

Methods: H. influenzae strains isolated from abscesses during an eleven-year period were determined retrospectively and the stored strains were tested for ampicillin, amoxicillin/calvulanic acid, cefuroxime, cefotaxime, ceftriaxone, ciprofloxacin, azithromycin, tetracycline, and imipenem resistance by broth microdilution method.

The prevalence of enterotoxin and antibiotic resistance genes in clinical and intestinal Bacteroides fragilis group isolates in Turkey.

This study was conducted to measure the antibiotic susceptibilities, corresponding gene contents, and the enterotoxin gene bft, in 50 Bacteroides fragilis group isolates, 25 of which were clinical and 25 intestinal. The resistance rates to amoxicillin/clavulanic acid, imipenem and metronidazole were low; ampicillin and tetracyclin resistance was high; clindamycin resistance and ermF gene presence was also high. Regarding phenotypical bacterial resistance and the presence of resistance genes, there was not statistically significant difference between clinical and intestinal isolates and bft positive and negative isolates.

Antimicrobial resistance of Helicobacter pylori strains to five antibiotics, including levofloxacin, in Northwestern Turkey.

Introduction: Antibiotic resistance is the main factor that affects the efficacy of current therapeutic regimens against Helicobacter pylori. This study aimed to determine the rates of resistance to efficacy clarithromycin, amoxicillin, tetracycline, levofloxacin and metronidazole among H. pylori strains isolated from Turkish patients with dyspepsia.

The cytokine response in THP-1 (monocyte) and HL-60 (neutrophil-differentiated) cells infected with different genotypes of Helicobacter pylori strains.

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.

Isolation and diagnosis of Helicobacter pylori by a new method: microcapillary culture.

Aim: To investigate the performance of the microcapillary culture method (MCM) in Helicobacter pylori (H. pylori) isolation and diagnosis.

Methods: Microcapillary culture (MC), classical culture (CC), rapid urease (CLO) test, and histopathologic examination (HE) were performed with biopsy samples.

Prevalence and antimicrobial susceptibilities of anaerobic bacteria isolated from perforated corneal ulcers by culture and multiplex PCR: an evaluation in cases with keratitis and endophthalmitis.

Background: Anaerobic bacteria play an important role in eye infections; however, there is limited epidemiologic data based on the the role of these bacteria in the etiology of keratitis and endophthalmitis. The aim of this re- search is to determine the prevalence of anaerobic bacteria in perforated corneal ulcers of patients with keratitis and endophthalmitis and to evaluate their antimicrobial susceptibilities.

Methods: Corneal scrapings were taken by the ophthalmologist using sterile needles.

An in Vitro Experimental Study on the Antimicrobial Activity of Silicone Oil against Anaerobic Bacteria.

Purpose: To investigate the in vitro antimicrobial activity of silicone oil against anaerobic agents, specifically Propionibacterium acnes, Peptostreptococcus spp., Peptostreptococcus anaerobius, Bacteroides fragilis, Fuobacterium spp., and Clostridium tertium.

Microorganisms in respiratory tract of patients diagnosed with atypical pneumonia: results of a research based on the use of reverse transcription polymerase chain reaction (RT-PCR) DNA microarray method and enzyme-linked immunosorbent assay.

Background: Numerous molecular-based tests were applied for the laboratory-based diagnosis of viruses. In this cross-sectional case control study, in addition to bacteria, we aimed to determine respiratory viruses using, for the first time in our country, the Reverse Transcription PCR DNA Microarray method, and we also aimed to evaluate its diagnostic performance.

Methods: Respiratory viruses were investigated from nasopharyngeal swabs of 76 patients diagnosed with atypical pneumonia and 64 healthy controls using the CLART Pneumovir (Genomica, Spain) kit and from 10 mL blood samples of the same subjects.