Tıp Fakültesi, Tıbbi Mikrobiyoloji Anabilim Dalı Koleksiyonu

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Berrak hücreli renal hücreli karsinom hastalarında BAP1, PBRM1, SETD2 mutasyonlarının varlığının araştırılması ve immünohistokimyasal olarak korelasyonunun değerlendirilmesi
(İnönü Üniversitesi, 2022) Eren, Şeyma
Hastaları doğru tedaviye yönlendirmek için tümör örneklerinin moleküler testi giderek önem kazanmaktadır. Bu çalışmanın amacı klinikopatolojik, histomorfolojik özellikler ile BAP1, PBRM1 ve SETD2 genlerindeki mutasyonların etkilerini ve bunların immünohistokimya ile korelasyonunu incelemek ve berrak hücreli renal hücreli karsinom hastalarının tedavisine, prognozuna ve yönetimine rehberlik etmesini araştırmaktır. Materyal ve Metod: Çalışmaya 2015-2021 yılları arasında nefrektomi uygulanmış, İnönü üniversitesi Turgut Özal Tıp Merkezi Tıbbi Patoloji laboratuvarında değerlendirilmiş 80 adet ccRCC olgusu alınmıştır. Bu olgular BAP-1, PBRM-1, SETD-2 immünohistokimyasal boyanmaları ile değerlendirilmiştir. 12 olgu ise tüm ekzom dizileme yöntemiyle moleküler olarak mutasyonlar açısından araştırılmıştır. Bulgular: 80 olgunun %41'inde PBRM-1, %17,5'inde BAP-1, %47,5'inde SETD-2 ile immünohistokimyasal olarak boyanma kaybı bulundu. PBRM-1 ve BAP-1 ile cinsiyet, yaş, tümör lokalizasyonu, tümör boyutu, evre, grade, metastaz, arasında ilişki saptanmadı. BAP-1 negatifliği kötü genel sağkalım ile ilişkili bulundu. SETD-2 negatifliği ile ileri evre ve tümör boyutu arasında korelasyon saptandı. PBRM-1 ve BAP-1 negatifliğinin birlikteliği anlamlı bulundu; PBRM1/SETD2, BAP1/SETD2 birlikteliği istatistiksel olarak anlamlı değildi. Ekzom sekanslama işlemi ile 12 olgunun hiçbirinde VHL, PBRM-1, BAP-1, SETD-2 için anlamlı mutasyon saptanmadı. 7 olguda ARSD, 9 olguda SLC25A5 geninde SNP mutasyonlar saptanmıştır. Sonuç: BAP-1 ve PBRM-1 ile immünohistokimyasal olarak boyanma oranları literatür ile benzer oranda saptanırken, SETD-2 ile oran literatüre göre daha yüksek oranda saptandı. Ekzom sekanslama ile 12 olgunun hiçbirinde her 3 gene ait anlamlı mutasyon saptanmazken ARSD ve SLC25A5 genlerinde yüksek oranda mutasyonlar izlenmiştir. Bu genlerle ilgili çalışmalar RCC'nin hem moleküler makanizmasını hem de olası hedefe yönelik tedavileri yönlendirmeye katkı sunacaktır.
Thymoquinone is protective against 2,3,7,8-tetrachlorodibenzo-p-dioxininduced hepatotoxicity
(Taylor & francıs ltd, 2-4 park kare, mılton park, abıngdon or14 4rn, oxon, ingiltere, 2018) Erdemli, ME; Yigitcan, B.; Gül, M.; Çanta, HG; Gül, S.; Aksungur, Z.
We investigated changes in rat liver tissues following administration of thymoquinone (TQ) against 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) induced hepatotoxicity. Fifty rats were assigned randomly to five groups of 10 as follows: control, corn oil, TCDD, TQ and TCDD + TQ. Biochemical and histopathological analyses were conducted on liver tissue. We found that 30 day TCDD administration caused histopathological changes in liver including thickening of Glisson's capsule, intracytoplasmic vacuolization in hepatocytes, sinusoidal dilation, vascular and sinusoidal congestion and inflammatory cell infiltration. TCDD administration increased malondialdehyde (MDA), total oxidant status (TOS), alanine aminotransferase (ALT), aspartate aminotransferase (AST) and alkaline phosphatase (ALP) levels in rat liver tissue and reduced glutathione (GSH), superoxide dismutase (SOD), catalase (CAT) and total antioxidant status (TAS) levels compared to all other groups. In the TQ treated group, GSH, SOD, CAT and TAS levels increased compared to all other groups. MDA, TOS, ALT, AST, ALP levels decreased compared to all other groups. Our histological findings were consistent with the biochemical findings. The oxidative and histologic effects of TCDD were eliminated by TQ treatment. TCDD administration caused oxidative stress in rat liver and TQ administered with TCDD prevented TCDD induced hepatotoxicity. TQ could be considered an alternative anti-TCDD toxicity agent.
Investigation of the protective effects of crocin on acrylamide induced small and large intestine damage in rats
(TAYLOR & FRANCIS INC, 530 WALNUT STREET, STE 850, PHILADELPHIA, PA 19106 USA, 2018) Gül, Mehmet; Yiğitcan, B.; Bağ, Harika Gözükara; Aksungur, Z
We investigated repair of acrylamide (AA) induced damage in intestines by administration of crocin. We used 40 male Wistar rats in four groups of 10 animals: control, AA, crocin, and AA + crocin groups. We investigated biochemical and histological changes to small and large intestine. AA ingestion decreased glutathione (GSH) levels and total antioxidant status (TAS) in the intestine compared to the control group, while superoxide dismutase (SOD) and catalase (CAT) activities, and total oxidant status (TOS) and malondialdehyde (MDA) levels were increased. Villi were shortened and villus degeneration was observed in ileum of the AA group. Degeneration of surface epithelium and Liberkuhn crypts were observed in colon sections. GSH and TAS levels increased after administration of AA together with crocin, while SOD and CAT levels and TOS and MDA levels decreased; significant recovery of histological damage also was observed. We found that crocin exhibits protective effects on AA induced small and large intestine damage by inhibiting oxidative stress.
Investigation of high-risk st131 clone in esbl-producing escherichia coli isolates isolated from urine and non-urinary clinical specimens with maldı-tof ms and real time pcr
(Ankara Microbiology Society, 2018) Otlu, B.
In recent years, the ST131 clone was identified as a high risk pandemic clone among Escherichia coli isolates by multilocus sequence typing (MIST) studies and has been associated with extended spectrum beta-lactamase (ESBL) production (often with CTX-M-15) and antibiotic resistance especially against fluoroquinolones. The aim of this study was to determine the rate of high risk ST131 clone in ESBL producing E.coli isolates in our region, to investigate the sensitivity of MALDI-TOF MS in the detection of ST131 clone, and to compare the frequency of antimicrobial resistance among ST131 and non-ST131 isolates. A total of 251 urinary and 50 non-urinary E.coli isolates identified in our hospital central laboratory between February 2016-February 2017 were included in the study. Real-time PCR and MALDI-TOF MS methods were used for the detection of E.coli ST131 clone. For the statistical evaluation of the rate of antibiotic resistance among isolates of ST131 and non-STI 31 clones, chi-square test was used. p value under 0.05 was considered as significant. Of the 301 isolates, 110 (36.6%) and 92 (30.6%) isolates were identified as ST131 clone by real-time PCR and MALDI-TOF MS, respectively. According to real-time PCR results, 91 (36.3%) of 251 urinary isolates and 19 (38%) of 50 non-urinary isolates were found as ST131 clone; there was no statistically significant difference between the groups. Ciprofloxacin resistance was found to be significantly higher in ST131 isolates than the non-STI 31 isolates (78.2%, n= 86 vs. 53.4%, n= 102). No statistically significant difference was determined for the other antibiotics tested. For the detection of E.coli ST131 clone; sensitivity of MALDI-TOF MS was 84%, specificity was 100% while positive predictive value was 100% and negative predictive value was 92%. In conclusion, further investigation of the high risk E.coli ST131 clone in our country, in which ESBL ratios and antibiotic resistance rates, especially in fluoroquinolones, are high, is important for the development of new strategies to control antibiotic resistance. MALDI-TOF MS method is particularly useful for easy and fast detection of the high risk E.coli ST131 clone.
Letter to the editor: a rarely isolated gram-negative bacterium in microbiology laboratories: leclercia adecarboxylata
(Akademiai Kiado Rt., 2018) Çiçek, M.; Tuncer, Ö.; Biçakçigil, A; Gürsoy, N.C.; Otlu, B.; Sancak, B.
High Genetic Diversity among Stenotrophomonas maltophilia Isolates from Single Hospital: Nosocomial Outbreaks or Genotypic Profile Changes during Subcultures
(Unıv saıns malaysıa, sch medıcal scıences, health campus, 16150 kubang kerıan, kelantan, 00000, malaysıa, 2018) Guvenir, Meryem; Otlu, Baris; Tunc, Emine; Aktas, Elif; Suer, Kaya
Background: Stenotrophomonas maltophilia is a non-fermentative gram-negative bacillus which is widely recognised as an important nosocomial pathogen causing pneumonia, blood-stream, wound and urinary tract infections, particularly in immunosuppressed patients. The aim of this study was to evaluate a nosocomial outbreak of by S. maltophilia in an intensive care unit of a tertiary hospital and evaluate unexpected multiclonality. Methods: A total of 11 isolates from respiratory cultures in intensive care unit of a 24 bed tertiary hospital obtained over a one months period and one isolate obtained from the nebuliser during environmental screening were investigated. The bacteria were identified by Phoenix 100 system. The clonal relatedness was evaluated by PFGE and semi-automated repetitive sequence-based PCR. Genotyping tests were repeated for 10 serial subcultures. Results: PFGE and DiversiLab yielded 10 genotypic profiles for 12 isolates. Four to eight different genotypes were observed from 10 subcultures of the same isolate. Conclusion: We conclude that, high genetic diversity and supposed multiclonal appearance of the outbreak isolates may be due to changing profiles during subcultures most probably depending on hypermutation.
Nosocomial Infections in a New Medical Center Turkey
(Infection Control and Hospital Epidemiology, 2000) Durmaz, Bengül; Durmaz, Rıza; Otlu, Barış; Sönmez, Emine
Serum leptin concentration is increased in patients with Behcet s syndrome and is correlated with disease activity
(British Journal of Dermatology, 2002) Evereklioğlu, Cem; İnalöz, H. S.; Kırtak, N.; Doğanay, Selim; Bülbül, M.; Özerol, Elif; Er, Hamdi; Özbek, Emin
Background Behc¸et’s syndrome is a systemic, relapsing immuno-inflammatory disease with a generalized vasculitis of the microvasculature endothelial dysfunction. Leptin, a recently discovered neuroendocrine hormone, is a metabolic peptide that appears to be involved. Serum proinflammatory cytokines upregulate leptin levels and leptin itself directly induces nitric oxide production from endothelial cells with its specific receptors. Objectives To detect changes of serum leptin concentrations in patients with Behc¸et’s syndrome compared with age- and sex-matched healthy volunteers by using enzyme-linked immunosorbent assay. We also investigated whether disease activity or the duration of Behc¸et’s syndrome correlates with leptin concentration. Methods Thirty-five consecutive patients with Behc¸et’s syndrome (41Æ2±8Æ4 years, 16 male, 19 female) and 20 age- and sex-matched healthy control subjects (40Æ4 ± 10Æ91 years, nine male, 11 female) were included in this study. The body mass index (BMI) [weight (kg) height)1 (m2 )] was calculated for subjects at study enrolment. We measured serum leptin with a leptin enzyme immunoassay kit, and acute-phase reactants, including erythrocyte sedimentation rate, a1-antitrypsin, a2-macroglobulin and neutrophil count. The Mann–Whitney U-test was used for statistical analysis and P < 0Æ05 was considered significant. Values were expressed as mean ± SD. Results The gender ratio, age and BMI were not substantially different among Behc¸et’s patients and controls. The mean serum leptin concentrations in patients with Behc¸et’s syndrome (16Æ8±7Æ49 ng mL)1 ) were significantly (P < 0Æ001) higher than in healthy control volunteers (7Æ5±2Æ77 ng mL)1 ). Active Behc¸et’s patients had significantly (P ¼ 0Æ001) higher leptin concentrations (20Æ5±7Æ99 ng mL)1 ) when compared with patients in inactive periods (12Æ8 ± 4Æ43 ng mL)1 ). In addition, patients with longer disease duration (mean, 20Æ1±5Æ15 years) had also significantly (P ¼ 0Æ013) higher leptin concentrations (20Æ2±8Æ52 ng mL)1 ) than those with shorter disease duration (13Æ4±4Æ52 ng mL)1 ) (mean, 7Æ4±3Æ29 years). All acute-phase reaction parameters were found to be significantly (for each, P < 0Æ01) increased in active disease. Conclusions Leptin may have a role in modulating endothelial function and may be involved in mechanisms for vessel endothelium repair, during an exacerbation as well as in chronic disease.
Effects of valproate and carbamazepine on serum levels of homocysteine vitamin B12 and folic acid
(Brain and Development, 2003) Karabiber, Hamza; Sönmez, Ergün; Özerol, Elif; Yakıncı, Mehmet Cengiz; Otlu, Barış; Yoloğlu, Saim
Homocysteine (HMC) is a sulfur containing amino acid, which plays a role in methionine metabolism. Folic acid (FA) and vitamin B12 (B12) are essential for remethylization of HMC to methionine. HMC level increases in the deficiency of these vitamins. Hyperhomocysteinemia causes vascular endothelial damage, which causes atherosclerosis. The aim of this study is to investigate the effect of valproate (VA) and carbamazepine (CBZ) on the serum levels of HMC, B12, and FA. Thirty-six children receiving CBZ and 30 children receiving VA for epilepsy for the last 1-year period and 29 healthy children as control were the population of this study. After 6 h of fasting serum HMC, B12, and FA levels were measured and results were compared statistically. Mean values of HMC, FA, and B12 levels in control group were 9.2 ^ 2.7 mmol/l, 9.0 ^ 2.0 ng/ml, and 342 ^ 162 pg/ml, in VA group 14.0 ^ 6.8 mmol/l, 7.3 ^ 2.9 ng/ml, and 368 ^ 159 pg/ml, in CBZ group 16.0 ^ 13.1 mmol/l, 7.5 ^ 3.3 ng/ml, and 285 ^ 158 pg/ml, respectively. Serum HMC levels were higher in VA and CBZ groups than control group (P , 0:01 and P , 0:05, respectively). Serum FA levels were lower in VA and CBZ groups compared to control group (P , 0:05). Serum levels of B12 were not different between VA and control groups (P . 0:05). In CBZ group serum B12 levels were lower than control group (P , 0:05). FA may be added to the treatment protocol (if the patients take only CBZ, then B12 should also be added) for patients taking these antiepileptic drugs to decrease the degenerative effect of VA and CBZ on vascular endothelium.
Nitric oxide and lipid peroxidation are increased and associated with decreased antioxidant enzyme activities in patients with age related macular degeneration
(Documenta Ophthalmologica, 2003) Evereklioğlu, Cem; Er, Hamdi; Doğanay, Selim; Çekmen, Mustafa Baki; Otlu, Barış; Özerol, Elif
Background: Nitric oxide (NO), hydroxyl radical (OH. ), superoxide anion (O2 −) and hydrogen peroxide (H2O2) are free-radicals released in oxidative stress. Superoxide dismutase (SOD), glutathione peroxidase (GSHPx) and catalase (CAT) are antioxidant enzymes, mediating defense against oxidative stress. Excess NO and/or defective antioxidants cause lipid peroxidation, cellular dysfunction and death. Age-related maculopathy (ARM) or degeneration (ARMD) is the leading cause of irreversible blindness in developed countries. The etiology is unclear and the molecular factors contributing this disease remain to be specified. Aims: This multicenter, double-blind, crosssectional study aimed to investigate plasma NO and lipid peroxidation levels with relation to antioxidant enzyme activities in erythrocyte and plasma of patients with ARMD compared with healthy control subjects. Methods: NO, lipid peroxidation (measured as plasma malondialdehyde [MDA] levels) and the catalytic activity of SOD, GSHPx and CAT were measured in a group of 41 patients with maculopathy (19 men, 22 women; 67.12 ± 3.70 years) and compared with 25 age- and sex-matched healthy control subjects without maculopathy (12 men, 13 women; 68.04 ± 3.02 years). NO and MDA levels were measured in plasma, CAT in red blood cells (RBCs), and SOD and GSHPx in both plasma and RBCs. Color fundus photographs were used to assess the presence of maculopathy, and the patients were divided into two groups using clinical examination and grading of photographs; early-ARM (n = 22) and late-ARMD (n = 19). Results: All patients with maculopathy had significantly (p < 0.001) higher plasma NO levels over control subjects (mean ± SD, 48.58 ± 8.81 vs. 28.22 ± 3.39 µmol/l). Plasma MDA levels in patients and control subjects were 4.99 ± 1.00 and 2.16 ± 0.24 µmol/l, respectively, and the difference was significant (p < 0.001). On the other hand, SOD and GSHPx activities were significantly lower in both RBCs and plasma of patients with maculopathy than in control subjects (RBCs-SOD, 3509.30 ± 478.22 vs. 5033.30 ± 363.98 U/g Hb, p < 0.001; plasma-SOD, 560.95 ± 52.52 vs. 704.76 ± 24.59 U/g protein, p < 0.001; RBCs-GSHPx, 663.43 ± 41.74 vs. 748.80 ± 25.50 U/g Hb, p < 0.001; plasma-GSHPx, 98.26 ± 15.67 vs. 131.80 ± 8.73 U/g protein, p < 0.001). RBCs-CAT levels were not different between groups (131.68 ± 12.89 vs. 133.00 ± 13.29 k/g Hb, p = 0.811). Late-ARMD patients had significantly lower antioxidant enzyme levels and higher MDA levels when compared with early-ARM patients (for each, p < 0.001). In addition, plasma NO and MDA levels were negatively correlated with SOD and GSHPx activities. Conclusions: This study demonstrated for the first time that NO, the most abundant free-radical in the body, might be implicated in the pathophysiology of ARMD in association with decreased antioxidant enzymes and increased lipid peroxidation status.
Serum leptin concentrations are decreased and correlated with disease severity in age related macular degeneration a preliminary study
(Eye, 2003) Evereklioğlu, Cem; Doğanay,Selim; Er, Hamdi; Çekmen, Mustafa Baki; Özerol, Elif; Otlu, Barış
Background Age-related maculopathy (ARM) or degeneration (ARMD) is the leading cause of irreversible blindness in developed countries. Despite several studies on the morphology of ARMD, the aetiology is unknown and factor(s) contributing to the pathogenesis remain to be characterised. More recent studies have demonstrated that cholesterol esters and lipids are present within Bruch’s membrane deposits and drusen, and dietary fat intake is associated with ARMD. The product of Ob gene, leptin, is a recently discovered peptide participating in human metabolism. There is a direct relationship between serum leptin and diet, and lipoprotein metabolism, but the role of leptin in the course of ARMD has not previously been investigated. Purpose This cross-sectional case–control study investigated whether serum leptin level was associated with ARMD as a new possible risk factor and to assess its relationship with disease severity. Methods A total of 32 patients with ARM or ARMD (17 men, 15 women) and 20 age- and sex-matched healthy control subjects without ARMD (11 men, nine women) from a similar ethnic background were enrolled in this multicentre study. Body mass index (BMI) (weight (kg)/height (m2 )) was calculated for each group. The presence of maculopathy was assessed on the basis of colour fundus photographs using an international classification system. Patients were classified as early-ARM (n ¼ 16) or late-ARMD (n ¼ 16) using clinical examination and grading of photographs. Serum leptin levels were measured by an enzyme-linked immunosorbent assay kit. The Mann–Whitney U test or w2 test was used for statistics as indicated, and Po0.05 was considered to be significant. Results The age, sex ratio, and BMI between groups were comparable. Patients with maculopathy had significantly (Po0.001) lower leptin levels (mean7SD, 6.0172.55 ng/ ml) than control subjects (13.2172.27 ng/ml). In addition, late-ARMD patients had significantly lower leptin levels (3.8170.58 ng/ ml) than early-ARM patients (8.2171.68 ng/ml, Po0.001) or control subjects (Po0.001). Conclusion Leptin seems to be a possible newly associated factor in the course of ARM and may be involved in the lipid composition of the macular lesions, especially in late-ARMD.
Clinical microbiologic and epidemiologic characteristics of Pseudomonas aeruginosa infections in a University Hospital Malatya Turkey
(American Journal of Infection Control, 2006) Yetkin, Gülay; Otlu, Barış; Çiçek, Ayşegül; Kuzucu, Çiğdem; Durmaz, Rıza
Background: Pseudomonas aeruginosa strains are generally resistant to many antibiotics, and nosocomial infections because of this species are one of the major problems in many hospitals. Molecular typing provides very useful information about origin and transmission of the strains. The aims of the present study were to investigate clinical and microbiologic characteristics of the nosocomial infections caused by P aeruginosa strains in a medical center and to bring up the cross-transmission level of this opportunistic pathogen in a university hospital by analyzing the clonal relationship among the isolates. Methods: A total of 105 P aeruginosa strains had been identified among the 80 inpatients in a 1-year period from August 2003 to August 2004. Demographic, clinical, and epidemiologic data of the patients were prospectively recorded. The standardized diskdiffusion method was used to determine resistance of the strains to imipenem, ceftazidime, aztreonam, amikacin, gentamicin, mezlocillin, cefepime, tobramycin, meropenem, ceftriaxone, and ciprofloxacin. Clonal relatedness of the strains was investigated by pulsed-field gel electrophoresis (PFGE). Results: Of the 105 P aeruginosa strains identified, 45 (43%) were isolated from the patients hospitalized in intensive care units. Thirteen patients had repeated pseudomonas infection (total 38 infections/13 patients); 26 of these repeated infections in 9 patients showed the same localization. Half of the patients had at least 1 underlying disease such as burn (48%), chronic illness (32%), and malignancy (20%). Fifty-seven patients (71%) had urinary and/or other catheterization. Urinary tract infection (35%) was the most frequent infection encountered, followed by respiratory tract infection (34%) and sepsis (13%). Resistance to the antibiotics tested was in the 12% to 88% range; amikacin was the most effective and ceftriaxone was the least effective antibiotic. The PFGE typing method showed that 28 of the 80 patients’ isolates were clonally related, including 23 indistinguishable or closely related strains (29%), and 5 possibly related strains (6%). Epidemiologic data of the 16 patients (20% of the patients) confirmed a clonal relationship among the strains. Of the 26 isolates of the 9 patients having repeated infection in the same location, 18 (69%) were in the clonally related groups, whereas 11 of the 12 strains isolated from repeated infections on different body sites were clonally different. Conclusion: Our results indicated that P aeruginosa infections in our hospital mainly affected the patients hospitalized in intensive care units and those having catheterization, burn, and/or chronic illness. Amikacin was the best antibiotic as far as bacterial resistance was considered. Although lack of major PFGE type confirmed no P aeruginosa outbreak, typing results showed that cross transmission and treatment failure are the 2 main problems, which should be consider together to prevent this bacterial infection in medical centers.
Acute otitis media and respiratory viruses
(European Journal of Pediatrics, 2007) Bulut, Yunus; Güven, Mehmet; Otlu, Barış; Yenişehirli, Gülgün; Aladağ, İbrahim; Eyibilen, Ahmet; Doğru, Salim
Abstract The present study was performed to elucidate the clinical outcome, and etiology of acute otitis media (AOM) in children based on virologic and bacteriologic tests. The study group consisted of 120 children aged 6 to 144 months with AOM. Middle ear fluid (MEF) was tested for viral pathogens by reverse transcriptase polymerase chain reaction (RT-PCR) and for bacteria by gram-staining and culture. Clinical response was assessed on day 2 to 4, 11 to 13, 26 to 28. Respiratory viruses were isolated in 39 patients (32.5%). Respiratory syncytial virus (RSV) (46.5%) was the most common virus identified in MEF samples, followed by human rhinovirus (HRV) (25.6%), human coronavirus (HCV) (11.6%), influenza (IV) type A (9.3%), adenovirus type sub type A (AV) (4%), and parainfluenza (PIV) type -3 (2%) by RT-PCR. In total 69 bacterial species were isolated from 65 (54.8%) of 120 patients. Streptococcus pneumoniae (S. pneumoniae) was the most frequently isolated bacteria. Viral RNA was detected in 31 (56.3%) of 55 bacteria-negative specimens and in 8 (12.3%) of 65 bacteria-positive MEF samples. No significant differences were found between children representing viral infection alone, combined viral and bacterial infection, bacterial infection alone, and neither viral nor bacterial infection, regarding clinical cure, relapse and reinfection rates. A significantly higher rate of secretory otitis media (SOM) was observed in alone or combined RSV infection with S. pneumonia or Haemophilus influenzae (H. influenzae) than in other viruses infection. Conclusion. This study provides information about etiologic agents and diagnosis of AOM in Turkish children. The findings highlight the importance of common respiratory viruses and bacterial pathogens, particularly RSV, HRV, S. pneumoniae and H. influenzae, in predisposing to and causing AOM in children.
Transfusion transmitted virus DNA in serum tear and aqueous humour of patients undergoing cataract operation
(Clinical & Experimental Ophthalmology, 2007) Emre, Sinan; Otlu, Barış; Çankaya, Cem; Doğanay, Selim; Durmaz, Rıza
Purpose: Transfusion-transmitted virus (TTV) is a novel non-enveloped, single-stranded DNA virus with unclear pathogenesis throughout the world. Many studies were conducted to determine this virus in various body fluids and different primer sets have been tested for accurate diagnosis.This study aimed to collect data on the prevalence of TTV in serum, tear and aqueous humour of patients undergoing planned cataract surgery and to determine effi- cacy of three different polymerase chain reaction (PCR) techniques. Methods: A total of 72 specimens (24 each of serum, tear and aqueous humour specimens) were collected from 24 patients (11 male and 13 female) having age-related cataract. The patients did not have any other ocular pathology. TTV DNA was investigated by three different PCR methods: a seminested PCR performed with Okamato’s primers, a one-step PCR performed with degenerative Takashi’s primers and a commercial real-time PCR system. Results: TTV DNA was detected in 20 (83.3%) of the 24 serum specimens by the one-step PCR and real-time PCR system. However, seminested PCR yielded a positivity rate of 25%.TTV DNA positivities of the one-step PCR and the real-time PCR system were 33.3% and 66.6% of the 24 tear specimens, respectively. Seminested PCR did not yield positive result in these specimens. From aqueous humour specimens, TTV DNA was detected in 3 (12.5%) of the 24 specimens only by the real-time PCR.TTV DNA positivity of seminested PCR was significantly low in all specimens. Conclusions: TTV DNA was detected in serum, tear and aqueous humour of patients undergoing cataract surgery, suppor ting the idea that this virus can be detected almost all of the body fluids but at different rates under various PCR conditions and primer sets. Using commercial real-time PCR significantly increased the TTV DNA positivity.
Two possible cases of Trichosporon infections in bone marrow transplanted children the first case of T japonicum isolated from clinical specimens
(Jpn J Infect Dis., 2008) Ağırbaşlı, Handan; Keçeli Özcan, Sema; Otlu, Barış; Sınık, Gülce; Çerikoğlu, Nilgün; Durmaz, Rıza; Can, Emine; Gedikoğlu, Gündüz; Sugita, Takashi; Selva Bilgen, Hülya
Species distribution antifungal susceptibility andclonal relatedness of Candida isolates frompatients in neonatal and pediatric intensive careunits at a medical center in Turkey
(New Microbiologıca, 2008) Kuzucu, Çiğdem; Durmaz, Rıza; Otlu, Barış; Aktaş, Elif; Gülcan, Hande; Çizmeci, Zeynep
The aim of this study was to assess species distribution, antifungal susceptibility and clonal relationships among Candida strains isolated from a group of pediatric/neonatal intensive care (PICU/NICU) patients that had a very high mortality rate (76%). The cases of 21 patients (19 with candidemia, 2 with Candida meningitides) treated over a 1-year period in a Turkish hospital PICU and NICU were retrospectively analyzed. Twenty-eight Candida isolates were detected from blood (20), cerebrospinal fluid (CSF) (2) and other specimens (6). Candida species were identified using the API ID 32C System. Susceptibility testing was done (all 28 isolates) for amphotericin B, fluconazole and itraconazole using the broth microdilution method. Arbitrarily primed polymerase chain reaction (AP-PCR) was used for molecular typing of the 3 most common ones; C. albicans (15), C. parapsilosis (6), and C. pelliculosa (4). Electrophoretic karyotyping (EK) was done to check clonal identity obtained by AP-PCR. Of the 20 blood isolates, 8 (40%) were C. albicans, 12 (60%) were non-albicans Candida, and one of the 2 CSF isolates was C. albicans. The overall species distribution was as follows: 15 C. albicans isolates, 6 C. parapsilosis isolates, 4 C. pelliculosa isolates, 2 C. famata isolates and 1 C. tropicalis isolate. Amphotericin B had the best antifungal activity with a MIC90 of 0.125 µg/ml, and the rates of susceptibility to fluconazole and itraconazole were 93% and 82%, respectively. AP-PCR revealed 11 genotypes (4 were identical pairs, 7 were distinct) among the 15 C. albicans isolates, 2 genotypes (5 were classified in the same type) among the 6 C. parapsilosis isolates, and 4 separate genotypes for the 4 C. pelliculosa isolates. Karyotyping results correlated well with the AP-PCR findings. As indicated in the previous research, our results confirmed that non-albicans Candida species have become more frequently causative agents for invasive fungal infections in the ICU. Transmission of C. albicans and C. pelliculosa was relatively low, but transmission of C. parapsilosis was high, suggesting that more effective control and very strict treatment protocols are needed for patients having high mortality and invasive fungal infection in ICU.
An outbreak of pseudomonas aeruginosa because of inadequate disinfection procedures in a urology unit: A pulsed- field gel electrophoresis-based epidemiologic study
(American Journal of Infection Control, 2008) Kayabaş, Üner; Bayraktar, Mehmet; Otlu, Barış; Uğraş, Murat; Ersoy, Yasemin; Bayındır, Yaşar; Durmaz, Rıza
Background: Pseudomonas aeruginosa is an opportunistic pathogen causing nosocomial infections in many hospitals. We aimed to investigate the source of urinary tract infections by determining clonal relationship of Pseudomonas aeruginosa strains with pulsed-field gel electrophoresis (PFGE). Methods: During a 2-month period, all postoperative infections because of P aeruginosa were investigated in the Urology Department. Patient data were collected from medical records. Surveillance samples were obtained from various places in urological operating rooms. PFGE typing was performed for all P aeruginosa isolates. Results: A total of 14 P aeruginosa strains (12 from patients and 2 from environmental samples) were isolated. PFGE typing of these 14 strains yielded 2 possibly related clones, which differed from each other by 4 major bands. Ten of the patient isolates were clonally identical with the strains of 2 forceps. Conclusion: Typing results confirmed that inadequately disinfected surgical devices can be the source of outbreak. After institution of infection control measures and education, no further clusters of P aeruginosa infection were detected in the Urology Department.
Investigation of human papillomavirus and epstein barr virus DNAs in pterygium tissue
(European Journal of Ophthalmology, 2009) Otlu, Barış; Emre, Sinan; Türkçüoğlu, Peykan; Doğanay, Selim; Durmaz, Rıza
Recent studies postulated the presence of a probable relationship between pterygium and neoplasia. This study aimed to investigate the role of two oncogenic viruses, human papillomavirus (HPV) and Epstein-Barr virus (EBV), in the development of conjunctival pterygia. METHODS. Polymerase chain reaction was used to identify the presence of HPV and EBV in 30 primary and 10 recurrent pterygia samples. Twenty conjunctival samples obtained from patients undergoing cataract surgeries were used as the control group. Patient groups had similar sex, race, and age distribution to eliminate bias. For exploration of HPV in groups, two different PCR methods (in-house PCR with two different primer sets and one real-time PCR method) were studied. The presence of EBV was shown by real-time PCR method. RESULTS. HPV was identified in none of the pterygia and control group patients. However, EBV was detected in 3 out of 30 (10%) primary pterygia patients and in none of the recurrent pterygia and control patients. CONCLUSIONS. Up to now, HPV has been blamed as the major viral pathogen in the etiopathogenesis of pterygium. The current results suggest that EBV may also be involved in the pathogenesis of pterygium, but further larger studies with larger cohorts are required to confirm this hypothesis.
Beijing W and major spoligotype families of mycobacterium tuberculosis strains isolated from tuberculosis patients in eastern Turkey
(New Microbiologica, 2009) Otlu, Barış; Durmaz, Rıza; Günal, Selami; Sola, Christophe; Zozio, Thierry; Rastogi, Nalin
The aim of this study was to determine the Beijing/W family and major phylogenetic clades of Mycobacterium tuberculosis strains of tuberculosis patients in a city with a tuberculosis incidence higher than the country average. A total of 220 M. tuberculosis strains isolated over a period of more than four years were typed by spoligotyping. Spoligotyping resulted in 64 different patterns, 38 (17.3%) of which were unique, and 26 were clusters including 182 (82.7%) strains. The major shared types were ST 53 (n=55, 25%), ST 41 (LAM7-TUR; n=19, 8.6%), and ST 284 (n=15, 6.8%). The major clades observed ranked in the following order: ill-defined T superfamily (n=112, 50.9%); LatinoAmerican-Mediterranean (LAM; n=33, 15%); Haarlem (n=24, 10.9%); and the S family (n=9, 4.1%). Three strains were in the Beijing family. A high number of strains (33 strains) showed patterns that did not fall within any of the major clades described. M. tuberculosis strains in Malatya have both STs showing a widespread distribution over the world and those restricted to this city, confirming the highly diverse nature of tuberculosis. Our results suggest that the Beijing clade, which is more prevalent among the strains with MDR and isoniazid resistance, is currently not a problem in Eastern Turkey.
Epidemiologic characterization of nosocomial Acinetobacter baumannii infections in a Turkish university hospital by pulsed field gel electrophoresis
(American Journal of Infection Control, 2009) Sesli Çetin, Emel; Durmaz, Rıza; Tetik, Tülay; Otlu, Barış; Kaya, Selçuk; Çalışkan, Ahmet
Background: Although members of the Acinetobacter genus are not commonly part of the human flora, their relatively high prevalence in hospital environment frequently results in colonization of the skin and respiratory tract. Objectives: The present investigation was carried out to elucidate epidemiologic characteristics of nosocomial Acinetobacter baumannii infections in a teaching hospital. Methods: Epidemiologic, clinical, and demographic features of the 66 patients with A baumannii infection during a 14-month period were recorded. Antibiotic susceptibilities of the isolates were determined by the standardized disk-diffusion method, and the clonal relationship of the isolates was analyzed by pulsed-field gel electrophoresis (PFGE). Results: The incidence of A baumannii infection was especially high in January, April, May, and June 2006. The isolates were most frequently obtained from blood and tracheal aspirates sent from the intensive care unit and neurosurgery ward. Although the most frequently identified predisposing factors were cerebrovascular disease and surgical operation, the main risk factors identified in these patients were catheterization and mechanical ventilation. Genotype analysis of the 66 A baumannii strains by PFGE revealed the circulation of 36 different PFGE types, of which type A (12) and K (17) accounted for 44% of the isolates. We found high clonal relationship (80.3%) among the typed strains. Thirteen antibiotypes were observed. Most of the isolates were multidrug resistant. Resistance to imipenem, meropenem, gentamicin, amikacin, tobramycin, netilmicin, ampicillin-sulbactam, trimethoprimsulfamethoxazole, piperacillin-tazobactam, cefoperazone-sulbactam, ciprofloxacin, and levofloxacin were found in 44%, 47%, 47%, 84.8%, 21.2%, 3%, 62.1%, 57.6%, 94%, 62.1%, 95.5%, and 95.5% of the isolates, respectively. Conclusion: The epidemiologic data obtained suggested that the increase in the number of A baumannii infections in our hospital was caused by the interhospital spread of especially 2 epidemic clones. We determined that clonally related strains can survive for a long time in our hospital and cause nosocomial infections in the predisposed patients.

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