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    Comparison of GeneXpert® vanA/vanB PCR System and Culture Methods in the Surveillance of Vancomycin-Resistant Enterococci
    (Ankara Microbiology Soc, 2014) Altun, Hatice Uludag; Hatipoglu, Cigdem Ataman; Bulut, Cemal; Eser, Ozgen Koseoglu; Demiroz, Ali Pekcan
    Vancomycin-resistant enterococci (VRE) are important agents of hospital infections worldwide. Early recognition of VRE colonization is important in the control of hospital infections. The aim of this study was to compare a real-time PCR (Rt-PCR) system and culture methods in the detection of VRE colonization. A total of 210 perirectal swab samples obtained from the patients (142 were in internal and 68 were in surgical intensive care units) hospitalized at Ankara Training and Research Hospital, Turkey between January-September 201 3 were included in the study. The samples were simultaneously evaluated with both Rt-PCR (GeneXpert (R) vanA/vanB, Cepheid, USA) and the culture methods. The samples were cultivated in enterococcosel agar and incubated at 37 degrees C for culture. Culture plates were evaluated for three days on a daily basis. Bacterial identification was done by conventional methods and automated Vitek 2.0 system (BioMerieux, France). Antibiotic susceptibility testing was performed by the E-test. VRE was detected in 76 (36.1%) of the samples by the Rt-PCR method; of them 70 were positive for vanA, two for vanB, and four for vanA + vanB. On the other hand, VRE was detected in 71(33.8%) of the samples by the culture method. Out of 71 samples, colony growth was observed on the first day in 39 cases, on the second day in 29 cases, and on the third day in three cases. The two strains identified as vancomycin-sensitive enterococci by the Vitek 2 Compact system were determined as vanB positive by PCR. These samples were also confirmed as VRE by E-test. The PCR result of a sample which was found to be invalid, also yielded negative result by culture. Five out of the seven culture-negative samples were positive for vanA, and two for vanB by the GeneXpert (R) system. In our study, the sensitivity, specificity, positive and negative predictive values of the GeneXpert vanA/vanB PCR system were determined as 97.4%, 98.4%, 97.4%, and 97.4%, respectively. Although the GeneXpert (R) vanA/vanB RT-PCR method seems to be more attractive regarding the turn around time, it has a higher cost than the culture method. Thus, it was concluded that all laboratories should choose the most appropriate method for screening VRE in the hospital setting according to their own capacities.
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    Evaluation of Common Commercial Systems for the Identification of Yeast Isolates in Microbiology Laboratories: A Multicenter Study
    (Ankara Microbiology Soc, 2015) Karabicak, Nilgun; Altun, Hatice Uludag; Karatuna, Onur; Hazirolan, Gulsen; Aksu, Neriman; Adiloglu, Ali; Akyar, Isin
    Accurate and rapid identification of yeast isolates have become important in recent years for not only antifungal susceptibility testing due to the species-specific clinical resistance breakpoints but also early initiation of appropriate antifungal therapy. In clinical microbiology laboratories species identification of yeasts is often performed with several commercial systems based on biochemical properties and rarely according to the physiological and morphological characteristics. The aim of this study was to compare the two common commercial systems, VITEK 2 YST ID Card (Vitek; bioMerieux, France) and API 20C AUX (API; bioMerieux, France) with conventional mycological methods. A total of 473 clinical yeast strains isolated from clinical specimens in different university and training/research hospitals and identified by Vitek system were included in the study. The isolates were re-identified with API and conventional methods including morphological identification in the Mycology Reference Laboratory of the Public Health Institute of Turkey. Candida dubliniensis MYA 583, Candida krusei ATCC 6258, Candida parapsilosis ATCC 22019, Candida albicans ATCC 10231 and Cryptococcus neoformans ATCC 32268 were used as quality control strains and those standard strains were studied consecutively 10 days with both of the methods. The results of identification by Vitek and API were compared with the results of conventional methods for those 473 yeast isolates [6 genus (Candida, Cryptococcus, Blastoshizomyces, Rhodotorula, Saccharomyces, Trichosporon), 17 species (5 common and 12 rarely isolated)]. The performances of the systems were better (Vitek: 95%; API: 96%) for the commonly detected species (C.albicans, C.parapsilosis, C.glabrata, C.tropicalis and C.krusei) than those for rarely detected species (Vitek: 78.4%; API: 71.6%) (p= 0.155). Misidentification or unidentification were mostly detected for C.parapsilosis (Vitek: 6/87; API: 7/87) and C.glabrata (Vitek: 9/104; API: 3/104) by both of the systems. For rarely detected yeast isolates, misidentification or unidentification were most frequently observed in species of C.pelliculosa (Vitek: 3/11; API: 6/11) and C.dubliniensis (API and Vitek: 2/5) isolates. Candida guilliermondii (API: 2/5) isolates had lower rate of identification with API compared to other species. Blastoschizomyces capitatus and Saccharomyces cerevisiae isolates could not be identified by both of the systems. As a result, the accurate diagnosis of Vitek and API systems were similar in terms of consistency (86.3%). Two systems performed well in correct identification of common clinical yeast species (at least 95%), while the identification of rare species was more challenging indicating that they require further morphological and physiological testing. The addition of morphological identification to commercial systems will be useful for accurate diagnosis and treatment of mixed infections.
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    Invasive pneumococci before the introduction of pneumococcal conjugate vaccine in Turkey: antimicrobial susceptibility, serotype distribution, and molecular identification of macrolide resistance
    (Taylor & Francis Ltd, 2015) Altun, Hatice Uludag; Hascelik, Gulsen; Gur, Deniz; Eser, Ozgen Koseoglu
    This study evaluates the antimicrobial susceptibilities and serotype distributions of invasive Streptococcus pneumoniae (SP) isolates identified in a Turkish hospital before the introduction of the 7-valent pneumococcal conjugate vaccine (PCV7). The susceptibilities of all isolates were determined by evaluating six antibiotics: penicillin (PEN), ceftriaxone (CRO), levofloxacin (LEV), erythromycin (ERY), clindamycin (CD), and vancomycin (VAN). Serotyping and amplification of macrolide resistance genes were performed. Sixteen (50%) and four (2%) isolates were resistant to PEN and LEV, respectively. No isolates demonstrated VAN resistance. Intermediate resistance to CRO was found in 4% of all invasive isolates. Twenty-three (12.6%) isolates were resistant to ERY. Four (2%) invasive SP isolates demonstrated multidrug resistance. Serogroups 3, 5, 6, 8, 9, and 23 were the most common in both age groups. The potential coverage rates of PCV7 and PCV13 were 44.1 and 66.1% in children and 39.8 and 71.5% in adults, respectively. Continuous surveillance of antimicrobial resistance is required.
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    Matrix Metalloproteinases 2 and 9 Polymorphism in Patients With Myeloproliferative Diseases A STROBE-Compliant Observational Study
    (Lippincott Williams & Wilkins, 2015) Maral, Senem; Acar, Muradiye; Balcik, Ozlem Sahin; Uctepe, Eyyup; Hatipoglu, Omer Faruk; Akdeniz, Derya; Altun, Hatice Uludag
    Chronic myeloproliferative disorders such as polycythemia vera (PV), essential thrombocytosis (ET), and idiopathic myelofibrosis arise from clonal proliferation of neoplastic stem cells in the bone marrow. Matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases that have potential to degrade all types of extracellular matrix (ECM) and also play a role in remodeling of the ECM. It is known that MMPs play a role in bone marrow remodeling. The primary goal of our study is to explore the relationship between chronic myeloproliferative diseases and some of MMP gene polymorphisms. The demonstration of a relationship will help to understand whether these polymorphisms may be a potential early diagnosis marker of the diseases. Patients were selected from outpatient clinks of Turgut Ozal University Hospital, Ankara, Turkey, between December 2010 and May 2011. Twenty-eight patients that previously diagnosed and followed-up with PV, 17 with secondary polycythemia (SP), and 12 with ET were enrolled in the study, along with a control group of 22 healthy people. DNA was isolated from peripheral blood. Using polymerase chain reaction restriction fragment length polymorphism method, MMP2 and MMP9 gene polymorphisms were analyzed with agarose gel electrophoresis. There was a statistically significant difference between the study groups and the control group in terms of Gin279Arg polymoiphisms rates of MMP9. The highest MMP9 Gln279Arg polymorphism rate was observed in the ET group. But nobody from the control group had polymorphic MMP9. There was no statistically significant difference between the groups in terms of MMP2-735 C > T polymorphism rates. In conclusion, MMP9 gene Gln279Arg polymorphism was associated with ET, SP, and PV diseases. Hence, we believe that these gene polymorphisms may play a role in the mechanism of bone marrow fibrosis and may be a factor that increases the risk of thrombosis. Illumination of the molecular basis of the relationship between MMP-thrombosis and MMP-librosis provides a better understanding of the pathophysiology of PV and ET diseases mid will allow new approaches to diagnosis and treatment.
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    THE SPECIFICITY AND SENSITIVITY RESULTS OF THE RAPID ANTIGEN TEST USED IN THE DIAGNOSIS OF GROUP A BETA HEMOLYTIC STREPTOCOCCAL TONSILLOPHARYNGITIS
    (Carbone Editore, 2015) Altun, Hatice Uludag; Meral, Tuba; Aribas, Emel Turk
    Aims: The rapid antigen detection test and throat culture can be used for the diagnosis of group A beta hemolytic streptococcus (GABHS) infections. The aim of this study was to determine the sensitivity and specificity ratios of the rapid antigen test for GABHS in the laboratory setting. Materials and methods: In this study, the throat culture and rapid antigen test results were evaluated for 5120 patients between the ages of 0-18 years, who were admitted between January and June 2014 to the pediatric outpatient clinic with a diagnosis of clinical exudative tonsillopharyngitis. The tests of these patients were performed at the microbiology laboratory of Turgut Ozal University Hospital. Patients with only a throat culture or a rapid antigen test result were excluded from the study. Thus, 1243 patients were included in the current study, in which both tests had been performed. Two throat swab samples were collected from these patients. Culture tests and rapid antigen tests were both performed for the patient samples. The Strep A Abon kit [Hangzhou, China] was used as the rapid antigen test. Results: Nine hundred thirty-six patients had no bacterial growth in their throat cultures, while 307 throat cultures were positive for GABHS. The sensitivity and specificity of the rapid antigen test were 73% and 96.8%, respectively. The positive and negative predictive values for the rapid. antigen test were 88.2% and 91.6%, respectively. Conclusion: Although the specificity of the rapid antigen test used in this study Was high (96.8%), its sensitivity was determined to be lower (73%). Therefore, for patients in whom negative test results are obtained, it would be appropriate to confirm the test results with throat cultures.