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    Analysis of peripheral blood lymphocyte phenotypes and Th1 Th2 cytokines profile in the systemic immune responses ofHelicobacter pylori infected individuals
    (Microbiology and Immunology, 2008) Kayhan, Başak; Araslı, Mehmet; Eren, Hacı; Aydemir, Selim; Aktaş, Elif
    H. pylori elicits specific humoral and cellularimmune responsesin themucosalimmune system.However, the type and extent of T lymphocyte response in the systemic immune system is not clear for H. pylori positive patients. In this study, peripheral blood T lymphocyte phenotypes and serum Th1/Th2 based cytokines of 32 H. pylori positive patients were analyzed and compared to those of healthy controls. While αβ TCR+ lymphocytes and their phenotype analysis were not significantly different to those of healthy controls, the percentage of pan γδ TCR+ lymphocytes was up to 2.4 times greater in the H. pylori positive group then in healthy controls. Furthermore, significant increases in IL-10 concentrations in serum samples of H. pylori patients indicated that their immune systems had switched toward a Th2 type immune response. The correlation between phenotype and type of T cell response in the peripheral blood during H. pylori infection is discussed.
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    Evaluation of emm gene types toxin gene profiles and clonal relatedness of group A streptococci
    (Bosnian Journal of Basic Medical Sciences, 2013) Mengeloğlu, Fırat Zafer; Aktaş, Elif; Otlu, Barış; Cömert, Füsun; Külah, Canan; Taş, Ebru; Sümbüloğlu, Vildan
    Th e aim of this study is to evaluate antibiotic susceptibilities, emm gene types, toxin gene profi les and clonal relatedness of group A streptococci (GAS) isolates obtained from patients and carriers. A total of  clinical isolates from patients and  isolates from carriers were included in the study. Emm typing, toxin gene detection for speA, speB, speC, speG and smeZ genes and pulsed-fi eld gel electrophoresis (PFGE) was performed. Twenty-one distinct emm types were detected; the most common types were emm, emm, emm, emm, emm and emm. Th e detection rates of both emm types and the toxin genes didn’t diff er signifi cantly between patients and carriers. Th e presence of speA and smeZ was signifi cantly higher in emm and speG was signifi cantly lower in emm when compared to the other emm types. Th e rate of clustering obtained with PFGE wasn’t signifi cantly diff erent in patients and carriers. As a result, twelve of the  emm types detected in this study were covered by the -valent vaccine, constituting . of the emm typeable isolates; however the emm type which is one of the most common types in the present study is not among this coverage.
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    Evaluation of the Carbapenem Inactivation Method for Detection of Carbapenemase Producing Gram Negative Bacteria in Comparison with the RAPIDEC CARBA NP
    (Microbial Drug Resistance, 2016) Aktaş, Elif; Malkoçoğlu, Gülşah; Otlu, Barış; Çopur Çiçek, Ayşegül; Külah, Canan; Cömert, Füsun; Sandallı, Cemal; Gürsoy, Nafia Canan; Erdemir, Duygu; Bulut, Mehmet Emin
    Timely detection of carbapenemases by both phenotypic and genotypic methods is essential for developing strategies to control the spread of infections by carbapenem-resistant isolates and related morbidity and mortality. The aim of this study was to compare the performance of a commercial kit, the RAPIDEC® CARBA NP, and an in-house technique, the carbapenem inactivation method (CIM), against a panel of 136 carbapenemase- and noncarbapenemase-producing Enterobacteriaceae, Acinetobacter baumannii, and Pseudomonas aeruginosa isolates. RAPIDEC CARBA NP displayed 99% sensitivity and 100% specificity, whereas the sensitivity and specificity were 78% and 100% for the CIM test, respectively. A slight modification of the CIM test, a prolonged incubation time of 4 hours instead of two, increased the sensitivity of the test to 90% by diminishing false negativity particularly for A. baumannii. In conclusion, both tests possess a high performance and are practical for the detection of carbapenemases. Although RAPIDEC CARBA NP is a more rapid and reliable method, the CIM test may represent a useful tool for microbiology laboratories due to its simplicity and availability at any laboratory with low cost.
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    Femoral Hemodiyaliz Kateteri ile İlişkili Globicatella sanguinis Bakteremisi: Tür Düzeyinde Tanımlamada Karşılaşılan Sorunlar
    (2017) Aktaş, Elif; Gürsoy, Nafia Canan; Koç, Yener; Hamidi, Aziz Ahmad; Bulut, Emin; Erdemir, Duygu; Otlu, Barış
    Öz: Bu olguda diyabetik nefropati tanısıyla kronik hemodiyaliz programına alınan 43 yaşında kadın hastada saptanan Globicatella sanguinis'e bağlı kateterle ilişkili bakteremi olgusu sunulmuştur. Fırsatçı ve nadir bir patojen olan Globicatella cinsinin laboratuvar tanısında kullanılan yöntemler irdelenmiştir. Mayıs 2016 tarihinde hastanın bir set periferik kan kültürü ve eş zamanlı olarak kateter kültürü alınmıştır. Üreyen bakterinin tanımlanması için biyokimyasal testler, Phoenix (BectonDickinson, ABD) ve MicroScan (BeckmanCoulter, ABD) otomatik identifikasyon sistemleri, matriks aracılı lazer desorpsiyon/iyonizasyonuçuş zamanlı kütle spektrometresi (MALDI-TOF MS) temelli Microflex MS (Bruker, Daltonics, Almanya) ve VITEK MS (database v2.0) (bioMérieux, Fransa) sistemleri kullanılmıştır. Etkene özgül p8FPL 5'-AGT TTG ATC ATG GCT CAG-3' ve p806R 5'-GGA CTA CCA GGG TAT CTA AT-3' primerleriyle kısmi 16S rDNA dizi analizi yapılmıştır. Vankomisin, eritromisin, imipenem, sefotaksim ve benzipenisilin için minimum inhibitör konsantrasyonu (MİK) agar gradient yöntemiyle belirlenmiştir. Hastanın kan ve kateter kültürlerinde aynı koloni üremesi tespit edilmiştir. Kanlı besiyerlerinde bir gecelik inkübasyon sonrası gözlenen alfa-hemolitik, katalaz-negatif koloniler, Gram boyama ile gram-pozitif zincir yapan koklar şeklinde görülmüştür. İzolat, Şişli Hamidiye Etfal Eğitim ve Araştırma Hastanesinde; Bruker MS sistemi ile G.sulfidifaciens (skor değeri > 2), Phoenix otomatik identifikasyon sistemi ile G.sanguinis olarak tanımlanmıştır. İnönü Üniversitesi Tıp Fakültesinde; Microscan otomatize sistemiyle tanımlama yapılamamış, VITEK MS ile izolat %99.9 G.sanguinis ve %98.3 G.sulfidifaciens olarak isimlendirilmiştir. 16S rDNA dizi analiziyle izolat %100 Globicatella sanguinis (GenBank accessionno. KJ680157.1) olarak tanımlanmıştır. MİK değerleri vankomisin için 0.38 µg/ml, eritromisin için 1.5 µg/ml, imipenem için 0.38 µg/ml, sefotaksim için > 32 µg/ml ve benzipenisilin için 64 µg/ml olarak belirlenmiştir. Hastada katetere bağlı kan dolaşımı enfeksiyonu olarak düşünüldüğü için, tedaviye vankomisin 1 x 1 g IV/72 saat olarak 10 güne kadar devam edilmiştir. Hastanın kontrollerinde ateş ve üreme olmamıştır. G.sanguinis, sıklıkla karşılaşılan patojenler içerisinde yer almadığından ve laboratuvar tanısında karşılaşılan güçlükler nedeniyle belki de gözden kaçabilmekte veya yanlış tanımlanabilmektedir. BD Phoenix veritabanında G.sulfidifaciens, Bruker MS veritabanında G.sanguinis ve MicroScan veritabanında Globicatella cinsinin mevcut olmadığı görülmüştür. Son yıllarda gelişen tıbbi uygulamalar ve immün sistemi baskılanmış hasta popülasyonundaki artış nedeniyle nadir bakteri türleri daha da sık görülecektir. Klinik mikrobiyoloji laboratuvarlarının, hem klasik mikrobiyolojik yöntemlerle hem de moleküler yöntemlerle tanı gücünün artırılması, ticari identifikasyon sistemi geliştiren şirketlerin patojen spektrumunu genişleterek veritabanlarını yenilemeleri bu tür etkenlerle oluşabilecek ciddi enfeksiyonların önlenmesi açısından önem taşımaktadır.
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    Mycobacterium tuberculosis klinik suşlarındaki izoniazid ve rifampin direncinin moleküler karakterizasyonu
    (İnönü Üniversitesi, 2004) Aktaş, Elif
    M-tuberculosis'in rifampin (RIF) ve izoniazid (INH)’e dirençli olması tüberküloz kontrolü için ciddi bir tehdit oluşturmaktadır. İlaca dirençli tüberkülozun kontrolü, dirençli vakaların hızlı ve uygun tedavisine dayanır. Farklı kaynaklardan elde edilen INH ve RIF dirençli M.tuberculosis klinik suşlannm moleküler özellikleri, yaygm olarak kullanılabilecek hızlı moleküler tam metodlanmn geliştirilmesinde yararlı bilgiler sağlayabilir. Bu çalışmada; Malatya bölgesinde toplanan 29 ilaca dirençli klinik izolat arasından INH ve RIF direncine neden olan iki gen, otomatize DNA dizi analizi ve multipleks alele özgül PZR(MAS-PZR) kullanılarak incelendi. îzolatlann 19’u çoğul ilaçlara dirençli, ikisi yalmzca RIF dirençli ve sekizi yalmzca INH dirençli izolatlardı. RIF direnci karakterizasyonu için, RIF direnci göstergesi olarak bilinen 81 bç’lik bölgeyi de içeren RNA polimerazın P alt ünitesini kodlayan gen olan rpoB geninin 250 bç’lik merkezi bölgesinin dizi analizi yapıldı. MAS-PZR, kodon 516, 526 ve 531 ’i hedef alıyordu. INH direnci karakterizasyonu katalaz-peroksidaz enzimini kodlayan gen olan katG geninin 435 bç’lik bölgesinin dizi analizi yapıldı. Bu bölge INH direnci ile en sık ilişki gösteren kodon 315’i de içeriyordu ve MAS-PZR’de kodon 315’teki mutasyonlann tespiti için kullanıldı.
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    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.
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    VIM-1, VIM-2, and GES-5 Carbapenemases Among Pseudomonas aeruginosa Isolates at a Tertiary Hospital in Istanbul, Turkey.
    (Microbial Drug Resistance, 2017) Malkoçoğlu, Gülşah; Aktaş, Elif; Bayraktar, Banu; Otlu, Barış; Bulut, Mehmet Emin
    Worldwide increase in carbapenem resistance and transferable carbapenemases are significant challenges in treatment of Pseudomonas aeruginosa infections. In this study, investigation of carbapenemase production in carbapenem-resistant P. aeruginosa isolates recovered from clinical specimens in a tertiary hospital was aimed. A total of 84 carbapenem-resistant P. aeruginosa isolates were examined. "Carbapenem inactivation method" (CIM) was used for phenotypic detection of carbapenemase production. The existence of blaKPC, blaNDM, blaIMP, blaVIM, blaOXA-48, and blaGES genes was investigated by polymerase chain reaction (PCR). Subtypes of the detected genes were identified by sequence analysis. Arbitrarily primed PCR (AP-PCR) was performed to evaluate the clonal relationship among the isolates. The presence of high-risk clones in carbapenemase producers was investigated by Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). Three isolates (3.5%) were identified as carbapenemase producers by CIM tests, while PCR tests demonstrated three isolates carrying carbapenemase genes as well. blaVIM gene was found in two isolates and blaGES gene was found in one isolate. Sequence analysis demonstrated that the carbapenemases were VIM-1, VIM-2, and GES-5. AP-PCR yielded high clonal diversity among the isolates. According to MALDI-TOF MS analysis, none of the carbapenemase-producing strains belonged to the high-risk clones. In conclusion, the presence of VIM-1, VIM-2, and GES-5 type carbapenemases in P. aeruginosa isolates was demonstrated for the first time in our hospital, GES-5 being reported for the second time in Turkey. Our results will lead strategies for controlling the spread of carbapenemases and contribute to epidemiological data from Turkey.