Browsing by Author "Özkütük N."
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Item Atlas of cell organelles fluorescence(CRC Press, 2003) Kohen E.; Santus R.; Hirschberg J.G.; Özkütük N.Containing over 150 original photomicrographs accompanied by protocol information, Atlas of Cell Organelles Fluorescence delineates organelles’ structures, interaction, and organization into complexes. It provides a collection that shows living cells under physiopathological conditions and in the context of treatment with carcinogens, xenobiotics, and chemotherapeutic drugs as well as photosensitizers. A guide for therapeutic, diagnostic, or prognostic interpretation of images, and for further research, the atlas helps you identify critical points of attack and suggests possible strategies for investigation. Each section provides a brief introduction and the technical details of the staining methods used. The text identifies the organelles and gives explanations of unusual appearances and the cytochemical reactions when necessary. Additional text is provided where appropriate for extension and implementation of methods being utilized to generate similar results. In all cases the normal and pathological markers and content are presented. The atlas includes a color insert that illustrates characteristic organelle features, microcompartmentalization, and alterations as investigated by one or more probes simultaneously. The book, an exhaustive list of cellular events observed using microfluorometry, supplies a compilation of information spread throughout the literature of the last 30 years. Atlas of Cell Organelles Fluorescence brings the information together and puts it in an easily accessible format. © 2004 by Taylor & Francis Group, LLC.Item Assessment of performance of "amplified Mycobacterium tuberculosis direct test" in pulmonary and extrapulmonary specimens; [Akci̇ǧer ve akci̇ǧer dişi örneklerde "ampli̇fi̇ye Mycobacterium tuberculosis di̇rek test" i̇n güveni̇li̇rli̇ǧi̇ni̇n deǧerlendi̇ri̇lmesi̇](2007) Sürücüoǧlu S.; Özkütük N.; Gazi H.; Çelik P.Since rapid diagnosis is critical in control of tuberculosis, nucleic acid amplification techniques have been widely used. The purpose of the present study was to assess the performance of Amplified Mycobacterium tuberculosis Direct Test (Amplified MTD Test, Gen-Probe) for the diagnosis of pulmonary and extrapulmonary tuberculosis in our laboratory. A total of 267 specimens (170 pulmonary and 97 extrapulmonary) were tested in the Clinical Mycobacteriology Laboratory of Manisa (a province located in Aegean part of Turkey) University Hospital from September 2001 to March 2005. When Amplified MTD (AMTD) test results were compared to the culture results taken as the gold standard, the sensitivity, specificity, positive and negative predictive values (PPV, NPV) for pulmonary specimens were found to be 84%, 96%, 73%, and 98%, respectively. When AMTD test positive, culture negative discrepant results were evaluated against the clinical history of the patients, these rates were detected as; 88%, 100%, 100%, and 98%, respectively. For 97 extrapulmonary specimens, sensitivity, specificity, PPV and NPV of AMTD test were 60%, 100%, 100%, and 98%, respectively. In conclusion, the results of the AMTD assay were reliable for the rapid diagnosis of pulmonary tuberculosis; if the results were evaluated together with the clinical status of patients, the performance of the test would be increased. However, even though the culture positive extrapulmonary specimens were sparse in our study (5%), the sensitivity of the AMTD test in extrapulmonary specimens was found less than that in pulmonary specimens. Therefore it is thought that AMTD test results should be evaluated carefully for the diagnosis of extrapulmonary tuberculosis.Item Comparison of interferon-gamma whole blood assay with tuberculin skin test for the diagnosis of tuberculosis infection in tuberculosis contacts; [Temaslιlarda tüberküloz enfeksiyonunun tanιsι için interferon-gama tam kan testi ile tüberkülin deri testinin karşιlaştιrιlmasι](2007) Öztürk N.; Sürücüoǧlu S.; Özkütük N.; Gazi H.; Akçali S.; Köroǧlu G.; Çiçek C.Tuberculin skin test which is used for the detection of latent tuberculosis (TB), has many disadvantages such as false positivities due to cross reactions between environmental mycobacteria and BCG strain, false negativities due to immunosuppression and malpractice, and also difficulties in application and evaluation. Recently a new diagnostic test which measures the production of interferon (IFN)-gamma in whole blood upon stimulation with specific ESAT-6 and CFP-10 antigens of Mycobacterium tuberculosis has been introduced. Since most of the mycobacteria other than tuberculosis and BCG strain do not contain these antigens, the detection of IFN-gamma levels indicates the specific T-cell response against M.tuberculosis. The aim of the study was to compare the tuberculin skin test and whole blood IFN-gamma assay (QuantiFERON®-TB Gold, Cellestis Ltd, Carnegie, Victoria, Australia) for the identification of latent TB infection in the contacts with active TB patients. The tests results were evaluated by using Kappa (K) analysis, and K coefficients of <0.4, 0.4-0.75 and >0.75 were accepted as poor, moderate and excellent agreements, respectively. A total of 233 subjects from three risk groups were included to the study. Group 1 included the household members (n=133) who had contact with smear positive index cases, Group 2 included the subjects from community (n=46) who had contact with smear positive index cases, and Group 3 included health care workers (n=74) who had contact with TB patients or their specimens. The positivity rates of tuberculin skin test and IFN-gamma assay in the cases were found as 37% and 42%, respectively. There were no significant differences among the three patient groups with regard to the results of the tuberculin skin test (p>0.05). However, the positive result of the IFN-gamma assay in Group 1 was found statistically higher than the other groups (51.3%, p=0.013). A poor agreement between the two tests was detected in the results taken from 233 subjects (65.7%, K=0.28), while agreement was moderate in unvaccinated group (72.7%, K=0.44). Evaluation of agreement rates of the tests according to the risk groups yielded 64.6% (K=0.3) for Group 1, 71.7% (K=0.32) for Group 2, and 63.5% (K=0.21) for Group 3, which all coefficients showed poor agreement. Although IFN-gamma blood assay has many advantages such as objective and quantitative results, no interference with vaccination due to the use of specific antigens and being practical, the high cost and the need for well-equipped laboratory are its disadvantages. As a result it was concluded that, IFN-gamma blood assay has limited value for the detection of latent TB infection in our country, since the prevalence of TB infection and BCG vaccination rates are high in Turkey.Item Two novel serum-free media for the culture of Trichomonas vaginalis(2007) Limoncu M.E.; Kilimcioǧlu A.A.; Kurt Ö.; Östan I.; Özkütük N.; Özbilgin A.Definitive diagnosis of Trichomonas vaginalis, one of the common causes of sexually transmitted diseases in Turkey, relies on the microscopic examination of both fresh preparations and culture material of genital secretions and urine. The aim of this study was to compare the diagnostic efficacies of two culture media, serum-free TB1 and TB2, including iron and vitamin B12, respectively, with the well-known medium, TYM. Growth rate reached peak levels 48 h in TYM and 72 h in both TB1 and TB2 after inoculation. The highest amount of viable trophozoites has been obtained from TB1, almost equal to TYM but significantly higher than TB2. Fresh preparations obtained from the vaginal secretions of 119 patients have been examined and vaginal samples have been inoculated in TB1, TB2, and TYM. Viable T. vaginalis trophozoites have been detected in ten (8.4%) of fresh preparations and 11 (9.9%) of each medium. It is concluded that serum-free TB1 medium could be used effectively in both the isolation and maintenance of T. vaginalis culture in vitro. © 2006 Springer-Verlag.Item Pyrazinamide monoresistant Mycobacterium tuberculosis in Manisa region, Turkey; [Manisa bölgesinde pirazinamid-monorezistan Mycobacterium tuberculosis](2008) Özkütük N.; Ecemiš T.; Sürücüoǧlu S.Pyrazinamide (PZA) is a primary antituberculous drug. BACTEC 460TB is the recommended reference method for the detection of PZA resistance in Mycobacterium tuberculosis. This method is more expensive than the conventional susceptibility methods and therefore, it is recommended that each laboratory should establish their own protocol for the inclusion of PZA in the panel of primary drugs tested. One of the most important factors that help this decision is the prevalence of PZA resistance, particularly PZA monoresistance in the related community. The aim of the present study was to determine the extent of PZA monoresistance in M.tuberculosis complex (MTBC) isolates in our region. In this study, PZA susceptibility testing of 109 MTBC strains (susceptible to isoniazid, rifampicin, ethambutol and streptomycin) isolated from Manisa province in the Aegean region of Turkey was performed by using the BACTEC 460TB radiometric system (Becton Dickinson, MD). Two (1.8%) of the 109 isolates which were susceptible to all primary drugs revealed monoresistance against PZA. One of the PZA-monoresistant isolates has been identified as M.bovis and the other as M.tuberculosis by molecular method (Genotype MTBC, Hain Lifescience, Germany). The results of our study indicated that since the rate of PZA monoresistance was low, susceptibility testing of a panel of primary drugs without PZA may be an economical alternative in our region.Item Second-line drug susceptibilities of multidrug-resistant Mycobacterium tuberculosis isolates in Aegean Region - Turkey(2008) Özkütük N.; Sürücüoǧlu S.; Gazi H.; Coşkun M.; Özkütük A.; Özbakkaloǧlu B.Aim: The emergence of multidrug-resistant tuberculosis (MDR-TB) is increasing, and the standard shortcourse regimen used for the treatment of TB is likely to be ineffective against MDR-TB, leading to the need for second-line drugs. In such situations, drug susceptibility testing is necessary to select an appropriate treatment regimen. Unfortunately, there are few studies showing the pattern of the second-line drug resistance in Turkey. We aimed to analyze the resistance to second-line anti-tuberculosis drugs of MDR strains of Mycobacterium tuberculosis isolated from the Aegean region of Turkey. Materials and Methods: In this study, drug susceptibility testing of 40 MDR-TB strains isolated from the Aegean region of Turkey was performed using the BACTEC 460 TB radiometric system. Capreomycin, ethionamide, kanamycin, amikacin, clofazimine and ofloxacin were tested in 1.25 μg/ml, 1.25 μg/ml, 5.0 μg/ml, 1.0 μg/ml, 0.5 μg/ml, and 2.0 μg/ml concentrations, respectively. Results: The results showed that 37.5% of the strains were resistant to ethionamide, 25% to capreomycin, 5% to kanamycin, amikacin and ofloxacin, and 2.5% to clofazimine. One (2.5%) of the 40 MDR-TB cases was defined as extensively drug-resistant tuberculosis (XDR-TB). Conclusions: The results of the study indicate that the high rates of resistance to ethionamide and capreomycin may be a problem in the treatment of patients with MDR-TB; XDR-TB is not yet a serious problem in our region. © TÜBİTAK.Item Seroprevalance of chlamydophila pneumoniae in patients with alzheimer's disease and vascular dementia; [Alzheimer ve vasküler demanslı hastalarda chlamydophila pneumonaie seroprevalansı](Ege University Press, 2010) Ecemiş T.; Mavioǧlu H.; Özkütük N.; Akçali S.; Karaçam M.; Şanlidaǧ T.In recent years, it was been argued that Chlamydophila pneumoniae, which is an intracellular pathogen capable of causing chronic infection, might be effective in some forms of dementia, an argument confirmed or rejected by some studies. The objective of this study was to determine if there was an association between C. pneumoniae infection and Alzheimer's disease and vascular dementia. We tested 54 patients with Alzheimer and 29 patients with vascular dementia and 50 controls for C. pneumoniae IgG and IgA antibodies and analyzed the results statistically. C. pneumoniae IgG antibodies were found in 25 patients (49.2%) with Alzheimer's disease, 15 patients (51.8%) with vascular dementia and 22 controls (44%) whereas 6 patients (11.1%), 2 patients (6.9%) and 3 controls (6%), respectively, tested positive for IgA. It was found no serological evidence for a significant association between C. pneumoniae and Alzheimer's disease as well as vascular dementia.Item Pott's disease with scrofuloderma and psoas abscess misdiagnosed and treated as hidradenitis suppurativa(2011) Ermertcan A.T.; Öztürk F.; Gençoǧlan G.; Nanir I.; Özkütük N.; Temiz P.A 29-year-old man with painless ulcers on the lumbar and inguinal regions associated with purulent discharge of 1.5 years' duration presented to our outpatient clinic. Dermatological examination revealed palpable nodules, discharging sinuses and scars on the left lumbar, gluteal and inguinal regions. According to the clinical, histopathological, scintigraphy, and magnetic resonance imaging findings as well as mycobacteriological examinations, the patient was diagnosed with Pott's disease with scrofuloderma and psoas abscess. Herein, we present an interesting case of Pott's disease with scrofuloderma and psoas abscess mistreated as hidradenitis suppurativa for a long time. © 2011 Informa Healthcare USA on behalf of Informa UK Ltd.Item Roles of phospholipase, esterase and slime activities of Candida albicans strains in infection-colonisation differentiation; [Candida albicans suşlarının fosfolipaz, esteraz ve slime aktivitelerinin enfeksiyon-kolonizasyon ayrımındaki rolleri](Turkiye Klinikleri, 2012) Pekintürk N.; Deǧerli K.; Özkütük N.; Ecemiş T.; Kurutepe S.; Özbakkaloǧlu B.Objective: This study investigated slime factor, phospholipase and esterase activities of C. albicans strains isolated as the infectious agent from healthy individuals, their effectiveness as virulen-ce factors and interactions between each other. For this purpose, virulence factors of 50 C.albicans stra-ins isolated from specimens as infectious agent (infection group) and 50 C.albicans isolates obtained from oral smears of the control group (control group) were analyzed and roles of virulence factors in differentiation of colonisation and infection were investigated. Material and Methods: C.albicans ATCC 10039 and 50 C.albicans strains isolated from clinical specimes of patients who were treated in various clinics of our hospital were used as reference strains. The strains isolated from sterile body sites and from clinical specimens containing pseuduhyphe on direct examination were considered as infectious agent and were identified as C.albicans by germ tube test and chlamidospore formation. Yolc sac agar medi-um was used to detect phospholipase activity, Tween 80 agar medium was used to detect esterase acti-vity and Kongo red brain-heart infusion agar medium was used to detect slime activity. Results: There was no significant difference in terms of slime, phospholipase and esterase activities of C. albicans stra-ins isolated from patients compared to controls (p= 0.357, p= 0.842, p= 0.841). Consistency analysis be-tween virulence factors revealed no significant difference in the patient group. In the other hand, in the control group, esterase/phospholipase coexistence consistency was significant (K value= +0.35, p= 0.001). Conclusion: In conclusion, we suggest that many virulence factors of C. albicans have impor-tant roles in the development of C. albicans-related infections. © 2012 by Türkiye Klinikleri.Item Molecular diversity of drug resistant Mycobacterium tuberculosis strains in Western Turkey(Galenos Publishing House, 2012) Sürücüoǧlu S.; Günal S.; Özkütük N.; Biçmen C.; Özsöz A.; Gazi H.; Durmaz R.Objective: The aim of this study was to investigate the molecular diversity and clonal relationship of drug resistant Mycobacterium tuberculosis strains isolated in Western Turkey. Materials and Methods: A total of 87 strains isolated between 2006 and 2009, eight of which were rifampicin monoresistant and 79 were multidrug resistant, were analyzed with IS6110 RFLP and spoligotyping methods. Results: The results of spoligotyping showed that 7% of the strains were orphans, and 8% were undefined for family in the SpolDB4 database. Major families of the strains were LAM (38%), T (35%), Haarlem (7%), Beijing (2%), S (2%) and U (1%) families. The clustering rate by spoligotyping was calculated as 75%. The most predominant SIT cluster was SIT41 (29%). According to the results of IS6110 RFLP, 71 different patterns of IS6110 were observed. Low copy number was found in 26% of the strains. When the results of two methods were combined, the final clustering rate was calculated as 26%. Conclusions: The genotypical distribution of drug resistant tuberculosis isolates in our region indicates genetic diversity and the clustering rate was found low in our region. However, more comprehensive and long-term molecular epidemiological studies are needed to control the drug resistant strains. © Trakya University Faculty of Medicine.Item T030 is the most common spa type among methicillin-resistant staphylococcus aureus strains isolated from Turkish hospitals; [T030, Türkiye'deki hastanelerden izole edilen metisiline dirençli staphylococcus aureus izolatlari arasinda en yaygin spa tipidir](Ankara Microbiology Society, 2013) Bozdoǧan B.; Yildiz Ö.; Oryaşin E.; Kirdar S.; Gülcü B.; Aktepe O.; Arslan U.; Bayramoǧlu C.; Çoban A.Y.; Coşkuner S.A.; Güdücüoǧlu H.; Karablber N.; Öncü S.; Tatman Otkun M.; Özkütük N.; Özyurt M.; Şener A.G.Staphylococcus aureus is one of the most frequent agents causing hospital infections. S.aureus has a great ability to adapt itself to variety of conditions and successful clones can be epidemic and even pandemic by its ability spread from one continent to another. The aims of this study were to detect spa types of 397 methicillin-resistant S.aureus (MRSA) strains isolated from 12 centers in different geographical regions of Turkey from 2006 to 2008, and to investigate their clonality by PFCE and MLST typing. Additionally, 91 MRSA from four of those 12 centers isolated during 2011 were also studied for their spa types. PFGE profiles indicated the presence of a major pulsotype, namely pulsotype A with a rate of 91.4% (363/397), followed by pulsotype B (n= 18, 4.5%) and pulsotype C (n= 11, 2.8%). Among isolates tested 363 (91.4%) were SCCmec type III, 30 (7.6%) were SCCmec type IV. Sequence analysis of representative isolates revealed that ST239 (85.1%) was the most common MLST type followed by two MLST types ST737 (4%), and ST97 (2.8%), both SCCmec type IV. Two isolates were ST80 with SCCmec type IV. Of 397 isolates, 338 (85.1%) were t030, followed by t005 (2.5%) and t632 (2%). Among MRSA isolated during 2011, 64 (70.3%) of 91 were t030, 4 (4.4%) were tOOS, 2 (2.2%) were t015, and 2 (2.2%) were t1094. Among centers the t030 prevalence of 2006-2008 isolates ranged from 59-100%. The highest t030 prevalence was found in Ankara (100%) and lowest in Trabzon (59%) provinces which are located at central and northestern Anatolia, respectively. In Istanbul province, the prevalence of t030 was 94.5% among 2006-2008 isolates which decreased to 55.5% among 2011 isolates. Also a decrease in t030 rates was observed among samples from Konya and Trabzon but not from Aydin. Our results showed that the most common MRSA clone in Turkey is ST 239-SCCmec type III, t030 which persisted during the six years of the study period. Presence of PVL toxin gene was tested by PCR and 5 (3%) isolates found to be positive, of them two were SCCmec Type IV-ST80 and three were SCCmec Type III-ST239. This study is the largest epidemiological survey ever done in Turkey which showed presence of a hospital Turkish clone TR09 (ST239-SCC meclll-t030) and a community clone TR10 (ST737-SCCmedV-t005) largely disseminated in Turkey.Item Investigation of extensive drug resistance in multidrug resistance tuberculosis isolates; [Çok İlaca Dirençli Tüberküloz İzolatlarinda Yaygin İlaç Direncinin Araştirilmasi](Ankara Microbiology Society, 2013) Bektöre B.; Haznedaroǧlu T.; Baylan O.; Özyurt M.; Özkütük N.; Şatana D.; Çavuşoǧlu C.; Seber E.Increasing number of drug resistant tuberculosis (TB) cases, observed in recent years, is an important public health problem. Extensively drug resistant TB (XDR-TB) is the development of resistance against any fluoroquinolones and at least one of the injectable second line anti-TB drugs in addition to resistance against isoniazide and rifampicin which are the first line anti-TB drugs [definition of multidrug resistant TB (MDR-TB)]. Anti-TB therapy failed with first-line anti-TB drugs due to MDR-TB cases is being planned according to second-line anti-TB drug susceptibility test results if available and if not, standart treatment protocols are used. Although it is recommended that individual anti-TB therapy should be designed according to the isolate's susceptibility test results, standart therapeutic protocols are always needed since second-line anti-TB drug susceptibility testing generally could not be performed in developing countries like Turkey. For this reason, nationwide and regional surveillance studies to determine the resistance patterns are always needed to make decisions about the standard therapy algorithms. In this study, it was aimed to investigate the presence of extensive drug resistance among 81 MDR-TB isolates obtained from various health care facilities from Istanbul, Izmir and Manisa and to determine the XDR-TB incidence in Marmara and Aegean regions. Furthermore, we aimed to provide epidemiological data to clinicians to support their choice of second-line anti-TB drugs for MDR-TB infections. Susceptibility testing of isolates for the first and the second-line anti-TB drugs were performed by using modified Middlebrook 7H9 broth in fluorometric BACTEC MCIT 960 system (Becton Dickinson, USA). Eighty-one MDR-TB isolates included in this study were isolated from 43 (53.1%) patients residing in Istanbul, 26 (32.1%) in Izmir and 12 (14.8%) in Manisa provinces. We could not find any isolate consistent with XDR-TB definition in this study. Second-line drug resistance rates of MDR-TB isolates to amikacin and kanamycin were 1.2%, ofloxacin and levofloxacin were 2.5%, capreomycin was 14.8%, ethionamide was 37% whereas linezolid resistance was not detected. Statistically significant correlation was detected between resistance rates of these antibiotic pairs; levofloxacin-ofloxacin (p< 0.01), amikacin-kanamycin (p= 0.01) and streptomycin-ethionamide (p= 0.04). In our study, extensive drug resistance was not encountered in any MDR-TB isolates while high resistance rates was observed against ethionamide and capreomycin. It can be concluded that parenteral aminoglycosides amikasin and kanamycin, fluoroquinolones and linezolid seemed to be reliable anti-TB agents in MDR-TB treatment, however, further larger scale studies are needed.Item Pyrazinamide monoresistance in clinical isolates(2013) Kalir N.; Özkütük A.A.; Esen N.; Özkütük N.Aim: To determine pyrazinamide (PZA) monoresistance in clinical isolates of Mycobacterium tuberculosis complex (MTBC) isolated in hospitals in and around İzmir. Materials and methods: The study was performed between 2004 and 2009 with 150 streptomycin, isoniazid, rifampicin, and ethambutol susceptible MTBC clinical strains isolated in the university hospitals of İzmir and Manisa. The PZA susceptibility of the isolates was determined by the BACTEC 460 TB test. Results: The results indicated that resistance to PZA was present in 5 (3.3%) of the 150 MTBC isolates susceptible to all primary drugs except PZA. Conclusion: It is not essential to perform PZA susceptibility tests routinely along with other primary drugs due to the low PZA monoresistance level in our region. © TÜBİTAK.Item Antimicrobial susceptibility and resistance mechanisms of methicillin resistant Staphylococcus aureus isolated from 12 Hospitals in Turkey(BioMed Central Ltd., 2014) Yildiz T.; Çoban A.Y.; Şener A.G.; Coşkuner S.A.; Bayramoğlu G.; Güdücüoğlu H.; Özyurt M.; Tatman-Otkun M.; Karabiber N.; Özkütük N.; Aktepe O.; Öncü S.; Arslan U.; Bozdoğan B.Introduction: Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most important nosocomial pathogens and is also emerging in Turkish hospitals. The aim of this study was to determine the antimicrobial susceptibility profiles of MRSA isolated from Turkish hospitals. Materials and methods: A total of 397 MRSA strains isolated from 12 hospitals in Turkey were included to present study. Antimicrobial susceptibilities were tested using agar dilution method. Presence of ermA, ermB, ermC, msrA, tetM, tetK, linA and aac-aph genes were studied by PCR. Results: All strains were susceptible to vancomycin and linezolid. The susceptibility rates for fusidic acid, lincomycin, erythromycin, tetracyclin, gentamycin, kanamycin, and, ciprofloxacin were 91.9%, 41.1%, 27.2%, 11.8%, 8.5%, 8.3% and 6.8%, respectively. Lincomycin inactivation was positive for 3 isolates. Of 225 erythromycin resistant isolates 48 had ermA, 20 had ermC, and 128 had ermA-C. PCR was negative for 15 strains. Of 3 isolates with lincomycin inactivation one had linA and msrA. Of 358 gentamycin resistant isolates 334 had aac-aph and 24 were negatives. Among 350 tetracyclin resistant isolates 314 had tetM. Of 36 tetM negative isolates 10 had tetK. Conclusion: MRSA isolates from Turkish hospitals were multiresistant to antimicrobials. Quinolone and gentamycin resistance levels were high and macrolide and lincosamide resistance were relatively low. Susceptibility rates for fusidic asid were high. Linezolide and vancomycin resistance are not emerged. The most common resistance genes were ermA, tetM and aac-aph. Evolution of antimicrobial susceptibilities and resistance genes profiles of MRSA isolates should be surveyed at regional and national level for accurate treatment of patients and to control dissemination of resistance genes. © 2014 Yildiz et al.; licensee BioMed Central Ltd.Item Evaluation of the Xpert MTB/RIF assay for the diagnosis of pulmonary and extrapulmonary tuberculosis in an intermediate-prevalence setting; [Orta Prevalansli Bölgede Akciǧer ve Akciǧer DIŞI Tüberküloz Tanisinda Xpert MTB/RIF Testinin Deǧerlendirilmesi](Ankara Microbiology Society, 2014) Özkütük N.; Sürücüog̈lu S.Early and accurate detection of tuberculosis (TB) is a global priority for TB control. In order to obtain results in a short period of time, nucleic acid amplification tests are increasingly used worldwide for the rapid diagnosis of tuberculosis. The Xpert MTB/RIF® (Cepheid, USA) is a commercially available, real-time PCR-based assay, which can detect both TB and resistance to rifampicin directly in clinical samples. The aim of this study was to evaluate the performance of Xpert MTB/RIF assay for M. tuberculosis detection in pulmonary and extrapulmonary clinical samples in routine laboratory practice in Turkey, an intermediate-prevalence setting. A total of 2639 clinical specimens, 1611 of which were pulmonary and 1028 were extrapulmonary, were included in the study. The results of Xpert MTB/RIF assay were evaluated by comparing the results with those obtained by culture [BACTEC MGIT 960 (Becton Dickinson, USA) and Löwenstein Jensen medium]. Overall sensitivity, specificity, positive and negative predictive values of Xpert MTB/RIF assay were determined as 73.9%, 98.6%, 79.6% and 98.1%, respectively. These values were calculated as 80.8%, 98.8%, 84.9% and 98.4% for pulmonary specimens, and 58.2%, 98.4%, 66.7% and 97.7% for extrapulmonary specimens. The sensitivity and specificity were 100% and 58.1%, respectively, for acid-fast bacilli (AFB) smear-positive specimens, 39.7% and 99.1%, respectively for smear-negative specimens. The sensitivity and specificity were 100% and 76.2% for smear-positive pulmonary specimens; 100% and 20% for smear-positive extrapulmonary specimens; 47.8% and 99.1% for smear-negative pulmonary specimens; and 28.2% and 99.2% for smear-negative extrapulmonary specimens, respectively. The sensitivity and specificity of microscopic examination were found to be 56.7% and 98.7% for all specimens; 63.2% and 98.6% for pulmonary specimens; and 41.8% and 99% for extrapulmonary specimens, respectively. Rifampicin resistance was detected by Xpert MTB/RIF assay in only two specimens, however, rifampicin resistance was failed to be detected by BACTEC MGIT 960 TB method in one of these samples. Xpert MTB/RIF assay appeared to be a reliable method for the diagnosis of TB for AFB smear-positive samples, but less sensitive for smear-negative samples, particularly for extrapulmonary samples which include low numbers of bacilli. However, we concluded that the MTB/ RIF is a useful assay for rapid diagnosis of tuberculosis, considering that the results can be given in the same day of sample collection and the assay is superior in sensitivity than microscopic examination.Item Distribution of nontuberculous mycobacteria isolated from clinical specimens and identified with DNA sequence analysis; [Klinik Örneklerden Soyutlanan ve DNA Dizi Analizi ile Tanimlanan Tüberküloz Dişi Mikobakterilerin Daʇilimi](Ankara Microbiology Society, 2015) Özçolpan O.O.; Sürücüoʇlu S.; Özkütük N.; Çavuşoʇlu C.The aims of the study were to perform the identification of nontuberculous mycobacteria (NTM) isolated from different clinical specimens in the Mycobacteriology Laboratory of Celal Bayar University, Manisa (located at Aegean region of Turkey), by DNA sequence analysis, and to discuss the epidemiological aspects of the data obtained. Out of 5122 clinical specimens sent to the laboratory with the initial diagnosis of tuberculosis in the period April 2007 to July 2011, M.tuberculosis complex and NTM were identified in 225 (4.39%) and 126 (2.46%) samples, respectively. DNA sequence analysis by targeting hsp65 and 16S rDNA gene regions was performed on 101 of the NTM strains in Mycobacteriology Laboratory of Ege University, Izmir. DNA sequence analysis data was evaluated using RIDOM and GenBLAST data bases. NTM strains were identified as 40 M.porcinum (39.60%), 36 M.lentiflavum (35.65%), six M.abscessus (5.64%), five M.peregrinum (4.95%), four M.gordonae (3.96%), three M.fortuitum (2.97%), two M.chelonae (1.98%), and one for each M.alvei (0.99%), M.scrofulaceum (0.99%), M.kansasii (0.99%) species. Two strains which were both 95-98% compatible with other mycobacteria in the data bases could not be identified with certainty. Seventy-two (94.73%) strains of M.lentiflavum and M.porcinum, which were the most frequent (75.24%) species in the study, were isolated from bronchoalveolar lavage (BAL) specimens. The remaining 99 strains examined could not be proven as the cause of the disease due to absence of patients' clinical data, whereas two M.abscessus strains isolated from the sputum were considered as the cause of the disease according to the ATS/IDSA criteria. The isolation rate of NTM in 2010 was found significantly higher (5.33%) than previous years. Review of the 2010 data showed that all strains of M.porcinum and M.lentiflavum, which were the most frequently identified strains were isolated from BAL specimens. This situation is in line with the start of using of an automatic bronchoscope washing machine in our hospital in the same year. In conclusion, NTM were isolated in 2.46% of the clinical specimens of the patients with the initial diagnosis of tuberculosis and these strains belonged to 10 different NTM species. The two NTM species most frequently isolated in our study were M.lentiflavum and M.porcinum which are known for their potential to cause human infections and antibiotic resistance. As these strains were mostly isolated in BAL specimens, it is concluded that automatic bronchoscope washing machines and water delivery system in the hospitals should be examined in terms of contamination by NTM. The isolated NTM strains could not be distinguished as the cause of the disease or a contaminant, which is the limiting factor in this study. However, knowing that the environmental mycobacteria can cause hospital infections, the data obtained in this study can contribute to epidemiology of NTM infections in Turkey.Item Multicentef evaluation of the indirect nitrate reductase assay for the rapid detection of multidrug-resistant tuberculosis; [Çok ilaca dirençli tüberkulozun hizli tespiti için dolayli nitrat redüktaz testinin çok merkezli deǧerlendirilmesi](Ankara Microbiology Society, 2016) Çoban A.Y.; Taştekin B.; Uzun M.; Kalayci F.; Ceyhan I.; Biçmen C.; Albay A.; Siǧ A.K.; Özkütük N.; Sürücuoglü S.; Ozkütük A.; Esen N.; Albayrak N.; Aslanturk A.; Saribaş Z.; Alp A.Multidrug-resistant tuberculosis (MDR-TB) is defined as resistance to at least isoniazid (INH) and rifampicin (RIF), and it complicates the implementation of tuberculosis control programmes. The rapid detection of MDR-TB is crucial to reduce the transmission of disease. The nitrate reductase assay (NRA) is one of the colorimetric susceptibility test methods for rapid detection of MDR-TB and based on the ability of reduction of nitrate to nitrite by Mycobacterium tuberculosis. The aim of this study was to evaluate the performance of the NRA for the rapid detection of MDR-TB. A total of 237 M.tuberculosis complex (MTC) isolates that were identified by the same method (BD MGIT™ TBc Identification Test, USA) from nine different medical centers in Turkey were included in the study. The susceptibility results of the isolates against INH and RIF obtained by reference test (Bactec MGIT™ 960, BD, USA) were then compared with NRA. In order to ensure consistency between centers, Lowenstein-jensen (Lj) medium with antibiotics and without antibiotics (growth control) and Griess reagent solution were prepared in a single center (Ondokuz Mayis University School of Medicine, Medical Microbiology Department) and sent to all participant centers with the standardized test procedure. After the inoculation of bacteria into the test tubes, the tubes were incubated at 37°C, and after seven days of incubation, 500 pi Griess reagent was added to the L) medium without antibiotics. If a color change was observed, an equal volume of Griess reagent was added to test L) media with antibiotics. When a color change was observed in L) media with antibiotics, it was considered that the isolate was resistant to tested antibiotics. Among 237 MTC isolates, 16 were resistant only to INH and nine were resistant only to RIF; 93 isolates (39.2%) were resistant (MDR) and 119 isolates (50.2%) were susceptible to both of the drugs determined with the reference susceptibility test. In the study, five INH-resistant isolates determined with reference method were found susceptible with NRT and eight INH-susceptible isolates determined with reference method were found resistant with NRT. In contrast, one RIF-resistant isolate determined with reference method was found susceptible with NRT and three RIF-susceptible determined isolates were found resistant with NRT. Accordingly, the concordance rate between the reference method and NRA were estimated as 94.5% for INH and 98.3% for RIF. The sensitivity, specificity, positive and negative predictive values of NRA were detected as 95.4%, 93.7%, 92.8% and 96% for INH, and 99%, 97.8%, 97.1% and 99.2% for RIF, respectively. The results of the 111 isolates were obtained on the seventh day, while the rest of the results were obtained between 10-14 days. In conclusion, the data of this multicenter study showed that NRA is a reliable, relatively inexpensive and practical method to perform for the rapid detection of MDR-TB.Item Seroprevalence of west nile virus, crimean-congo hemorrhagic fever virus, francisella tularensis and borrelia burgdorferi in rural population of Manisa, Western Turkey(Malaria Research Center, 2016) Gazi H.; Özkütük N.; Ecemis T.; Atasoylu G.; Köroglu G.; Kurutepe S.; Horasan G.D.Background & objectives: Zoonotic diseases are well recognised threat to public health globally. The information of regional prevalence and associated risk factors allow the national programmes to determine and frame better strategies for their control, as they also provide the actual status of zoonosis in the region. The aim of this study was to determine the seroprevalence of West Nile virus (WNV), Crimean-Congo hemorrhagic fever virus (CCHFV), Francisella tularensis and Borrelia burgdorferi among the rural residents of Manisa region, Turkey and to identify the associated risk factors. Methods: Cross sectional study was conducted in rural parts of Manisa, Aegean region of western Turkey in 2012. Blood samples from 324 randomly selected subjects were screened for the presence of IgG antibodies to WNV, CCHFV, F. tularensis and B. burgdorferi with commercially available kits. The demographic structure of the rural residents and risk factors related to lifestyle such as outdoor agriculture activities, animal husbandry, hunting and history of tick bite were questioned and their relationships with positive results were analyzed statistically. Results: It was observed that 49 subjects (15%) had IgG antibodies to at least one of the zoonotic agents studied. The seroprevalence of F. tularensis was highest with a percentage of 7.1% (n = 23). Distribution of the positive results for WNV, CCHFV and B. burgdorferi were 4.3% (n = 14), 3.7% (n = 12) and 0.9% (n = 3), respectively. Older age and uncompleted secondary education were the statistically significant risk factors for seropositivity to at least one zoonotic agent investigated. Logistic regression analyses confirmed that older age (over 50) increased the risk of WNV and CCHFV seropositivity. Interpretation & conclusion: Seropositivity rates were not found to be higher than the expected rates. Further, studies are needed to evaluate the threat of vector borne zoonoses and associated risk factors in the study area. © 2016, Malaria Research Center. All rights reserved.Item Chronic subcutaneous nodules, plaques and ulcers of the hand(Medknow Publications, 2017) Ermertcan A.; Özkütük N.; Temiz P.; Çavuşoǧlu C.; Sürücüoǧlu S.[No abstract available]Item The reliability of tuberculin skin test in the diagnosis of latent tuberculosis infection in psoriasis patients: A case-control study(Blackwell Publishing Inc., 2020) Sürücüoğlu S.; Türel Ermertcan A.; Çetinarslan T.; Özkütük N.Tuberculin skin test (TST), which is used in the diagnosis of latent tuberculosis infection, may cause Koebner's phenomenon and false-positive results in psoriasis patients. The purpose of this study is to compare TST with QuantiFERON-TB Gold Plus (QFT-plus) test in psoriasis patients and to determine the effects of psoriasis on TST results. Ninety-two psoriasis patients and 30 control subjects were included in the study. QFT-plus test, TST, and prick test to distinguish the increase of induration because of the skin trauma were performed on both groups. The demographics, risk factors for latent tuberculosis infection, BCG vaccination history, Koebner's history, psoriasis severity, and treatment history of the patients were recorded. The effects of these variables on test results were investigated by comparing those with control group. The criteria of National Tuberculosis Diagnosis and Treatment Guidelines were used in the evaluation of test results, and threshold value of positivity for TST was taken as 10 mm in BCG-vaccinated patients who are planned to start biological treatment. Prick test results were negative in the control group. There was no significant relation between the results of prick test and TST induration diameters in the patient group. Although TST positivity was significantly higher in patients (62%) compared with control group (33%), QFT-plus test results were not statistically different between two groups. Agreement between two tests was determined to be low in patient group with 48% (K = 0.1), and it was determined to be moderate with 77% in control group (K = 0.4). QFT-plus test was found to be negative in 46 of 57 TST-positive patients (80.7%) in patient group. It was determined in both groups that vaccination did not have any effect on test results. When threshold value was lowered to 5 mm in patient group without considering BCG reaction, the number of TST-positive patients increased from 57 to 65. Mean TST induration diameter was 10 mm and 14 mm in cases with mild and moderate to severe clinical manifestation, respectively (P =.04). However, no effect of disease period and treatment was determined on both test results. TST positivity was higher in psoriasis patients compared with control group. It was considered due to the increased reaction of the skin to mycobacterial antigens rather than the Koebner's response. Although TST results were not affected by BCG, it was concluded that a 10-mm threshold value of positivity was a suitable approach in order to reduce the number of patients receiving unnecessary preventive treatment in patients who are considered to initiate biologic agents. Furthermore, it was also concluded that QFT-plus test may be preferred in psoriasis patients since it is applied in vitro and its specificity is higher and not affected by disease severity. © 2020 Wiley Periodicals LLC.