Browsing by Author "Çiçek C."

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    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.
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    Development of a database for tracking HIV positive/AIDS patients; [HIV pozi̇ti̇f/aids hastalarinin tani ve i̇zlemi̇ i̇çi̇n geli̇şti̇ri̇len veri̇ tabani ortami]
    (2007) Altuǧlu I.; Çavuşoǧlu C.; Çiçek C.; Tünger Ö.
    The collection of reliable data is the first step to assess the status of HIV/AIDS in a community. HIV recording systems are necessary for organizing and analyzing the patients' data. The aim of the study was to develop a database to be used to track HIV positive/AIDS patients. The database includes general demographic fields as well as specific fields such as health history, laboratory and other clinical history, current and past drug regimens (both antiretroviral and non-antiretroviral drugs). It is also possible to organize and maintain a patient database according to specific diseases, laboratory tests and/or medication treatments.
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    Detection of human metapneumovirus prevalence in pediatric patients with lower respiratory tract infections; [Alt solunum yolu enfeksiyonu olan pediatrik hastalarda insan metapnömovlrus prevalansinin saptanmasi]
    (2012) Gökmen A.A.; Çiçek C.; Saz E.U.; Özananar Y.; Duyu M.
    Human metapneumovirus (hMPV) which is classified in Paramyxoviridae family has been identified in 2001 as the etiological agent of lower respiratory tract infection (LRTI) especially in children. Previous studies indicated that hMPV prevalence in LRTI is between 2-25%, being resposible for 10% of childhood LRTIs and its isolation rate is approximately 6% in hospitalized patients under age three years. The aim of this study was to investigate the hMPV prevalence in children with LRTI in our region. A total of 100 patients (41 female, 59 male) ages between 0-10 years old (median age: 4.8) and who were admitted to Pediatric Clinics of Ege University Medical Faculty Hospital with the diagnosis of LRTI between )a-nuary-December 2009 were included in the study. Nasopharyngeal swab samples were taken from those patients during the first three days of their symptoms. The presence of hMPV in the samples were investigated by rapid (shell vial) cell culture method using HEp-2 cell line and by real-time reverse transcriptase polymerase chain reaction (rRT-PCR). The methods were performed to the clinical samples simultaneously. In both methods, a standard strain of hMPV provided by Erasmus University was used as positive control and QCMD-2009 hMPV panel was used as external quality control. In our study, 11 and 2 samples were found positive with cell culture and rRT-PCR methods, respectively. Two of rRT-PCR positive samples were also positive in cell culture, while the other nine were positive by only cell culture method. Both of the methods were performed twice due to inconsistent results, however, the same results were obtained in both runs. Studies with QCMD-2009 panel yielded compatible results for five samples, however a positive standard sample (hMPV A subtype, Ct value: 37.31) was found as negative by rRT-PCR test used in this study (RealAccurateTM, Pathofinder, The Netherlands). Our data showed that the prevalence of hMPV detected by rapid cell culture method was 11 % in pediatric patients with LRTIs, the age range of hMPV positive cases was 6 months to 7 years old (median age: 20 months), the majority of the admissions was in winter season and the main clinical picture was bronchiolitis. In addition, rRT-PCR assay used in this study was thought to be insufficient to detect the viral RNA in the event of low levels of hMPV A subtypes. Thereby the cell culture method should be used in addition to the new developing molecular methods for the detection of hMPV until standardization is achieved.
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    Molecular typing of adenoviruses isolated from clinical specimens by pcr and dna sequencing methods; [Klinik ömeiklerden izole edilen adenoviruslarin pcr ve dna dizi analizi yöntemiyle tiplendirilmesi]
    (2012) Çiçek C.; Şanlidaĝ T.; Akçau S.; Sayan M.; Yalaz M.; Metin D.Y.
    Adenoviruses are responsible for a broad spectrum of diseases, including upper and lower respiratory tract infections (UI^TIs and LRTIs, respectively), conjunctivitis, gastroenteritis, and hemorrhagic cystitis. The aim of this study was to determine the adenovirus (AdV) types isolated from clinical specimens by polymerase chain reaction (PCR) and DNA sequencing methods. A total of 22 AdV strains isolated between January 1 2011 to May 31 2011, from various samples (295 nasopharyngeal swabs, 42 conjunctival swabs, 13 stool) sent to our routine virology laboratory were included in the study. Of the 22 patients whose samples yielded adenovirus positivity, 8 were adult (4 were male; median age: 32.5 years) and 14 (7 were male; median age: 1 year) were children. Those specimens (14 nasopharyngeal swabs, 7 conjunctival swabs, 1 stool) were obtained from patients with URTIs (n= 6), LRTIs (n= 8), conjunctivitis (n= 7) and gastroenteritis (n= 1). For the isolation and identification of adenoviruses, rapid (shell vial) cell culture and direct immunofluorescence antibody methods were used, respectively. Molecular typing of adenoviruses were performed by PCR and sequencing of a partial region (hipervariable region 1 -6) of the hexon gene. PCR primers (Adhex FI, Adhex R1) used for DNA amplification were from those described by Lu and Erdman, previously. If insufficient DNA was amplified from the first reaction for sequencing, a nested PCR was performed using Adhex F2 and Adhex R2 primers. Sequencing was performed using the amplification primers and Sequence Reagent Mix-DYEnamic ET Terminator Cycle Sequencing Kit (Amersham Pharmacia Biotech Inc, USA) on ABI PRISM 310 Genetic Analyzer (Applied Biosystems, USA). Obtained adenovirus sequences were typed by BLAST analysis and three AdV types namely type 3, 4, and 8 were identified. In our study, AdV type 3 was detected in a gastroenteritis case and six cases with URTIs and LRTIs (n= 7, 31.8%). AdV type 8 was identified as the cause of conjunctivitis in seven patients and of URTIs and LRTIs in five patients (n= 12, 54.5%). AdV type 4 was found to be associated with URTI in one, and LRTIs in two patients (n= 3; 13.7%). Our data indicated that AdV type 8 was the most prevalent type in patients with conjunctivitis and URTIs, while AdV type 3 was the most prevalent type in patients with LRTI. BLAST analysis was thought to be useful for the molecular typing of adenoviruses. In conclusion, advanced studies with large number of specimens are necessary to achive a reliable, detailed national adenovirus database.
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    Molecular typing and sequencing of adenovirus isolated from a conjunctivitis outbreak in a neonatal intensive care unit by PCR
    (2012) Çiçek C.; Şanlidaǧ T.; Siyah Bilgin B.; Pullukçu H.; Akçali S.; Altun Köroǧlu O.; Yalaz M.; Kültürsay N.
    Aim: We aimed to evaluate the molecular typing of adenovirus isolated during an epidemic at the Ege University Children's Hospital neonatal intensive care unit (NICU). Materials and methods: During the NICU outbreak management, 40 clinical samples (from 15 newborn infants and 25 health care providers) were sent to a microbiology laboratory in viral transport media. All the samples were processed using a direct fluorescent antibody (DFA) test and a shell vial cell culture followed by adenovirus polymerase chain reaction (PCR) and DNA sequencing. PCR and DNA sequencing for adenovirus hexon gene hypervariable regions 1-6 were done after DNA extraction from clinical specimens. Adenovirus typing was done using BLAST analysis. Results: Ten adenoviruses were isolated from 4 out of 10 infants, 3 out of 5 hospital staff with conjunctivitis, and 3 asymptomatic staff. Ten positive samples were identified as adenovirus type 8 by using BLAST analysis. Conclusion: We isolated adenovirus type 8, one of the most common serotypes causing conjunctivitis, during an adenovirus outbreak in our NICU. The highest positivity was obtained using the PCR method. Although DFA was positive in a limited number of cases, this test was applied rapidly at the beginning of the epidemic and contributed to the prevention of further spread. © TÜBİTAK.