Browsing by Author "Ozkutuk, N"

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    Drug-resistant pulmonary tuberculosis in western Turkey: prevalence, clinical characteristics and treatment outcome
    Surucuoglu, S; Ozkutuk, N; Celik, P; Gazi, H; Dinc, G; Kurutepe, S; Koroglu, G; Havlucu, Y; Tuncay, G
    BACKGROUND: Although high antituberculosis (anti-TB) drug resistance rates have been reported in Turkey, the clinical characteristics and implications for the outcome of anti-TB treatment have not been fully investigated. We determined the prevalence of anti-TB drug resistance and examined demographic data, clinical characteristics and treatment outcome in relation to patterns of resistance. METHODS: From the TB case registry of a university hospital and the two largest dispensaries in Manisa city, we identified all pulmonary TB cases with a culture-proven definitive diagnosis and antimicrobial susceptibility results for a 7-year period. We collected and analyzed demographic and clinical data and information on treatment outcome for those cases in relationship to anti-TB drug resistance. RESULTS: Of 355 M. tuberculosis strains, 71.5% were susceptible to streptomycin, isoniazid, rifampicin and ethambutol. Any drug resistance and multi-drug resistance (MDR) rates were 21.1% and 7.3% and were higher in males (53% and 9%, respectively) than in females (22% and 1%, respectively). Drug resistance was significantly higher in old cases (acquired drug resistance) vs new cases (primary drug resistance), and was associated with treatment failure (P<0.001). The prevalence of MDR was significantly higher in the old cases (22.4%) than in the new cases (4.4%) (P<0.001). Symptoms, radiographic findings, associated diseases, and sputum smear positivity were unrelated to the development of resistance. The prevalence of any drug resistance and MDR was significantly higher in those with treatment failure than in patients with treatment success. CONCLUSION: High resistance rates, particularly for acquired MDR, indicate a need for improvement in the TB control programme in our region.
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    Molecular identification and characterization of rifampicin-resistant Mycobacterium tuberculosis isolates by line probe assay
    Bicmen, C; Gunduz, AT; Coskun, M; Senol, G; Ozkutuk, N; Cirak, AK; Ozacar, R
    Aim: Early identification and characterization of rifampicin-resistant (R-r) Mycobacterium tuberculosis isolates recovered from the samples of tuberculosis (TB) patients in the Aegean (West Anatolian) Region was intended. Methods and Results: Sixty isolates [47 (78.3%) multidrug-resistant (MDR)], which were identified as M. tuberculosis complex and phenotypically resistant to rifampicin by both BACTEC mycobacteria growth indicator tube (MGIT) 960 and 460 systems were analysed by a commercial line probe assay (INNO-LiPA Rif TB). The concordance of LiPA with the in vitro susceptibility test was found as 98.3%. Among the isolates, S531L (R5 pattern; 46.7%) and L511P/R, S512T, Q513L/K (Delta S1 pattern; 11.7%) were the most frequent mutation patterns. As compared with the BACTEC systems and conventional techniques for cultivation, identification and in vitro susceptibility testing, INNO-LiPA Rif TB after cultivation in BACTEC MGIT 960 system provided an average of 20 days early diagnosis of (RM)-M-r. tuberculosis isolates. Conclusions: Rapid molecular identification and characterization of (RM)-M-r. tuberculosis isolates after BACTEC MGIT 960 cultivation would be useful for faster diagnosis, infection control and planning of accurate treatment in MDR-TB patients. Significance and Impact of the Study: Patients with MDR-TB need a specified treatment and efficient follow-up strategies. Rapid and practical methodologies to diagnose and follow these patients should be applied in routine use.
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    Characterization of rpoB mutations by line probe assay in rifampicin-resistant Mycobacterium tuberculosis clinical isolates from the Aegean region in Turkey
    Ozkutuk, N; Gazi, H; Surucuoglu, S; Gunduz, A; Ozbakkaloglu, B
    The nature and frequency of mutations in the rpoB gene of rifampicin (RIF)-resistant Mycobacterium tuberculosis clinical isolates vary considerably according to the geographical location, and very little information is available regarding specific mutational patterns in our country. The main objective of this study was to determine the frequency of mutations in the hypervariable region of the rpoB gene in RIF-resistant M. tuberculosis isolates recovered from tuberculosis patients in our region by using the INNO-LiPA Rif. TB kit and to evaluate the performance of the kit for the detection of RIF-resistance. Mutations associated with RIF resistance were studied by line probe assay (LiPA) in 65 RIF-resistant and 56 RIF-susceptible M. tuberculosis strains isolated from different patients in the Aegean region of Turkey. The LiPA identified all susceptible strains (100%) as RIF-sensitive and 63 of 65 (96.9%) phenotypically documented RIF-resistant M. tuberculosis isolates as RIF-resistant, with specific detection of mutation in 44 (67.7%) isolates, whilst 2 strains were identified as RIF-susceptible. The R5-pattern (Ser-531-Leu mutation) was the most frequently observed (35 of 65, 53.8%), followed by the Delta S2-pattern (7.7%) and Delta S4-pattern (7.7%).
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    Differences in the cellular and humoral immune system between middle-aged men with different intensity and duration of physically training
    Buyukyazi, G; Kutukculer, N; Kutlu, N; Genel, F; Karadeniz, G; Ozkutuk, N
    Aim. The effects of acute exercise on immune system and serum magnesium and iron have been investigated in recent years. However, data related to the comparisons of long-term physical training with different intensity and duration are limited. Methods. The association between long-term physical training and cellular (lymphocyte phenotyping) and humoral immune parameters (serum immunoglobulins) and serum magnesium and iron values in the middle-aged men was investigated. Eleven male master athletes (MA) performing high intensity and long duration training, 11 male recreational athletes (RA) performing moderate intensity and duration training (>10 years) participated. Eleven male sedentary individuals were enrolled as control group (CG). Results. The percentages of total CD3+ T cells, CD4+ T helper, CD8+ T suppressor/cytotoxic, CD19+ B cells, natural killer cells, HLA-DR+ active T cells and CD4/CD8 ratios did not show any significant difference among 3 groups. In MA, VO2max values showed a significant negative correlation with CD4+ T helper cells. There were no significant differences among MA, RA and CG in terms of IgG, IgA, and IgM concentrations. There was a significant correlation between VO2max and IgG in RA. Iron, iron binding capacity and ferritin were found similar in all groups, but serum magnesium level in MA was significantly lower than RA and CG. Conclusion. No exact data to support immunosuppression or immunostimulation could be obtained except a significant negative correlation between CD4+ T helper cells and VO2max values in MA and a positive correlation between serum IgG and VO2max ivalues in RA. These findings may be the indirect markers of cellular immune system suppression by intensive exercises and stimulation of IgG production by moderate exercises.
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    Low Mononuclear Cell IL-18 and IL-27 Response in Children: Susceptibility to Tuberculosis Infection after Contact
    Karabacak, HA; Yilmaz, O; Tuglu, I; Taneli, F; Surucuoglu, S; Kanik, ET; Ozkutuk, N; Gozukara, C; Ozkut, MM; Turkeli, A; Yuksel, H
    Background Identification of the immune response against tuberculosis is vital to develop new diagnostic and therapeutic modalities. The objective of this study was to determine IL (interleukin)-18 and IL-27 responses of peripheral blood mononuclear cells to early secreted antigen (ESAT-6) and culture filtrate protein-10 (CFP-10) stimulation in children with a (+) or (-) tuberculin skin test (TST) with in-house tuberculosis contact. Methods We enrolled 40 children aged 1 to 5 years who had an in-house contact with a tuberculous adult. Blood samples were obtained from all children for QuantiFERON tuberculosis (TB) gold in tube (QFT-GIT), and peripheral blood mononuclear blood cell culture tests. The subjects were grouped as TST (-) QFT-GIT (-), TST (+) QFT-GIT (-), and TST (+) QFT-GIT (+). Supernatant of peripheral blood mononuclear cell culture was separated with and without stimulation of ESAT-6 and CFP-10, and IL-18 and IL-27 levels were measured with enzyme linked immunoassay (ELISA) test. Results The study group included 22 boys and 18 girls with mean age 4.25 +/- 0.9 years. IL-18 and IL-27 levels were statistically significant in ESAT-6/CFP-10-stimulated supernatants of peripheral blood mononuclear cell (PBMC) samples among the three groups (p = 0.000,p = 0.007, respectively). IL-18 levels between the TST (-) QFT-GIT (-) and TST (+) QFT-GIT (+) groups were significantly different (p = 0.026). Both IL-18 and IL-27 levels were significantly different between ESAT-6/CFP-10 stimulated PBMC supernatants of TST (-) QFT-GIT (-) and TST (+) QFT-GIT (-) groups (p = 0.000,p = 0.003, respectively). Conclusion Low IL-18 and IL-27 responses of peripheral blood mononuclear cells in children with Bacillus Calmette-Guerin (BCG) vaccine may play a role inMycobacterium tuberculosisinfection after in-house contact.
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    Oropharyngeal carriage and penicillin resistance of Neisseria meningitidis in primary school children in Manisa, Turkey
    Gazi, H; Surucuoglu, S; Ozbakkaloglu, B; Akcali, S; Ozkutuk, N; Degerli, K; Kurutepe, S
    Introduction: To determine the oropharyngeal carriage rates and serogroups of Neisseria meningitidis in primary schoolchildren in Manisa, Turkey as well as the prevalence and penicillin resistance of N. meningitidis. Materials and Methods: Throat swabs obtained from 1128 children were cultured and recovered organisms were tested by disk diffusion method and the E-test for antimicrobial susceptibilities. Results: The carriage rate of N. meningitidis in our region was 6.2% (71 strains) and the serogroups identified were serogroups A (28.1%), B (22.5%), C (35.2%), D (2.8%) and W-135 (11.2%). Penicillin resistance was found in 16 strains (22.5%), while beta-lactamase activity was found in none. Conclusions: The carriage rate of N. meningitidis and serogroups are similar to the rates reported in other countries. Continued surveillance of meningococci for antimicrobial resistance will allow early detection of changes in susceptibility patterns that might affect recommendations for chemoprophylaxis as well as for treatment.
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    Multicenter evaluation of crystal violet decolorization assay (CVDA) for rapid detection of isoniazid and rifampicin resistance in Mycobacterium tuberculosis
    Coban, AY; Akbal, AU; Bicmen, C; Albay, A; Sig, AK; Uzun, M; Selale, DS; Ozkutuk, N; Surucuoglu, S; Albayrak, N; Ucarman, N; Ozkutuk, A; Esen, N; Ceyhan, I; Ozyurt, M; Bektore, B; Aslan, G; Delialioglu, N; Alp, A
    The aim of this multicenter study was to evaluate the performance of the crystal violet decolorization assay (CVDA) for detection of multidrug resistant tuberculosis (MDR-TB). This study was performed in 11 centers in two phases. A total of 156 isolates were tested for INH and RIF resistance. In the phase I, 106 clinical isolates were tested in the Center 1-7. In the phase 2, 156 clinical isolates were tested in the center 1-6, center 8-11. Eighty six of 156 tested isolates were the same in phase I. Agreements were 96.2-96.8% for INH and 98.1-98.7% for RIF in the phase I-II, respectively. Mean time to obtain the results in the phase I was 14.3 +/- 5.4 days. In the phase II, mean time to obtain the results was 11.6 +/- 3.5 days. Test results were obtained within 14days for 62.3% (66/106) of isolates in the phase I and 81.4% (127/156) of isolates in the phase II. In conclusion, CVDA is rapid, reliable, inexpensive, and easy to perform for rapid detection of MDR-TB isolates. In addition, it could be adapted for drug susceptibility testing with all drugs both in developed and developing countries.
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    A new colorimetric method for rapid detection of ethambutol and streptomycin resistance in Mycobacterium tuberculosis: crystal violet decolorization assay (CVDA)
    Coban, AY; Akbal, AU; Ceyhan, I; Uzun, M; Selale, DS; Aslan, G; Delialioglu, N; Ozyurt, M; Bektore, B; Bicmen, C; Aslanturk, A; Ucarman, N; Albay, A; Sig, AK; Ozkutuk, N; Surucuoglu, S
    Streptomycin (STR) and ethambutol (EMB) are important drugs used for the treatment of tuberculosis. There is a need for fast, reliable and inexpensive methods for detecting resistance to these drugs. The aim of this study was to evaluate the performance of the crystal violet decolorization assay (CVDA) for the detection of STR and EMB resistance that is important drugs in tuberculosis treatment. In this study, drug susceptibility testing was performed on 140 Mycobacterium tuberculosis isolates provided from nine centers. Three tubes were used for each isolate. One of the tubes had a concentration of 2mg/L STR and the other 5mg/L EMB. The third was drug-free control tube. Sensitivity, specificity, positive predictive value (PPD), negative predictive value (NPD) and agreement for STR were found to be 81.8%, 94.6%, 87.8%, 91.5% and 90.57%, respectively. For EMB, sensitivity, specificity, PPD, NPD, and agreement were found to be 76%, 98.23%, 90.47%, 94.87% and 94.2%, respectively. The results were obtained in 11.3 +/- 2.7days (8-21days). CVDA is rapid, reliable, inexpensive, and easy to perform for rapid detection of STR and EMB resistance, and it could be adapted for drug susceptibility testing.
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    Multicenter evaluation of AYC.2.2 agar for the isolation of mycobacteria from clinical samples
    Coban, AY; Ceyhan, I; Uzun, M; Genc, GE; Bicmen, C; Ozkutuk, N; Surucuoglu, S; Yanar, O; Aslan, G; Kurnaz, N; Cayci, YT
    Purpose: The aim of this multicenter study is to evaluate AYC.2.2 agar for the isolation of mycobacteria from clinical samples. Methods: Totally 5559 media were tested in 7 centers. AYC.2.2 agar media for the study were prepared by C1 and sent to other centers under appropriate conditions. Other media except AYC.2.2 agar were purchased commercially. The media were subjected to routine laboratory operations in the center where they were sent. After the samples received for routine processing (in all centers, samples were processed with the same method (NALC-NaOH)), they were cultivated on routine media and AYC.2.2 agar afterward. Results: C1: Average growth time was determined as 12.74 +/- 3.74 days with MGIT 960 system; 24.42 +/- 4.75 days with LJ and 24.37 +/- 4.96 days with AYC.2.2 agar. C2: Average growth time was determined as 18.25 +/- 9.32 days with TK-Medium, 28.73 +/- 7.44 days with LJ, and 31.72 +/- 6.35 days with AYC.2.2 agar. C3: Average growth time was determined as 20.48 +/- 7.24 days with Ogawa medium, 20.74 +/- 7.12 days with LJ, and 20.26 +/- 7.43 days with AYC.2.2 agar. C4: Average growth time was determined as 15.27 +/- 6.37 days with MGIT 960 system, 22.14 +/- 9.1 days with LJ, and 22 +/- 8.45 days with AYC.2.2 agar. C5: Average growth time was determined as 13 +/- 4.24 days with MGIT 960 system, 32.16 +/- 6.23 days with LJ, and 33 +/- 5.73 days with AYC.2.2 agar. C6: Average growth time was determined as 9 +/- 3.11 days with MGIT 960 system, 18.68 +/- 5.32 days with LJ, and 18.34 +/- 4.63 days AYC.2.2 agar. C7: Average growth time was determined as 14.74 +/- 7.65 with MGIT 960 system, 26.01 +/- 8.21 days with LJ, and 26.24 +/- 7.88 days with AYC.2.2 agar. Conclusions: In conclusion, similar results were obtained with LJ and Ogawa media and AYC.2.2 agar. Furthermore, more studies should be conducted for isolation of M. tuberculosis and performing antibiotic susceptibility tests using AYC.2.2 agar before it can be used as a routine media in the laboratories.
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    Diagnostic accuracy of the Xpert® MTB/RIF cycle threshold level to predict smear positivity: a meta-analysis
    Lange, B; Khan, P; Kalmambetova, G; Al-Darraji, HA; Alland, D; Antonenka, U; Brown, T; Balcells, ME; Blakemore, R; Denkinger, CM; Dheda, K; Hoffmann, H; Kadyrov, A; Lemaitre, N; Miller, MB; Nikolayevskyy, V; Ntinginya, EN; Ozkutuk, N; Palacios, JJ; Popowitch, EB; Porcel, JM; Teo, J; Theron, G; Kranzer, K
    SETTING: Xpert (R) MTB/RIF is the most widely used molecular assay for rapid diagnosis of tuberculosis (TB). The number of polymerase chain reaction cycles after which detectable product is generated (cycle threshold value, C-T) correlates with the bacillary burden. OBJECTIVE: To investigate the association between Xpert C-T values and smear status through a systematic review and individual-level data meta-analysis. DESIGN: Studies on the association between C-T values and smear status were included in a descriptive systematic review. Authors of studies including smear, culture and Xpert results were asked for individual-level data, and receiver operating characteristic curves were calculated. RESULTS: Of 918 citations, 10 were included in the descriptive systematic review. Fifteen data sets from studies potentially relevant for individual-level data meta-analysis provided individual-level data (7511 samples from 4447 patients); 1212 patients had positive Xpert results for at least one respiratory sample (1859 samples overall). ROC analysis revealed an area under the curve (AUC) of 0.85 (95%CI 0.82-0.87). Cut-off C-T values of 27.7 and 31.8 yielded sensitivities of 85% (95%CI 83-87) and 95% (95%C1 94-96) and specificities of 67% (95%CI 66-77) and 35% (95%CI 30-41) for smear-positive samples. CONCLUSION: Xpert CT values and smear status were strongly associated. However, diagnostic accuracy at set cut-off C-T values of 27.7 or 31.8 would not replace smear microscopy. How C-T values compare with smear microscopy in predicting infectiousness remains to be seen.
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    Antituberculosis drug resistance patterns in adults with tuberculous meningitis: results of haydarpasa-iv study
    Senbayrak, S; Ozkutuk, N; Erdem, H; Johansen, IS; Civljak, R; Inal, AS; Kayabas, U; Kursun, E; Elaldi, N; Savic, B; Simeon, S; Yilmaz, E; Dulovic, O; Ozturk-Engin, D; Ceran, N; Lakatos, B; Sipahi, OR; Sunbul, M; Yemisen, M; Alabay, S; Beovic, B; Ulu-Kilic, A; Cag, Y; Catroux, M; Inan, A; Dragovac, G; Deveci, O; Tekin, R; Gul, HC; Sengoz, G; Andre, K; Harxhi, A; Hansmann, Y; Oncu, S; Kose, S; Oncul, O; Parlak, E; Sener, A; Yilmaz, G; Savasci, U; Vahaboglu, H
    Background: Tuberculous meningitis (TBM) caused by Mycobacterium tuberculosis resistant to antituberculosis drugs is an increasingly common clinical problem. This study aimed to evaluate drug resistance profiles of TBM isolates in adult patients in nine European countries involving 32 centers to provide insight into the empiric treatment of TBM. Methods: Mycobacterium tuberculosis was cultured from the cerebrospinal fluid (CSF) of 142 patients and was tested for susceptibility to first-line antituberculosis drugs, streptomycin (SM), isoniazid (INH), rifampicin (RIF) and ethambutol (EMB). Results: Twenty of 142 isolates (14.1 %) were resistant to at least one antituberculosis drug, and five (3.5 %) were resistant to at least INH and RIF, [multidrug resistant (MDR)]. The resistance rate was 12, 4.9, 4.2 and 3.5 % for INH, SM, EMB and RIF, respectively. The monoresistance rate was 6.3, 1.4 and 0.7 % for INH, SM and EMB respectively. There was no monoresistance to RIF. The mortality rate was 23.8 % in fully susceptible cases while it was 33.3 % for those exhibiting monoresistance to INH, and 40 % in cases with MDR-TBM. In compared to patients without resistance to any firstline drug, the relative risk of death for INH-monoresistance and MDR-TBM was 1.60 (95 % CI, 0.38-6.82) and 2.14 (95 % CI, 0: 34-13: 42), respectively. Conclusion: INH-resistance and MDR rates seemed not to be worrisome in our study. However, considering their adverse effects on treatment, rapid detection of resistance to at least INH and RIF would be most beneficial for designing anti-TB therapy. Still, empiric TBM treatment should be started immediately without waiting the drug susceptibility testing.
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    Comparison of Four Different DNA Isolation Methods from MGIT Culture for Long-Read Whole Genome Sequencing of Mycobacterium tuberculosis
    Arslan, N; Demiray-Gurbuz, E; Ozkutuk, N; Esen, N; Özkütük, AA
    Background: Tuberculosis (TB) remains a global health challenge, particularly due to drug resistance and limitations in rapiddiagnosis. Next-generation sequencing (NGS), especially long-read whole genome sequencing (WGS), shows promise for rapidlydetecting TB and drug resistance, but it requires high-quality DNA, which is difficult to extract from Mycobacterium tuberculosisdue to its complex cell wall. Objectives: This study evaluated four DNA isolation methods for extracting pure DNA from M. tuberculosis, aiming tostandardize protocols for long-read WGS. Methods:Mycobacterium tuberculosis H37RV colonies were grown in BACTEC MGIT liquid medium. Two pellets were prepared asthe initial material for the DNA extraction protocol: Pellets from 1 mL McFarland 2 suspensions and all growing colonies fromtwo MGIT liquid cultures. Four DNA extraction methods were used: The cetyltrimethylammonium bromide (CTAB) method,GeneJET Genomic DNA Purification Kit, Quick-DNA Fecal/Soil Microbe Kit, and Genematrix Tissue/Bacterial DNA Purification Kit,with some modifications. DNA quality was assessed based on concentration, purity, and integrity. Results: Among the tested methods, the Quick-DNA Fecal/Soil Kit yielded approximately 85 ng/mL of DNA and a purity of 1.9 at260/280 nm from the colonial pellet of two MGIT tubes. However, lower intact DNA [DNA integrity number (DIN) similar to 6.8] wasobtained with this kit. The CTAB method provided the highest intact DNA (DIN similar to 9.5), although the purity of the DNA was notsufficient. Conclusions: Based on three repetitions of McF-2 and colonial pellet extractions, the Quick-DNA Fecal/Soil Kit yielded thehighest DNA quantity and purity but showed lower integrity compared to other methods, indicating the need for adjustments.A pellet from two MGIT cultures (similar to 100 mu L) is suitable for long-read WGS with this kit. However, a larger sample size is required togeneralize these findings. For effective long-read sequencing of M. tuberculosis, DNA extraction protocols must be optimized tobalance yield, fragment size, and purity for accurate sequencing and drug resistance analysis.