Browsing by Author "Biçmen, C"

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    Frequency of precore/core mutants in chronic Hepatitis B cases
    Akçali, S; Sanlidag, T; Biçmen, C; Özbakkaloglu, B; Alasehir, EA
    Objective: In recent years, the presence of precore/core region mutations were uncovered by the examination of Hepatitis B Virus (HBV) deoxyribonucleic acid (DNA) that is isolated from patient samples with anti-HBe seroconversion without viral replication loss. In this study, the frequency of precore/core mutations were investigated on serum samples obtained from chronic hepatitis B patients. Methods: From a total of 100 samples 69 anti-HBe and HBV DNA positive, and 31 HBeAg and HBV DNA positive samples were analyzed in the study to determine the mutations with the INNO-LIPA method at the Serology laboratory. Statistical analyses were bone with, SPSS v11.5 and chi-square and variance analysis (ANOVA) tests were conducted. Results: The precore mutations were detected in 68, while the core promoter mutations were present in 57 samples. Mutations were detected at the precore region in 11 out of 31 HBeAg positive (35%), and 57 out of 69 anti-HBe positive samples (83%). Likewise, the core promoter region was affected in 10 of 31 HBeAg (32%), and 47 out of 69 anti-HBe positive samples (68%). Both precore and core promoter mutations were substantially higher in the anti-HBe positive group (p<0.05). Conclusion: As a result, since precore/core mutations were prevalent in samples obtained from the study group, it is our opinion that careful attention must be paid to such mutations during the diagnosis and treatment phases of chronic hepatitis B patients.
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    Molecular Diversity of Drug Resistant Mycobacterium Tuberculosis Strains in Western Turkey
    Sürücüoglu, 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.
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    Comparison of Proportion Method in Lowenstein-Jensen Medium with the BACTEC 460 TB System for Antimycobacterial Susceptibility Testing of Mycobacterium tuberculosis Isolates
    Yurtsever, SG; Biçmen, C; Gündüz, AT; Özkütük, N; Salman, S; Demirci, M
    This study was conducted to compare BACTEC 460 TB system and the proportion method in commercially available and ready to use antibiotic added Loweinstein-Jensen (LJ) medium for susceptibility testing of first line drugs in Mycobacterium tuberculosis complex isolates. A total 238 M.tuberculosis strains isolated from clinical samples in our laboratory between 2006-2010 period were included in the study. Susceptibility testing for streptomycin, isoniazid, rifampicin and ethambutol in commercially provided LJ medium (Salubris Inc., Istanbul) was performed by the proportion method as recommended by the manufacturer, and the results were compared with the results of BACTEC 460 TB (Becton Dickinson, USA) system. Resistance rates of M.tuberculosis strains against streptomycin, isoniasid, rifampicin and ethambutol obtained by BACTEC 460 TB system were 19.7%, 42%, 40.8% and 18%, respectively. Those rates were 22.7%, 38.7%, 37% and 15.5%, respectively, by antibiotic added LJ proportion method. There was no statistically significant difference between the two methods in terms of resistance rates (p > 0.05). The rates of consistency between proportion method in LJ medium and BACTEC 460 TB system for streptomycin, isoniasid, rifampicin and ethambutol susceptibility were found as 85.3%, 92.4%, 95.4% and 92.4%, respectively. When comparing the reporting time (interval between beginning of the process to reporting of the results) of the methods, minimal, maximal and average reporting spans for BACTEC 460 TB system were 5, 12 and 8.08 +/- 2.65 days, and 15, 42 and 23.89 +/- 6.02 days for the proportion method in LJ medium, respectively, being statistically significant (p = 0.001). It was determined that the sensitivity test results of major antimycobacterial drugs in commercial LJ medium were compatible with the BACTEC 460 TB system. Nonetheless, the rate of incompatible results was higher for STR than the other drugs. Although there has been some disadvantages such as longer reporting time, need for experience in manual processing and visual evaluation, standardized LJ media approved for quality can be used for susceptibility testing of M.tuberculosis in the laboratories which do not have eligible conditions for the establishment of automated systems.
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    Investigation of Bacterial Etiology with Conventional and Multiplex PCR Methods in Adult Patients with Community-Acquired Pneumonia
    Kurutepe, S; Ecemis, T; Özgen, A; Biçmen, C; Çelik, P; Özkan, SA; Sürücüoglu, S
    Community-acquired pneumonia (CAP) is still a serious life-threatening disease, in which the etiologic agent cannot be identified in more than 50% of patients despite advanced diagnostic methods. The most commonly used methods in the determination of CAP etiology are culture and serological tests. Since early and accurate therapy reduces the mortality in CAP cases, rapid and reliable diagnostic methods are needed. The aim of this study was to determine the bacterial etiology in adult patients with CAP by implementing multiplex polymerase chain reaction/reverse line blot hybridization (M-PCR/RLBH) assay combined with conventional methods. A total of 128 cases (94 were male; age range: 19-81 years, mean age: 58) who were admitted to our hospital and clinically diagnosed as CAP between November 2008 - November 2010, were included in the study. Respiratory samples (sputum and/or bronchoalveolar lavage) obtained from patients were searched by M-PCR/RLBH method (Gen ID (R) Autoimmun Diagnostika GmbH, Germany) in terms of the presence of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Mycoplasma pneumoniae, Chlamydia pneumoniae and Legionella pneumophila nucleic acids. The samples were simultaneously inoculated onto 5% sheep blood agar, chocolate agar, haemophilus isolation agar, buffered charcoal yeast extract-selective agar and EMB agar media for cultivation. Serum samples obtained from the cases were tested for IgM and IgG antibodies against C.pneumoniae by microimmunofluorescence (Focus Diagnostic, USA) and against L.pneumophila and M.pneumoniae by indirect immunofluorescence (Euroimmun, Germany) methods. The bacterial etiology was identified in 59 (46.1%) of 128 patients with CAP and a total of 73 pathogens were detected. The leading organism was S.pneumoniae (n= 32, 25%), followed by H.influenzae and M.pneumoniae (n= 9, 7%), gram-negative bacilli (n= 10, 7.8%), M.catarrhalis (n= 6, 4.7%), C.pneumoniae (n= 4, 3.2%), L.pneumophila (n= 2, 1.6%) and Staphylococcus aureus (n= 1, 1.4%). Infection with atypical pathogens were detected in 15 (11.7%), and mixed infections in 14 (10.9%) patients. The detection rate of microorganisms (S.pneumoniae, H.influenzae, M.catarrhalis, C.pneumoniae, L.pneumophilia, M.pneumoniae) searched by M-PCR/RLBH method was 41.4% (53/128), while those microorganisms were detected in 23.4% (30/128) of the patients by conventional methods, representing a significant difference (p< 0.05). It was concluded that M-PCR/RLBH method supplemented the determination of bacterial etiology in CAP cases by increasing the rate of detection from 23.4% to 41.4%. The results indicated that empirical treatment of CAP should primarily include antibiotics against S.pneumoniae, M.pneumoniae and H.influenzae in our region.
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    Multicenter Evaluation of the Indirect Nitrate Reductase Assay for the Rapid Detection of Multidrug-Resistant Tuberculosis
    Çoban, AY; Tastekin, B; Uzun, M; Kalayci, F; Ceyhan, I; Biçmen, C; Albay, A; Sig, AK; Özkütük, N; Sürücüoglü, S; Ozkütük, A; Esen, N; Albayrak, N; Aslantürk, A; Saribas, 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 (TM) 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 (TM) 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 degrees C, and after seven days of incubation, 500 mu l Griess reagent was added to the LJ medium without antibiotics. If a color change was observed, an equal volume of Griess reagent was added to test LJ media with antibiotics. When a color change was observed in LJ 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.