Browsing by Author "Esen, N"

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    Microbiological results of bronchoalveolar lavage that was performed for opportunistic pulmonary infections
    Gülcü, A; Sevinç, C; Esen, N; Kilinç, O; Uçan, ES; Itil, O; Çimrin, AH; Kömüs, N; Sener, G; Akkoçlu, A; Gülay, Z; Yücesoy, M
    Between 2001-2002; in 62 cases, 33 (53%) male, 29 (47%) female, mean age 51.4 +/- 18.1 years) bronchoalveolar lavage (BAL) was performed for diagnosis of opportunistic pulmonary infection and specimens were evaluated for results of microbiological examinations. There was hematological malignancy in 18 (29%) and solid organ malignancy in 13 (21%) cases. Thirty-one (50%) cases were immuncompromised for reasons other than malignancy. By endoscopic evaluation endobronchial lesion was seen in 2 (3%) cases, indirect tumor signs were seen in 2 (3%) cases and signs of infection were seen in 11 (18%) cases. Fortyseven (76%) cases were endoscopically normal. Acid-fast bacilli (AFB) direct examination was positive in 3 (5%) cases. In 4 (6%) cases mycobacterial culture was positive, Mycobacterium tuberculosis-polymerase chain reaction (PCR) was also positive in these four cases. Examination of Gram-stained smears for bacteria was associated with infection in 14 (23%) cases. Bacteriologic cultures were positive for single potential pathogen in 10 (16%) cases, and for mixed pathogens in 7 (11%) cases for a total number of 17 (27%). Fungal cultures were positive in 3 (5%) cases all of which had hematological malignancy. As a result in 24 (39%) cases microbiological agent of infection is determined: in four mycobacteria, in 17 bacteria other than mycobacteria and in three fungi.
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    Pyrazinamide monoresistance in clinical isolates
    Kalir, N; Özkütük, AA; Esen, N; Özkütük, N
    Aim: To determine pyrazinamide (PZA) monoresistance in clinical isolates of Mycobacterium tuberculosis complex (MTBC) isolated in hospitals in and around Izmir. 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 Izmir 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.
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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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    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.
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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.