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Objective: In this study, nine commercial Nucleic Acid Amplification Test Systems (NAATs) were evaluated for diagnostic performance of Mycobacterium tuberculosis complex (MTBC) from smear positive sputum species (SPss) and smear negative sputum specimens (SNss). Methods: Sixty SPss and 55 SNss were examined microscopically by Ehrlich Ziehl Neelsen (EZN) staining method, and also inoculated on Löwenstein Jensen (LJ) medium for culture. The sensitivity and specificity of nine NAATs were calculated according to LJ culture method accepted as gold standard. Results: When LJ culture results were taken as gold standard; the sensitivity rates of method COBAS Amplicor MTB (Method A), GenProbe MTD (Method B), Cobas TaqMan MTB PCR (Method C), iCycler iQ RT PCR (Method D), TaqMan PCR AB 5700 (Method E), TaqMan PCR AB7700 (Method F), LightCycler® 480 RT PCR (Method G), Rotor Gene RT PCR (Method H) and the AdvanSure TB/NTM RT PCR (Method I) for SPss were 98.3 %, 93.3 %, 96.7 %, 100 %, 93.3 %, 100 %, 100 %, 100 % and 100 %, respectively. The sensitivity was 53.84% for the methods A, B, D, E, G and I; 38.46% for the method C and H; 61.5% for the method F for the method I in SNss. There were no statistical significant differences between the nine NAATs (p≥0.05). The specificity was 100% for all nine NAATs in SNss. The positivity rates of methods were 53.8% for methods A, B, D, E, G, I; 38.5% for methods C and H, and 61.5% for method F in SNss. These rates were 100% for D, F, G, H and I; 98.3% for method A; 96.7% for method C; 93,3% for methods B and E in SPss. Statistical analysis showed that there was no statistically significant differences among the nine NAATs (p≥0.05). Conclusion: It is concluded that the nine NAATs might be useful for detecting MTBC from SPss, but not effective for SNss.

Drug-resistant tuberculosis is a serious problem throughout the world. Resistance to Rifampicin (RIF) is mainly caused by the mutations in the rpoB gene coding the beta-subunit of RNA polymerase. In this study, we aimed to detect the distribution of rpoB gene mutations in 80 RIF-resistant clinical Mycobacterium tuberculosis (MTB) isolates from Turkey. The rpoB gene was amplified by PCR and mutations leading to RIF resistance were determined by automated sequence analysis. A total of 72 of the 80 isolates (90%) were found to carry mutations in the amplified region, whereas eight isolates (10%) carried no mutations. Overall, 24 different missense mutations affecting 14 codons, and two deletion mutants were identified. Nine new mutations, six in the hot-spot region and three outside this region, were found. The codon numbers of the most frequently encountered mutations were 531 (51.4%), 526 (18.1%), 516 (13.9%), and 513 (12.5%). As a result, 90% of the RIF-resistant MTB isolates from the Turkish patients were found to carry a mutation in the rpoB gene, Ser531Leu being the most frequent one. Although molecular methods identify mutations leading to RIF resistance very quickly, results of the antimycobacterial susceptibility tests must be taken into consideration for the patients carrying no mutations in this region.

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Objectives: Most important point for the control and effective treatment of multidrug resistant tuberculosis (MDR-TB) is early diagnosis and rapid determination of the resistance. The aim of this study is to assess the performance of the Genotype-MTBDR assay applied directly on sputum samples and compare the results with those obtained by DNA sequencing and phenotypic susceptibility testing. Materials and methods: Between November 2005 and February 2006, 93 smear and culture positive sputum samples were included in the study. Drug susceptibility results for rifampin (RIF) and isoniazid (INH), obtained by proportion method on L-J medium, Genotype-MTBDR and DNA sequencing were compared. Results: The rate of concordance between the results of the Genotype-MTBDR and DNA sequencing was 93.5% and 96.7% for RIF and INH, respectively. Moreover, Genotype-MTBDR detected all the RIF (24) and INH (18) resistant strains obtained by sequencing (100%). Compared to the DNA sequencing method; the sensitivity, specificity, positive predictive and negative predictive value for RIF and INH were 100%, 91.3%, 80%, 100% and 100%, 96%, 85.7%, 100% respectively. Conclusion: Genotype-MTBDR, one of molecular assays, distinctly shortens the time for diagnosis and detection of resistance to INH and RIF, essential for management of MDR-TB. The test appears to have good sensitivity and specificity when also used directly on sputum specimens.