Main Article Content
Tuberculosis (TB) is the crucial cause of death from infectious diseases worldwide. The causative agents of TB are a group of closely related bacteria known as the Mycobacterium tuberculosis complex (MTBC). Accurate and rapid diagnosis by PCR method is helpful for the successful treatment of tuberculosis. The aim of this study was to compare the efficiency between a more rapid method by a commercial kit (abTESTM MTB qPCR kit) and a cheaper but less rapid method by conventional polymerase chain reaction (C-PCR) for the detection of M. tuberculosis complex in FFPE tissue. Six hundred and forty formalin-fixed paraffin-embedded (FFPE) tissues that showed histomorphology suspected of tuberculous infection were collected from the Institute of Pathology, Department of Medical Services. DNA was isolated from the FFPE tissue and two methods of PCR were performed by using the abTESTM MTB qPCR kit and C-PCR for the detection of M. tuberculosis complex. The results showed that C-PCR was more sensitive for detection of M. tuberculosis complex than abTESTM MTB qPCR kit. There were 199 samples (30 %) positive for TB-DNA by C-PCR and 192 samples (28 %) positive for TB-DNA by abTESTM MTB qPCR kit. The comparison between these two methods by kappa analysis showed a very good agreement (K = 0.959, 95 % CI 0.936-0.983). In conclusion, C-PCR is more effective for the detection of TB DNA in FFPE tissue. This less costly method (even taking longer time) is an alternative method for the detection of MTBC infection in FFPE tissue.
 Gagneux, S., 2018, Ecology and evolution of Mycobacterium tuberculosis, Nat. Rev. Microbiol. 16: 202-213.
 Singh, K.K., Muralidhar, M., Kumar, A., Chattopadhyaya, T.K., Kapila, K., Singh, M.K., Sharma, S.K., Jain, N.K. and Tyagi, J.S., 2000, Comparison of in house polymerase chain reaction with conventional techniques for the detection of Mycobacterium tuberculosis DNA in granulomatous lymphadenopathy, J. Clin. Pathol. 53: 355-361.
 Inoue, M., Tang, W.Y., Wee, S.Y. and Barkham, T., 2011, Audit and improve evaluation of a real-time probe-based PCR assay with internal control for the direct detection of Mycobacterium tuberculosis complex, Eur. J. Clin. Microbiol. Infect. Dis. 30: 131-135.
 Cegielski, J.P., Devlin, B.H., Morris, A.J., Kitinya, J.N., Pulipaka, U.P., Lema, L.E., Wakatare, J.L. and Reller, L.B., 1997, Comparison of PCR, culture, and histopathology for diagnosis of tuberculous pericarditis, J. Clin. Microbiol. 35: 3254-3257.
 Nakiyingi, L., Kateete, D.P., Ocama, P., Worodria, W., Sempa, J.B., Asiimwe, B.B., Katabazi, F.A., Katamba, A., Huang, L., Joloba, M.L. and Mayanja-Kizza, H., 2012, Evaluation of in-house PCR for diagnosis of smear-negative pulmonary tuberculosis in Kampala, Uganda, BMC Res. Notes 5: 487.
 Hansen, W.L., Beuving. J., Bruggeman, C.A. and Wolffs, P.F., 2010, Molecular probes for diagnosis of clinically relevant bacterial infections in blood cultures, J. Clin. Microbiol. 48: 4432-4438.
 Wang, H.Y., Lu, J.J., Chang, C.Y., Chou, W.P. and Hsieh, J.C., 2019, Development of a high sensitivity TaqMan-based PCR assay for the specific detection of Mycobacterium tuberculosis complex in both pulmonary and extrapulmonary specimens, Sci. Rep. 9: 113.
 Zakham, F., Lahlou, O., Akrim, M., Bouklata, N., Jaouhari, S., Sadki, K., Seghrouchni, F., Elmzibri, M., Benjouad, A., Ennaji, M. and Elaouad, R., 2012, Comparison of a DNA based PCR approach with conventional methods for the detection of Mycobacterium tuberculosis in Morocco, Mediterr. J. Hematol. Infect. Dis. 4: e2012049.
 Chantranuwat, C., Assanasen, T., Shuangshoti, S. and Sampatanukul, P., 2006, Polymerase chain reaction for detection of Mycobacterium tuberculosis in papanicolaou-stained fine needle aspirated smears for diagnosis of cervical tuberculous lymphadenitis, Southeast Asian J. Trop. Med. Public Health 37: 940-947.
 Singh, H.B., Singh, P., Jadaun, G.P., Srivastava, K., Sharma, V.D., Chauhan, D.S., Sharma, S.K. and Katoch, V.M., 2006, Simultaneous use of two PCR systems targeting IS6110 and MPB64 for confirmation of diagnosis of tuberculous lymphadenitis, J. Commun. Dis. 38: 274-279.
 Thierry, D., Cave, M.D., Eisenach, K.D., Crawford, J.T., Bates, J.H., Gicquel, B. and Guesdon, J.L., 1990, IS6110, an IS-like element of Mycobacterium tuberculosis complex, Nucl. Acids Res. 18(1): 188.
 Das, N., Mendiratta, D., Narang, R., Thamke, D. and Narang, P., 2016, Suitability of IS6110 based polymerase chain reaction for the detection of Mycobacterium tuberculosis in sputum of new pulmonary tuberculosis cases, J. Mahatma Gandhi Inst. Med. Sci. 21: 35-39.
 Lee, H.S., Park, K.U., Park, J.O., Chang, H.E., Song, J. and Choe, G., 2011, Rapid, sensitive, and specific detection of Mycobacterium tuberculosis complex by real-time PCR on paraffin-embedded human tissues, J. Mol. Diagn. 13: 390-394.
 Thakur, R., Sarma, S. and Goyal, R., 2011, Comparison of DNA extraction protocols for Mycobacterium tuberculosis in diagnosis of tuberculous meningitis by real-time polymerase chain reaction, J. Glob. Infect Dis. 3: 353-356.
 Rao, X., Lai, D. and Huang, X., 2013, A new method for quantitative real-time polymerase chain reaction data analysis, J. Comput. Biol. 20: 703-711.
 Wilhelm, J. and Pingoud, A., 2003, Real-time polymerase chain reaction, ChemBioChem 4: 1120-1128.
 Yuan, J.S., Reed, A., Chen, F., Stewart, C.N.Jr., 2006, Statistical analysis of real-time PCR data, BMC Bioinform. 7: 85.
 Ruijter, J.M., Ramakers, C., Hoogaars, W.M., Karlen, Y., Bakker, O., van den Hoff, M.J. and Moorman, A.F.M., 2009, Amplification efficiency: Linking baseline and bias in the analysis of quantitative PCR data. Nucleic acids research 37: e45.
 Landis, J.R. and Koch, G.G., 1977, The measurement of observer agreement for categorical data, Biometrics 33: 159-174.
 Eisenach, K.D., Cave, M.D., Bates, J.H. and Crawford, J.T., 1990, Polymerase chain reaction amplification of a repetitive DNA sequence specific for Mycobacterium tuberculosis, J. Infect. Dis. 161: 977-981.
 Gilbert, M.T., Haselkorn, T., Bunce, M., Sanchez, J.J., Lucas, S.B., Jewell, L.D., Marck, E.V. and Worobey, M., 2007, The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when?, PLoS ONE 2: e537.
 Dietrich, D., Uhl, B., Sailer, V., Holmes, E.E., Jung, M., Meller, S. and Kristiansen, G., 2013, Improved PCR performance using template DNA from formalin-fixed and paraffin-embedded tissues by overcoming PCR inhibition, PLoS ONE 8: e77771.
 Ludyga, N., Grünwald, B., Azimzadeh, O., Englert, S., Höfler, H., Tapio, S. and Aubele, M., 2012, Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses, Virchows Archiv 460: 131-140.
 Bastien, P., Procop, G.W. and Reischl, U., 2008, Quantitative real-time PCR is not more sensitive than conventional PCR, J. Clin. Microbiol. 46: 1897-1900.