Comparative analysis of analytical sensitivity of qPCR methods for detecting isoniazid-resistant tuberculosis using SYBR Green and TaqMan Probe
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis and remains one of the leading causes of death worldwide. The increasing prevalence of TB strains resistant to multiple antibiotics, including isoniazid, highlights the urgent need for rapid and accurate molecular diagnostic methods. One such method is quantitative polymerase chain reaction (qPCR). This study aimed to compare the analytical sensitivity of qPCR assays for detecting isoniazid-resistant M. tuberculosis using SYBR Green and TaqMan Probe chemistries. Analytical sensitivity was evaluated using DNA from isoniazid-resistant M. tuberculosis carrying the S315G mutation, which was serially diluted up to 10⁻⁹. Primary data were analyzed using probit regression analysis. The results showed that the analytical sensitivity of the SYBR Green method was 1.5045 × 10⁻³ ng/µL, while that of the TaqMan Probe method was 1.0205 × 10⁻³ ng/µL. These findings indicate that the qPCR TaqMan Probe method is approximately 1.47 times more sensitive than the SYBR Green method. However, further studies evaluating additional validation parameters are required to determine the most suitable method for routine diagnostic application.
There is no Figure or data content available for this article
References
- 1. WHO. Global Tuberculosis Report 2020.; 2020. Accessed May 12, 2024. https://www.who.int/publications/i/item/9789240013
- 2. Kemenkes RI. Petunjuk Teknis Penatalaksanaan Tuberkulosis Resistan Obat Di Indonesia. KemenkesRI; 2020.
- 3. WHO. WHO consolidates guidelines on tuberculosis rapid diagnostic for tuberculosis detection; Module 3: Diagnosis. . https://www.who.int/publications/i/item/9789240029. Published online 2021.
- 4. WHO. Global Tuberculosis Report 2022.; 2022. Accessed May 12, 2024. https://www.who.int/publications/i/item/9789240061729
- 5. Kurniati A, Suameitra Dewi DNS, Purwani NN. Rapid and Specific Detection of Mycobacterium tuberculosis Using Polymerase Chain Reaction. Journal of Vocational Health Studies. 2019;3(2):83-88. doi:10.20473/jvhs.V3.I2.2019.83-88
- 6. Mullis KB, Faloona FA. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. In: Methods in Enzymology. Vol 155. Academic Press; 1987:335-350. doi:https://doi.org/10.1016/0076-6879(87)55023-6
- 7. Tajadini M, Panjehpour M, Javanmard SH. Comparison of SYBR Green and TaqMan methods in quantitative real-time polymerase chain reaction analysis of four adenosine receptor subtypes. Adv Biomed Res. 2014;3(1). https://journals.lww.com/adbm/fulltext/2014/03000/comparison_of_sybr_green_and_taqman_methods_in.85.aspx
- 8. ICH. Validation of Analytical Procedures Q2(R2). Published online March 31, 2022.
- 9. Burd E. Validation of Laboratory-Developed Molecular Assays for Infectious Diseases. Clin Microbiol Rev. 2010;23(3):550-576. doi:10.1128/cmr.00074-09
- 10. Sjahrurachman A. Diagnosis “Multidrug resistant mycobacterium” tuberculosis. Jurnal Tuberkulosis Indonesia. 2010;7(2):8-11.
- 11. Jagielski T, Grzeszczuk M, Kamiński M, et al. Identification and analysis of mutations in the katG gene in multidrug-resistant Mycobacterium tuberculosis clinical isolates. Pneumonol Alergol Pol. 2013;81(4):298-307.
- 12. Moaddab SR, Farajnia S, Kardan D, Zamanlou S, Alikhani MY. Isoniazid MIC and KatG Gene Mutations among Mycobacterium tuberculosis Isolates in Northwest of Iran. Iran J Basic Med Sci. 2011;14(6):540-545.
- 13. Narmandakh E, Tumenbayar O, Borolzoi T, Erkhembayar B, Boldoo T, Dambaa N, et al. Genetic Mutations Associated with Isoniazid Resistance in Mycobacterium tuberculosis in Mongolia. Antimicrob Agents Chemother. 2020;64(7):e00537-20. doi:10.1128/AAC.00537-20
- 14. Marahatta SB, Gautam S, Dhital S, et al. KatG (SER 315 THR) Gene Mutation in isoniazid resistant Mycobacterium tuberculosis. Kathmandu Univ Med J. 2011 Mar; 9(33):19-23. URL: https://www.kumj.com.np/issue/33/19-23.pdf
- 15. Boonaiam S, Chaiprasert A, Prammananan T, Leechawengwongs M. Genotypic analysis of genes associated with isoniazid and ethionamide resistance in MDR-TB isolates from Thailand. Clinical Microbiology and Infection. 2010;16(4):396–9. https://doi.org/10.1128/AAC.00537-20
- 16. Wang L, Lim DR, Phelan JE, Reyes LT, Palparan AG, Sanchez MGC, et al. Whole genome sequencing analysis of Mycobacterium tuberculosis reveals circulating strain types and drug-resistance mutations in the Philippines. Sci Rep. 2024;14(1):19602. https://doi.org/10.1038/s41598-024-70471-x
- 17. Gegia M, Winters N, Benedetti A, van Soolingen D, Menzies D. Treatment of isoniazid-resistant tuberculosis with first-line drugs: a systematic review and meta-analysis. Lancet Infect Dis. 2017;17(2):223-234. doi:10.1016/S1473-3099(16)30407-8
- 18. Alvarez ML, Doné SC. SYBR® Green and TaqMan® Quantitative PCR Arrays: Expression Profile of Genes Relevant to a Pathway or a Disease State. In: Alvarez ML, Nourbakhsh M, eds. RNA Mapping: Methods and Protocols. Springer New York; 2014:321-359. doi:10.1007/978-1-4939-1062-5_27
- 19. Marmiroli N, Maestri E. Chapter 6 - Polymerase chain reaction (PCR). In: Picó Y, ed. Food Toxicants Analysis. Elsevier; 2007:147-187. doi:https://doi.org/10.1016/B978-044452843-8/50007-9
- 20. Nagy A, Vitásková E, Černíková L, et al. Evaluation of TaqMan qPCR System Integrating Two Identically Labelled Hydrolysis Probes in Single Assay. Sci Rep. 2017;7(1):41392. doi:10.1038/srep41392
- 21. Rodriguez-Làzaro D, Hernàndez M. Real-time PCR in Food Science. Curr Issues Mol Biol. 2013;15:25-38. https://doi.org/10.21775/cimb.015.025
- 22. Ari O, Durmaz R, Vezir S, Arslanturk A. Development of a Multiplex Real-Time PCR for Diagnosis of Tuberculosis and Multidrug Resistance. Curr Microbiol. 2025;82(5):219. https://doi.org/10.1007/s00284-025-04196-z
- 23. Antonello M, Scutari R, Lauricella C, Renica S, Motta V, Torri S, et al. Rapid Detection and Quantification of Mycobacterium tuberculosis DNA in Paraffinized Samples by Droplet Digital PCR: A Preliminary Study. Front Microbiol. 2021;12:727774. https://doi.org/10.3389/fmicb.2021.727774
- 24. Vaks JE, Hemyari P, Rullkoetter M, Santulli MJ, Schoenbrunner N. Verification of Claimed Limit of Detection in Molecular Diagnostics. J Appl Lab Med. 2016;1(3):260-270. doi:10.1373/jalm.2016.020735
- 25. Vaks JE. New Method on Evaluation of Limit of Detection in Molecular Diagnostics. In: Medical Devices and Diagnostics. Proceeding of Joint Statistical Meetings; 2018.
- 26. Westgard J, Westgard S. Probit Analysis, Part One. https://westgard.com/lessons/basic-method-validation/893-probit-part-one.html.
- 27. Cao H, Shockey JM. Comparison of TaqMan and SYBR Green qPCR Methods for Quantitative Gene Expression in Tung Tree Tissues. J Agric Food Chem. 2012;60(50):12296–303. https://doi.org/10.1021/jf304690e
- 28. Zhou X, Zhang T, Song D, Huang T, Peng Q, Chen Y, et al. Comparison and evaluation of conventional RT-PCR, SYBR green I and TaqMan real-time RT-PCR assays for the detection of porcine epidemic diarrhea virus. Molecular and Cellular Probes. 2017;33:36–41. https://doi.org/10.1016/j.mcp.2017.02.002
- 29. Soltany-Rezaee-Rad M, Sepehrizadeh Z, Mottaghi-Dastjerdi N, Yazdi MT, Seyatesh N. Comparison of SYBR Green and TaqMan real-time PCR methods for quantitative detection of residual CHO host-cell DNA in biopharmaceuticals. Biologicals. 2015;43(2):130–5. https://doi.org/10.1016/j.biologicals.2014.11.004
- 30. Prencipe S, Sillo F, Garibaldi A, Gullino ML, Spadaro D. Development of a Sensitive TaqMan qPCR Assay for Detection and Quantification of Venturia inaequalis in Apple Leaves and Fruit and in Air Samples. Plant Disease. 2020;104(11):2851–9. https://doi.org/10.1094/PDIS-10-19-2160-RE
- 31. Ayalew S, Wegayehu T, Wondale B, Kebede D, Osman M, Niway S, et al. Detection of Mycobacterium tuberculosis complex in saliva by quantitative PCR: A potential alternative specimen for pulmonary tuberculosis diagnosis. Tuberculosis. 2024;148:102554. https://doi.org/10.1016/j.tube.2024.102554
- 32. Souza MB, Cergole-Novella MC, Molinari DA, et al. Multiplex real-time PCR using SYBR Green: Unspecific intercalating dye to detect antimicrobial resistance genes of Streptococcus pneumoniae in cerebrospinal fluid. PLoS One. 2022;17(6):e0269895-. https://doi.org/10.1371/journal.pone.0269895
- 33. Abdel Sater F, Younes M, Nassar H, Nguewa P, Hamze K. A rapid and low-cost protocol for the detection of B.1.1.7 lineage of SARS-CoV-2 by using SYBR Green-based RT-qPCR. Mol Biol Rep. 2021;48(11):7243-7249. doi:10.1007/s11033-021-06717-y
- 34. Cardoso GVF, Lima JS, Oliveira AC do S de, Silva JB da, Roos TB, Moraes CM de. SYBR Green qPCR Technique for the Detection of Trypanosoma cruzi in Açaí Pulp. Foodborne Pathog Dis. 2020;17(7):466-469. doi:10.1089/fpd.2019.2745
- 35. Zhou X, Zhang T, Song D, et al. Comparison and evaluation of conventional RT-PCR, SYBR green I and TaqMan real-time RT-PCR assays for the detection of porcine epidemic diarrhea virus. Mol Cell Probes. 2017;33:36-41. doi:10.1016/j.mcp.2017.02.002
- 36. Jakkul W, Chaisiri K, Saralamba N, et al. Newly developed SYBR Green-based quantitative real-time PCRs revealed coinfection evidence of Angiostrongylus cantonensis and A. malaysiensis in Achatina fulica existing in Bangkok Metropolitan, Thailand. Food Waterborne Parasitol. 2021;23:e00119. doi:https://doi.org/10.1016/j.fawpar.2021.e00119
- 37. Maggi RG, Richardson T, Breitschwerdt EB, Miller JC. Development and validation of a droplet digital PCR assay for the detection and quantification of Bartonella species within human clinical samples. J Microbiol Methods. 2020;176:106022. doi:https://doi.org/10.1016/j.mimet.2020.106022
- 38. Nicholson P, Rawiwan P, Surachetpong W. Detection of tilapia lake virus using conventional rt-pcr and sybr green rt-qpcr. Journal of Visualized Experiments. 2018;2018(141). doi:10.3791/58596
- 39. Zhang T, Chen J, Wang C, Zhai X, Zhang S. Establishment and application of real-time fluorescence-based quantitative PCR for detection of infectious laryngotracheitis virus using SYBR Green I. Poult Sci. 2018;97(11):3854-3859. doi:https://doi.org/10.3382/ps/pey277
- 40. Barbau-Piednoir E, Denayer S, Botteldoorn N, Dierick K, De Keersmaecker SCJ, Roosens NH. Detection and discrimination of five E. coli pathotypes using a combinatory SYBR® Green qPCR screening system. Appl Microbiol Biotechnol. 2018;102(7):3267-3285. doi:10.1007/s00253-018-8820-0
How to Cite This
Copyright and Permissions

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
Publishing your paper with Jurnal Teknologi Laboratorium (JTL) means that the author or authors retain the copyright in the paper. JTL granted an exclusive reuse license by the author(s), but the author(s) are able to put the paper onto a website, distribute it to colleagues, give it to students, use it in your thesis etc, even commercially. The author(s) can reuse the figures and tables and other information contained in their paper published by JTL in future papers or work without having to ask anyone for permission, provided that the figures, tables or other information that is included in the new paper or work properly references the published paper as the source of the figures, tables or other information, and the new paper or work is not direct at private monetary gain or commercial advantage.
JTL journal provides immediate open access to its content on the principle that making research freely available to the public supports a greater global exchange of knowledge. This journal is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License. This license lets others remix, transform, and build upon the material for any purpose, even commercially.
JTL journal Open Access articles are distributed under this Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA). Articles can be read and shared for All purposes under the following conditions:
- BY: You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
- SA: If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original.
