Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 May 10:15:1372647.
doi: 10.3389/fmicb.2024.1372647. eCollection 2024.

Evaluation of a real-time PCR assay performance to detect Mycobacterium tuberculosis, rifampicin, and isoniazid resistance in sputum specimens: a multicenter study in two major cities of Indonesia

Ida Parwati  1 , Lidya Chaidir  2 , Muhammad Yunus  3 , Maya Marinda Montain  4 , Dini Budhiarko  3 , Siti Fatimah Selasih  3 , Ryan Bayusantika Ristandi  5 , Rifky Waluyajati Rachman  5 , Raden Desy Nurhayati  6 , Imran Pambudi  7 , Akterono Dwi Budiyati  3
Affiliations

Evaluation of a real-time PCR assay performance to detect Mycobacterium tuberculosis, rifampicin, and isoniazid resistance in sputum specimens: a multicenter study in two major cities of Indonesia

Ida Parwati et al. Front Microbiol. .

Abstract

Background: Tuberculosis (TB) is one of the major global health issues due to its high mortality rate, especially in low- and middle-income countries. One of the key success points of the TB eradication program is early TB diagnosis, which requires rapid and accurate diagnostic testing. This study aimed to evaluate the performance of a newly developed RT-PCR kit (Indigen MTB/DR-TB RT-PCR) in a routine TB clinical setting.

Method: A multi-fluorescence RT-PCR assay was designed and developed to detect regions within IS6110, rpoB, katG, and inhA of the Mycobacterium tuberculosis (MTB) genes. Sputum specimens were obtained from suspected TB patients who visited TB healthcare facilities in two major cities of Indonesia from September 2022 to May 2023. Specimens were assessed using Indigen MTB/DR-TB RT-PCR, acid-fast bacillus (AFB) smear microscopy, MTB culture, and drug susceptibility testing (DST) methods. Fisher's exact test (χ2) was used to analyze the Indigen performance relative to culture methods.

Result: The performance of Indigen MTB/DR-TB RT-PCR to detect MTB was assessed using 610 sputum specimens obtained from suspected patients. The overall sensitivity and specificity were 94.12% (95% CI: 90.86-96.48%) and 98.32% (95% CI: 96.20-99.46%), respectively. When the analysis was performed on AFB smear-negative TB subjects (386 subjects), a lower sensitivity level was found at 78.57% (95% CI: 68.26-86.78%), while the specificity level remained similar at 98.34% (95% CI: 96.18-99.46%). The overall performance of Indigen MTB/DR-TB RT-PCR to detect MTB showed substantial agreement with the MTB culture method (kappa value 0.93). In comparison to DST, the sensitivity and specificity levels of Indigen to detect RIF resistance or INH resistance were 78.2% (95% CI: 61.8-90.2%) and 82.8% (95% CI: 64.2-94.2%), respectively, while the specificity level for both groups was at 100% (95% CI, 87.7-100%).

Conclusion: Indigen MTB/DR-TB RT-PCR demonstrated reliable performance for TB molecular diagnostic testing and can be implemented in routine TB diagnostic settings.

Keywords: INH resistance; Indigen; Mycobacterium tuberculosis; RIF resistance; diagnostic; real-time PCR.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Similar articles

See all similar articles

References

    1. Alisjahbana B., Koesoemadinata R. C., Hadisoemarto P. F., Lestari B. W., Hartati S., Chaidir L., et al. . (2021). Are neighbourhoods of tuberculosis cases a high-risk population for active intervention? A protocol for tuberculosis active case finding. PLoS One 16:e0256043. doi: 10.1371/journal.pone.0256043, PMID: - DOI - PMC - PubMed
    1. Araya B. T., Ali K. E., Geleta D. A., Tekele S. G., Tulu K. D. (2021). Performance of the Abbott RealTime MTB and RIF/INH resistance assays for the detection of mycobacterium tuberculosis and resistance markers in sputum specimens. PLoS One 16:e0251602. doi: 10.1371/journal.pone.0251602, PMID: - DOI - PMC - PubMed
    1. Armand S., Vanhuls P., Delcroix G., Courcol R., Lemaître N. (2011). Comparison of the Xpert MTB/RIF test with an IS6110-TaqMan real-time PCR assay for direct detection of Mycobacterium tuberculosis in respiratory and nonrespiratory specimens. J. Clin. Microbiol. 49, 1772–1776. doi: 10.1128/JCM.02157-10, PMID: - DOI - PMC - PubMed
    1. Babafemi E. O., Cherian B. P., Banting L., Mills G. A., Ngianga K. (2017). Effectiveness of real-time polymerase chain reaction assay for the detection of Mycobacterium tuberculosis in pathological samples: a systematic review and meta-analysis. Syst. Rev. 6:215. doi: 10.1186/s13643-017-0608-2, PMID: - DOI - PMC - PubMed
    1. Boehme C. C., Nabeta P., Hillemann D., Nicol M. P., Shenai S., Krapp F., et al. . (2010). Rapid molecular detection of tuberculosis and rifampin resistance. N. Engl. J. Med. 363, 1005–1015. doi: 10.1056/NEJMoa0907847, PMID: - DOI - PMC - PubMed

LinkOut - more resources