Comparison of Interpretation between Pyrosequencing and Xpert MTB/RIF Assay in Multidrug-Resistant Tuberculosis

Linda Choerunnisa, Coriejati Rita, Anna Tjandrawati, Lidya Chaidir, Ida Parwati


Indonesia is one of the countries with the highest multidrug-resistant tuberculosis cases in the world. Rapid molecular test using the Xpert MTB/RIF assay is one of the detection methods for MDR-TB. Early detection of MDR-TB is crucial for early initiation of treatment. However, Xpert MTB/RIF assay only detects the rpoB gene mutations associated with Rifampicin resistance. Recently, WHO recommends the use of Pyrosequencing, a DNA sequencing method that can detect not only the rpoB gene but also katG and/or inhA gene mutations associated with Isoniazid resistance. The aims of this study were to compare the interpretation between the two methods  and to determine the differences in codon mutation position detection of the rpoB gene and mutation detection of the katG and/or inhA gene. This was a cross-sectional comparative observational study on patients ≥18 years old interpreted as RR-TB patients based on Xpert MTB/RIF assay results who had not received MDR-TB drugs at Dr. Hasan Sadikin General Hospital, Bandung, Indonesia. Results showed there were 40 Rifampicin-resistant TB subjects interpreted by Xpert MTB/RIF assay while Pyrosequencing interpreted 30 MDR-TB, 9 RR-TB and one Isoniazid-resistant TB subjects in January - February 2020. The detection of rpoB gene codon mutation position between Xpert MTB/RIF assay and Pyrosequencing methods was not significantly different (p=0.389). Pyrosequencing had detected 27 katG gene mutations, 3 inhA gene mutations, one katG and inhA gene mutation. To conclude, Pyrosequencing can be used for accurate detection of Rifampicin and Isoniazid resistance in MDR-TB.


Perbandingan Hasil Interpretasi antara Pyrosequencing dengan Xpert MTB/RIF Assay pada Multidrug-Resistant Tuberculosis

Indonesia merupakan salah satu negara dengan kasus multidrug-resistant tuberculosis terbanyak. Penegakan diagnosis MDR-TB saat ini menggunakan tes cepat molekular Xpert MTB/RIF assay sehingga pasien segera mendapatkan pengobatan. Namun Xpert MTB/RIF assay hanya mendeteksi mutasi gen rpoB penyandi resistansi Rifampisin. World Health Organization merekomendasikan Pyrosequencing, metode sequencing nukleotida yang dapat mendeteksi mutasi gen rpoB, gen katG dan/atau inhA penyandi resistansi Isoniazid. Tujuan penelitian ini adalah menentukan apakah kedua alat ini memberikan hasil interpretasi yang sama, apakah ada perbedaan deteksi posisi mutasi kodon gen rpoB dan apakah ditemukan mutasi gen katG dan/atau inhA. Penelitian ini merupakan studi observasional komparatif dengan rancangan cross-sectional. Subjek penelitian adalah pasien usia ≥18 tahun yang diinterpretasi RR-TB berdasarkan Xpert MTB/RIF assay di RSUP Dr. Hasan Sadikin Bandung dan belum mendapat pengobatan. Xpert MTB/RIF assay menginterpretasi 40 subjek Rifampicin-resistant TB sedangkan Pyrosequencing menginterpretasi 30 subjek MDR-TB, 9 subjek RR-TB dan satu subjek Isoniazid-resistant TB pada bulan Januari-Februari 2020. Deteksi posisi mutasi kodon gen rpoB antara Xpert MTB/RIF assay dan Pyrosequencing tidak berbeda bermakna (p=0,389). Pyrosequencing mendeteksi 27 mutasi gen katG, 3 mutasi gen inhA, satu mutasi gen katG dan inhA. Kesimpulan, Pyrosequencing dapat digunakan untuk deteksi resistansi Rifampisin dan Isoniazid pada MDR-TB secara lebih akurat.


Multidrug-resistant tuberculosis, Pyrosequencing, Xpert MTB/RIF assay

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WHO. Global tuberculosis report 2019. France: WHO; 2019.

Hamze M, Ismail MB, Rahmo AK, Dabboussi F. Pyrosequencing for rapid detection of tuberculosis resistance to Rifampicin and Isoniazid in Syrian and Lebanese clinical isolates. Int J Mycobacteriol. 2015;4(3):228–32.

Lawn SD, Nicol MP. Xpert MTB/RIF assay: development, evaluation and implementation of a new rapid molecular diagnostic for tuberculosis and Rifampicin resistance. Future Microbiology. 2011;6(9):1067–82.

Albert H, Nathavitharana RR, Isaacs C, Pai M, Denkinger CM, Boehme CC. Development, roll-out and impact of Xpert MTB/RIF for tuberculosis: what lessons have we learnt and how can we do better?. Eur Respir J. 2016;48(2):516–25.

Bodmer T, Ströhle A. Diagnosing pulmonary tuberculosis with the Xpert MTB/RIF test. J Vis Exp. 2012;(62):e3547..

Ocheretina O, Byrt E, Mabou M, Royal-Mardi G, Merveille Y, Rouzier V, et al. False-positive Rifampin resistant results with Xpert MTB/RIF version 4 assay in clinical samples with a low bacterial load. Diagn Microbiol Infect Dis. 2016;85(1):53–5.

Kaur R, Jindal N, Arora S, Kataria S. Epidemiology of Rifampicin resistant tuberculosis and common mutations in rpoB gene of Mycobacterium tuberculosis: a retrospective study from six districts of Punjab (India) using Xpert MTB/RIF assay. J Lab Physicians. 2016;8(2):96–100.

Garza-Gonzalez E, Gonzalez GM, Renteria A, Cruz-Pulido WL, Rivera G, Bocanegra-Garcia V. A Pyrosequencing method for molecular monitoring of regions in the inhA, ahpC and rpoB genes of Mycobacterium tuberculosis. Clin Microbiol Infect. 2010;16(6):607–12.

Seifert M, Catanzaro D, Catanzaro A, Rodwell TC. Genetic mutations associated with Isoniazid resistance in Mycobacterium tuberculosis: a systematic review. PLoS ONE. 2015;10(3):1–13.

Harrington CT, Lin EI, Olson MT, Eshleman JR. Fundamentals of pyrosequencing. Arch Pathol Lab Med. 2013;137(9):1296-303.

Zheng R, Zhu C, Guo Q, Qin L, Wang J, Lu J, et al. Pyrosequencing for rapid detection of tuberculosis resistance in clinical isolates and sputum samples from re-treatment pulmonary tuberculosis patients. BMC Infect Dis. 2014;14:200.

USAID. International Standards for Tuberculosis Care. TB care I. 3rd ed. San Fransisco: United States Agency for International Development (USAID); 2014.

Pyrobett. MXDR-TB test user manual. Singapore: Pyrobett Joint Lab Genome Institute; 2017.

GeneXpert. Xpert MTB/RIF assay. Revision F ed. USA: Cepheid Innovation; 2019.

Ajbani K, Tornheim J, Naik S, Soman R, Shetty A, Rodrigues C. Pyrosequencing to resolve discrepant Xpert MTB/RIF and mycobacterial growth indicator tube 960. Lung India. 2018;35(2):168–70.

Zheng C, Li S, Luo Z, Pi R, Sun H, He Q, et al. Mixed infection and Rifampin heteroresistance among Mycobacterium tuberculosis clinical isolates. J Clin Microbiol. 2015;53(7):2138–47.

Folkvardsen DB, Thomsen VO, Rogouts L, Rasmussen EM, Bang D, Bernaerts G, et al. Rifampin heteroresistance in Mycobacterium tuberculosis cultures as detected by phenotypic and genotypic drug susceptibility test methods. J Clin Microbiol. 2013;51(12):4220–2.

Engstrom A, Hoffner S, Jureen P. Detection of heteroresistant Mycobacterium tuberculosis by Pyrosequencing. J Clin Microbiol. 2013;51(12):4210–2.

Baffoe-Bonnie A, Houpt ER, Turner L, Dodge D, Heysell SK. Drug-susceptible and multidrug-resistant Mycobacterium tuberculosis in a single patient. Emerging Infectious Diseases. 2019;25(11):2120–1.

Aung WW, Ei PW, Nyunt WW, Swe TL, Lwin T, Htwe MM, et al. Phenotypic and genotypic analysis of anti-tuberculosis drug resistance in Mycobacterium tuberculosis isolates in Myanmar. Ann Lab Medicin. 2015; 35(5):494–9.


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