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J Clin Microbiol. 2006 Jul; 44(7): 2605–2608.
PMCID: PMC1489488

Rapid Genotypic Detection of Rifampin- and Isoniazid-Resistant Mycobacterium tuberculosis Directly in Clinical Specimens


A multiplex PCR DNA strip assay (Genotype MTBDR) designed to detect rifampin (rpoB) and high-level isoniazid (katG) resistance mutations in Mycobacterium tuberculosis isolates was optimized for clinical specimens. Successful genotypic results were achieved with 36 of 38 (95%) smear-positive respiratory specimens, allowing rapid therapeutic adjustments in transmittable drug-resistant tuberculosis.

Multidrug-resistant tuberculosis (MDR TB) is defined as Mycobacterium tuberculosis resistant to rifampin (RIF) and isoniazid (INH). The spread of MDR TB has escalated worldwide (8). Drug susceptibility testing (DST) of M. tuberculosis in clinical specimens is time-consuming. INH and RIF are crucial elements of the standard treatment regimen of tuberculosis, and resistance to these drugs requires extension of therapy (4). The vast majority of RIF resistance is caused by mutations located in the 81-bp region of the rpoB gene (22). INH resistance is more complex, as the mutations conferring resistance are located in several genes and loci. INH resistance has been associated mainly with mutations in katG, inhA, ahpC, and kasA (2, 13, 15, 18). Studies investigating strains with high-level INH resistance have documented that 50 to 100% have mutations located in codon 315 of the katG gene (9, 16).

Genotype MTBDR, a commercially available multiplex PCR DNA strip assay (Hain Lifescience, Nehren, Germany), is designed to simultaneously detect the most important rpoB and katG gene mutations conferring RIF and high-level INH resistance in isolates (10). It is based on the hybridization between rpoB and katG amplicons to membrane-bound probes. The DNA strip covers five rpoB wild-type probes, four rpoB mutant probes (with D516V, H526Y, H526D, and S531L mutations), one katG wild-type probe, and two katG mutant probes (with S315T1 and S315T2 mutations). The aim of this study was to optimize and evaluate the application of the assay directly in clinical specimens. Furthermore, we compared the DNA strip results with phenotypic DST results.

The study was carried out at the International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Denmark. A total of 106 NaOH-N-acetyl-l-cysteine-pretreated clinical specimens submitted for M. tuberculosis examination were selected on the basis of susceptibility test result and acid-fast bacillus smear grade. A volume of surplus material from the selected specimens was collected. The respiratory specimens consisted of sputum, tracheal secretion, bronchoalveolar lavage fluid (n = 66), and pleural fluid (n = 4). The nonrespiratory specimens were obtained from lymph node (n = 12), gastric lavage fluid (n = 11), cerebrospinal/synovial fluid/urine (n = 6), and tissue biopsy samples (n = 7). None of the patients were registered in the Registry of Human Tissue Utilization, National Board of Health (prohibits tissue use for research). Of 90 culture-positive specimens, 62% (n = 56) were smear positive and 42% (n = 38) were RIF and/or INH resistant. All specimens were processed by conventional mycobacterial procedures as previously described (11). Smears were stained with auramine-rhodamine and examined by ×200 magnification (21). Specimens were incubated on Löwenstein-Jensen slants and MGIT (Becton Dickinson), and growth of Mycobacterium tuberculosis was confirmed by Inno-LiPA species assay (InnoGenetics). DST for RIF and INH was performed using a BACTEC 460 system (Becton Dickinson) according to the manufacturer's instructions (20). Critical drug concentrations were 2.0 μg/ml for RIF and 0.1 μg/ml for INH. In addition, INH was tested at 0.4 and 2.0 μg/ml. On request, strand displacement amplification (SDA) (Becton Dickinson) was performed as described elsewhere (12). Specimens were stored at −20°C prior to analysis.

Genotype MTBDR optimization.

An aliquot (500 μl) of pretreated specimen was centrifuged (10,000 × g, 15 min). The pellet was resuspended in sterile Milli-Q water (100 μl) and heat inactivated (100°C, 20 min). DNA was extracted by ultrasonication (60°C, 15 min) followed by centrifugation (10,000 × g, 5 min). We optimized the multiplex PCR targeting rpoB, and katG, and 23S rRNA with regard to sample volume (1, 3, and 5 μl), MgCl2 concentration (1.0, 1.5, and 2.0 mM), and the number of PCR cycles (20 and 30). Following optimization, the multiplex PCR conditions for the rest of the study consisted of a 50-μl reaction volume, 35 μl primer-nucleotide mix (kit), 10× PCR buffer without MgCl2, 3 μl of MgCl2 stock solution (25 mM), 2 U of FastStart Taq DNA polymerase (Roche Applied Science), and 5 μl of extracted DNA. With a Gene Amp PCR 9600 system (Applied Biosystems), the amplification profile consisted of a denaturation step (95°C, 5 min), 10 cycles of 95°C for 30 s and 58°C for 2 min, followed by 30 cycles of 95°C for 25 s, 53°C for 40 s, and 70°C for 40 s, and a final extension of 70°C for 8 min. Amplicons of 200 bp (universal control), 250 bp (rpoB), and 120 bp (katG) on an agarose gel were found in 47 of 56 (84%) smear-positive specimens. Hybridization utilizing a preprogrammed Auto-LiPA system (InnoGenetics) and interpretation of the DNA strip (Fig. (Fig.1)1) were performed according to the manufacturer's instructions.

FIG. 1.
Representative DNA strip patterns obtained with the optimized Genotype MTBDR assay. The positions of the oligonucleotide probes are given on the left. The target genes and specific probe lines are shown from top to bottom as follows: conjugate control; ...

Interpretable DNA strip readings correlated with smear grade and were obtained for 36 of 38 (95%) respiratory and 15 of 18 (83%) nonrespiratory smear-positive specimens, regardless of DST (Table (Table1).1). Genotypic results were concordant with those found with BACTEC in 54 of 57 (95%) samples (Tables (Tables11 and and2).2). Discordant results could be explained by the INH resistance mutations being located elsewhere than codon 315. All 10 MDR TB specimens had results concordant with BACTEC. Mutations and wild-type mismatch (katG) correlated in 17 of 20 (85%) samples with high-level INH resistance (MIC ≥ 0.4 μg/ml) as approved by CLSI (formerly NCCLS) standard M24-A (17). The S315T1 mutation was the most prevalent, accounting for 14 of 20 (70%) samples. Fourteen of 20 (70%) specimens with high-level INH resistance were also resistant at the higher concentration (2.0 μg/ml) tested. Similarly to our findings, high-level INH resistance (MIC > 2 μg/ml) has previously been associated with 89% of isolates with mutations in codon 315 (23). Samples with low-level INH resistance (0.1 μg/ml) had wild-type patterns, indicating that this mutation was located in another gene. As the modified assay is unable to determine the proportion of resistant bacteria and is limited to the detection of RIF and INH resistance mutations in smear-positive specimens, the assay cannot replace phenotypic DST, which remains the gold standard. In a few studies, mycobacteriophage-based assays for RIF resistance detection have also shown potential for direct application with sputum samples (1, 3, 5). However, the accuracy of these methods remains to be elucidated. Similarly to our findings, other PCR-based assays utilizing TaqMan, molecular beacons, and fluorescence resonance energy transfer probes (katG codon 315, inhA, and rpoB) demonstrated high sensitivities in smear-positive specimens (6, 7, 14, 19, 24).

Performance of the optimized assay with primary drug-susceptible and -resistant respiratory and nonrespiratory specimens
Comparison of genotypic and phenotypic drug resistance results for respiratory and nonrespiratory specimens

In conclusion, the optimized Genotype MTBDR assay was found to be directly applicable with smear-positive specimens. The assay is rapid (<48 h) and easy to perform and allows detection of multidrug resistance in tuberculosis patients suspected of treatment failure or reactivation of prior disease or originating from countries with high prevalences of MDR TB. A rapid tool that simultaneously detects RIF and the more prevalent high-level INH resistance may have a major impact on the future management of tuberculosis.


We thank Karin Øhrberg Lund for her skillful laboratory contribution and HAIN Lifescience, Nehren, Germany, for supplying kits and technical support.

We declare no conflicts of interest.


1. Albert, H., A. Trollip, T. Seaman, and R. J. Mole. 2004. Simple, phage-based (FASTPplaque) technology to determine rifampicin resistance of Mycobacterium tuberculosis directly from sputum. Int. J. Tuberc. Lung Dis. 8:1114-1119. [PubMed]
2. Banerjee, A., E. Dubnau, A. Quemard, V. Balasubramanian, K. S. Um, T. Wilson, D. Collins, G. de Lisle, and W. R. Jacobs, Jr. 1994. inhA, a gene encoding a target for isoniazid and ethionamide in Mycobacterium tuberculosis. Science 263:227-230. [PubMed]
3. Bardarov, S., Jr., H. Dou, K. Eisenach, N. Banaiee, S. Ya, J. Chan, W. R. Jacobs, Jr., and P. F. Riska. 2003. Detection and drug-susceptibility testing of M. tuberculosis from sputum samples using luciferase reporter phage: comparison with the Mycobacteria Growth Indicator Tube (MGIT) system. Diagn. Microbiol. Infect. Dis. 45:53-61. [PubMed]
4. Blanc, L., P. Chaulet, M. Espinal, S. Graham, M. Grzemska, A. Harries, F. Luelmo, D. Maher, R. O'Brien, M. Raviglione, H. Rieder, J. Starke, M. Uplekar, and C. Wells. 2003. Treatment of tuberculosis, guidelines for national programmes, 3rd ed. World Health Organization, Geneva, Switzerland.
5. Butt, T., R. N. Ahmad, R. K. Afzal, A. Mahmood, and M. Anwar. 2004. Rapid detection of rifampicin susceptibility of Mycobacterium tuberculosis in sputum specimens by mycobacteriophage assay. J. Pak. Med. Assoc. 54:379-382. [PubMed]
6. El Hajj, H. H., S. A. Marras, S. Tyagi, F. R. Kramer, and D. Alland. 2001. Detection of rifampin resistance in Mycobacterium tuberculosis in a single tube with molecular beacons. J. Clin. Microbiol. 39:4131-4137. [PMC free article] [PubMed]
7. Espasa, M., J. Gonzalez-Martin, F. Alcaide, L. M. Aragon, J. Lonca, J. M. Manterola, M. Salvado, G. Tudo, P. Orus, and P. Coll. 2005. Direct detection in clinical samples of multiple gene mutations causing resistance of Mycobacterium tuberculosis to isoniazid and rifampicin using fluorogenic probes. J. Antimicrob. Chemother. 55:860-865. [PubMed]
8. Espinal, M. A. 2003. The global situation of MDR-TB. Tuberculosis (Edinburgh) 83:44-51. [PubMed]
9. Hillemann, D., T. Kubica, R. Agzamova, B. Venera, S. Rusch-Gerdes, and S. Niemann. 2005. Rifampicin and isoniazid resistance mutations in Mycobacterium tuberculosis strains isolated from patients in Kazakhstan. Int. J. Tuberc. Lung Dis. 9:1161-1167. [PubMed]
10. Hillemann, D., M. Weizenegger, T. Kubica, E. Richter, and S. Niemann. 2005. Use of the Genotype MTBDR assay for rapid detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis complex isolates. J. Clin. Microbiol. 43:3699-3703. [PMC free article] [PubMed]
11. Johansen, I. S., B. H. Lundgren, J. P. Thyssen, and V. O. Thomsen. 2002. Rapid differentiation between clinically relevant mycobacteria in microscopy positive clinical specimens and mycobacterial isolates by line probe assay. Diagn. Microbiol. Infect. Dis. 43:297-302. [PubMed]
12. Johansen, I. S., V. O. Thomsen, A. Johansen, P. Andersen, and B. Lundgren. 2002. Evaluation of a new commercial assay for diagnosis of pulmonary and nonpulmonary tuberculosis. Eur. J. Clin. Microbiol. Infect. Dis. 21:455-460. [PubMed]
13. Kelley, C. L., D. A. Rouse, and S. L. Morris. 1997. Analysis of ahpC gene mutations in isoniazid-resistant clinical isolates of Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 41:2057-2058. [PMC free article] [PubMed]
14. Marín, M., D. García de Viedma, M. J. Ruíz-Serrano, and E. Bouza. 2004. Rapid direct detection of multiple rifampin and isoniazid resistance mutations in Mycobacterium tuberculosis in respiratory samples by real-time PCR. Antimicrob. Agents Chemother. 48:4293-4300. [PMC free article] [PubMed]
15. Mdluli, K., R. A. Slayden, Y. Zhu, S. Ramaswamy, X. Pan, D. Mead, D. D. Crane, J. M. Musser, and C. E. Barry III. 1998. Inhibition of a Mycobacterium tuberculosis beta-ketoacyl ACP synthase by isoniazid. Science 280:1607-1610. [PubMed]
16. Musser, J. M., V. Kapur, D. L. Williams, B. N. Kreiswirth, D. van Soolingen, and J. D. van Embden. 1996. Characterization of the catalase-peroxidase gene (katG) and inhA locus in isoniazid-resistant and -susceptible strains of Mycobacterium tuberculosis by automated DNA sequencing: restricted array of mutations associated with drug resistance. J. Infect. Dis. 173:196-202. [PubMed]
17. National Committee for Clinical Laboratory Standards. 2003. Susceptibility testing of mycobacteria, nocardiae, and other aerobic actinomycetes. Approved standard M24-A. National Committee for Clinical Laboratory Standards, Wayne, Pa.
18. Ramaswamy, S., and J. M. Musser. 1998. Molecular genetic basis of antimicrobial agent resistance in Mycobacterium tuberculosis: 1998 update. Tuber. Lung Dis. 79:3-29. [PubMed]
19. Ruiz, M., M. J. Torres, A. C. Llanos, A. Arroyo, J. C. Palomares, and J. Aznar. 2004. Direct detection of rifampin- and isoniazid-resistant Mycobacterium tuberculosis in auramine-rhodamine-positive sputum specimens by real-time PCR. J. Clin. Microbiol. 42:1585-1589. [PMC free article] [PubMed]
20. Siddiqi, S. H. 1996. BACTEC 460 TB system product and procedure manual. Becton Dickinson Microbiology Systems, Sparks, Md.
21. Smithwick, R. W. 1979. Laboratory manual for acid-fast microscopy. U.S. Department of Health, Education and Welfare, Centers for Disease Control and Prevention, Atlanta, Ga.
22. Telenti, A., P. Imboden, F. Marchesi, D. Lowrie, S. Cole, M. J. Colston, L. Matter, K. Schopfer, and T. Bodmer. 1993. Detection of rifampicin-resistance mutations in Mycobacterium tuberculosis. Lancet 341:647-650. [PubMed]
23. van Soolingen, D., P. E. de Haas, H. R. van Doorn, E. Kuijper, H. Rinder, and M. W. Borgdorff. 2000. Mutations at amino acid position 315 of the katG gene are associated with high-level resistance to isoniazid, other drug resistance, and successful transmission of Mycobacterium tuberculosis in the Netherlands. J. Infect. Dis. 182:1788-1790. [PubMed]
24. Wada, T., S. Maeda, A. Tamaru, S. Imai, A. Hase, and K. Kobayashi. 2004. Dual-probe assay for rapid detection of drug-resistant Mycobacterium tuberculosis by real-time PCR. J. Clin. Microbiol. 42:5277-5285. [PMC free article] [PubMed]

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