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http://dx.doi.org/10.4014/jmb.1501.01015

A Color-Reaction-Based Biochip Detection Assay for RIF and INH Resistance of Clinical Mycobacterial Specimens  

Xue, Wenfei (State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Fudan University)
Peng, Jingfu (State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Fudan University)
Yu, Xiaoli (School of Biology and Pharmaceutical Engineering,Wuhan Polytechnic University)
Zhang, Shulin (Department of Medical Microbiology and Parasitology, Shanghai Jiao Tong University School of Medicine)
Zhou, Boping (The Third People's Hospital of Shenzhen)
Jiang, Danqing (State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Fudan University)
Chen, Jianbo (The Third People's Hospital of Shenzhen)
Ding, Bingbing (School of Biology and Pharmaceutical Engineering,Wuhan Polytechnic University)
Zhu, Bin (Baio Technology Limited Company)
Li, Yao (State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Fudan University)
Publication Information
Journal of Microbiology and Biotechnology / v.26, no.1, 2016 , pp. 180-189 More about this Journal
Abstract
The widespread occurrence of drug-resistant Mycobacterium tuberculosis places importance on the detection of TB (tuberculosis) drug susceptibility. Conventional drug susceptibility testing (DST) is a lengthy process. We developed a rapid enzymatic color-reaction-based biochip assay. The process included asymmetric multiplex PCR/templex PCR, biochip hybridization, and an enzymatic color reaction, with specific software for data operating. Templex PCR (tem-PCR) was applied to avoid interference between different primers in conventional multiplex-PCR. We applied this assay to 276 clinical specimens (including 27 sputum, 4 alveolar lavage fluid, 2 pleural effusion, and 243 culture isolate specimens; 40 of the 276 were non-tuberculosis mycobacteria specimens and 236 were M. tuberculosis specimens). The testing process took 4.5 h. A sensitivity of 50 copies per PCR was achieved, while the sensitivity was 500 copies per PCR when tem-PCR was used. Allele sequences could be detected in mixed samples at a proportion of 10%. Detection results showed a concordance rate of 97.46% (230/236) in rifampicin resistance detection (sensitivity 95.40%, specificity 98.66%) and 96.19% (227/236) in isoniazid (sensitivity 93.59%, specificity 97.47%) detection with those of DST assay. Concordance rates of testing results for sputum, alveolar lavage fluid, and pleural effusion specimens were 100%. The assay provides a potential choice for TB diagnosis and treatment.
Keywords
Mycobacterium tuberculosis; drug resistance; biochip; enzymatic color reaction; mixed sample; templex PCR;
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1 Abebe G, Paasch F, Apers L, Rigouts L, Colebunders R. 2011. Tuberculosis drug resistance testing by molecular methods: opportunities and challenges in resource limited settings. J. Microbiol. Methods 84: 155-160.   DOI
2 Aziz MA, Wright A, Laszlo A, De Muynck A, Portaels F, Van Deun A, et al. 2006. Epidemiology of antituberculosis drug resistance (the global project on anti-tuberculosis drug resistance surveillance): an updated analysis. Lancet 368: 2142-2154.   DOI
3 Chen Q, Sun Y, Zhang L, Deng K, Xia H, Xing H, et al. 2011. Detection of C677T mutation of MTHFR in subject with coronary heart disease by hairpin probe with enzymatic color on microarray. Biosens. Bioelectron. 28: 84-90.   DOI
4 Benson R, Tondella ML, Bhatnagar J, Carvalho Mda G, Sampson JS, Talkington DF, et al. 2008. Development and evaluation of a novel multiplex PCR technology for molecular differential detection of bacterial respiratory disease pathogens. J. Clin. Microbiol. 46: 2074-2077.   DOI
5 Bobadilla-del-Valle M, Ponce-de-Leon A, Arenas-Huertero C, Vargas-Alarcon G, Kato-Maeda M, Small PM, et al. 2001. rpoB Gene mutations in rifampin-resistant Mycobacterium tuberculosis identified by polymerase chain reaction singlestranded conformational polymorphism. Emerg. Infect. Dis. 7: 1010-1013.   DOI
6 Caoili JC, Mayorova A, Sikes D, Hickman L, Plikaytis BB, Shinnick TM. 2006. Evaluation of the TB-Biochip oligonucleotide microarray system for rapid detection of rifampin resistance in Mycobacterium tuberculosis. J. Clin. Microbiol. 44: 2378-2381.   DOI
7 Cherkasova E, Laassri M, Chizhikov V, Korotkova E, Dragunsky E, Agol VI, Chumakov K. 2003. Microarray analysis of evolution of RNA viruses: evidence of circulation of virulent highly divergent vaccine-derived polioviruses. Proc. Natl. Acad. Sci. USA 100: 9398-9403.   DOI
8 Cruciani M, Scarparo C, Malena M, Bosco O, Serpelloni G, Mengoli C. 2004. Meta-analysis of BACTEC MGIT 960 and BACTEC 460 TB, with or without solid media, for detection of mycobacteria. J. Clin. Microbiol. 42: 2321-2325.   DOI
9 Donnabella V, Martiniuk F, Kinney D, Bacerdo M, Bonk S, Hanna B, Rom WN. 1994. Isolation of the gene for the beta subunit of RNA polymerase from rifampicin-resistant Mycobacterium tuberculosis and identification of new mutations. Am. J. Respir. Cell Mol. Biol. 11: 639-643.   DOI
10 Gryadunov D, Mikhailovich V, Lapa S, Roudinskii N, Donnikov M, Pan'kov S, et al. 2005. Evaluation of hybridisation on oligonucleotide microarrays for analysis of drug-resistant Mycobacterium tuberculosis. Clin. Microbiol. Infect. 11: 531-539.   DOI
11 Edwards KJ, Metherell LA, Yates M, Saunders NA. 2001. Detection of rpoB mutations in Mycobacterium tuberculosis by biprobe analysis. J. Clin. Microbiol. 39: 3350-3352.   DOI
12 Espasa M, Gonzalez-Martin J, Alcaide F, Aragon LM, Lonca J, Manterola JM, et al. 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.   DOI
13 Goble M, Iseman MD, Madsen LA, Waite D, Ackerson L, Horsburgh CR Jr. 1993. Treatment of 171 patients with pulmonary tuberculosis resistant to isoniazid and rifampin. N. Engl. J. Med. 328: 527-532.   DOI
14 Guo Y, Zhou Y, Wang C, Zhu L, Wang S, Li Q, et al. 2009. Rapid, accurate determination of multidrug resistance in M. tuberculosis isolates and sputum using a biochip system. Int. J. Tuberc. Lung Dis. 13: 914-920.
15 Han J, Swan DC, Smith SJ, Lum SH, Sefers SE, Unger ER, Tang YW. 2006. Simultaneous amplification and identification of 25 human papillomavirus types with Templex technology. J. Clin. Microbiol. 44: 4157-4162.   DOI
16 Heep M, Brandstatter B, Rieger U, Lehn N, Richter E Rusch-Gerdes S, Niemann S. 2001. Frequency of rpoB mutations inside and outside the cluster I region in rifampin-resistant clinical Mycobacterium tuberculosis isolates. J. Clin. Microbiol. 39: 107-110.   DOI
17 Laurenzo D, Mousa SA. 2011. Mechanisms of drug resistance in Mycobacterium tuberculosis and current status of rapid molecular diagnostic testing. Acta Trop. 119: 5-10.   DOI
18 Hemvani N, Patidar V, Chitnis DS. 2012. A simple and economical in-house phage technique for the rapid detection of rifampin, isoniazid, ethambutol, streptomycin, and ciprofloxacin drug resistance in Mycobacterium tuberculosis, directly on decontaminated sputum samples. Int. J. Infect. Dis. 16: e332-e336.   DOI
19 Higgs BW, Mohtashemi M, Grinsdale J, Kawamura LM. 2007. Early detection of tuberculosis outbreaks among the San Francisco homeless: trade-offs between spatial resolution and temporal scale. PLoS One 2: e1284.   DOI
20 Khue PM, Truffot-Pernot C, Texier-Maugein J, Jarlier V, Robert J. 2007. A 10-year prospective surveillance of Mycobacterium tuberculosis drug resistance in France 1995-2004. Eur. Respir. J. 30: 937-944.   DOI
21 Ling DI, Zwerling AA, Pai M. 2008. GenoType MTBDR assays for the diagnosis of multidrug-resistant tuberculosis: a meta-analysis. Eur. Respir. J. 32: 1165-1174.   DOI
22 Morgan M, Kalantri S, Flores L, Pai M. 2005. A commercial line probe assay for the rapid detection of rifampicin resistance in Mycobacterium tuberculosis: a systematic review and metaanalysis. BMC Infect. Dis. 5: 62.   DOI
23 Pang Y, Zhou Y, Zhao B, Liu G, Jiang G, Xia H, et al. 2012. Spoligotyping and drug resistance analysis of Mycobacterium tuberculosis strains from national survey in China. PLoS One 7: e32976.   DOI
24 Park H, Song EJ, Song ES, Lee EY, Kim CM, Jeong SH, et al. 2006. Comparison of a conventional antimicrobial susceptibility assay to an oligonucleotide chip system for detection of drug resistance in Mycobacterium tuberculosis isolates. J. Clin. Microbiol. 44: 1619-1624.   DOI
25 Telenti A, Honore N, Bernasconi C, March J, Ortega A, Heym B,et al. 1997. Genotypic assessment of isoniazid and rifampin resistance in Mycobacterium tuberculosis: a blind study at reference laboratory level. J. Clin. Microbiol. 35: 719-723.
26 Pholwat S, Ehdaie B, Foongladda S, Kelly K, Houpt E. 2012. Real-time PCR using mycobacteriophage DNA for rapid phenotypic drug susceptibility results forMycobacterium tuberculosis. J. Clin. Microbiol. 50: 754-761.   DOI
27 Piersimoni C, Olivieri A, Benacchio L, Scarparo C. 2006. Current perspectives on drug susceptibility testing of Mycobacterium tuberculosis complex: the automated nonradiometric systems. J. Clin. Microbiol. 44: 20-28.   DOI
28 Rondon L, Piuri M, Jacobs WR Jr, de Waard J, Hatfull GF, Takiff HE. 2011. Evaluation of fluoromycobacteriophages for detecting drug resistance in Mycobacterium tuberculosis. J. Clin. Microbiol. 49: 1838-1842.   DOI
29 Toit K, Mitchell S, Balabanova Y, Evans CA, Kummik T, Nikolayevskyy V, Drobniewski F. 2012. The colour test for drug susceptibility testing of Mycobacterium tuberculosis strains. Int. J. Tuberc. Lung Dis. 16: 1113-1118.   DOI
30 Varma-Basil M, El-Hajj H, Colangeli R, Hazbon MH, Kumar S, Bose M, et al. 2004. Rapid detection of rifampin resistance in Mycobacterium tuberculosis isolates from India and Mexico by a molecular beacon assay. J. Clin. Microbiol. 42: 5512-5516.   DOI
31 Williams DL, Spring L, Collins L, Miller LP, Heifets LB, Gangadharam PR, Gillis TP. 1998. Contribution of rpoB mutations to development of rifamycin cross-resistance in Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 42: 1853-1857.