2019 / 01

Next Paper
DOI: 10.24075/brsmu.2019.007

ORIGINAL RESEARCH

Detection of Ser450Leu mutation in rpoB gene of Mycobacterium tuberculosis by allele-specific loop-mediated isothermal DNA amplification method

Filipenko ML1, Oscorbin IP1, Khrapov EA1, Shamovskaya DA1, Cherednichenko AG2, Shvartz YaSh2
About authors

1 Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia

2 Novosibirsk Tuberculosis Research Institute, Novosibirsk, Russia

Correspondence should be addressed: Maxim L. Filipenko
Lavrentyev Prospect 8/2, Novosibirsk, 630090; moc.liamg@oknepiliflm

About paper

Funding: the study was done with the financial support of the basic budgetary financing project № VI.62.1.5 «Synthetic biology: development of tools for the genetic material manipulation and creation of promising drugs for therapy and diagnostics» (0309-2018-0003).

Author contribution: Filipenko ML created а general concept of the study, planned experiments, analyzed the results and participated in the writing of this article; Oscorbin IP participated in the writing of this article; Khrapov EA conducted experiments; Shamovskaya DV conducted experiments; Cherednichenko AG analyzed the experiments results; Shvartz YaSh was involved in planning and analyzed the experiments results.

Received: 2018-12-07 Accepted: 2019-02-25 Published online: 2019-03-09
|
  1. Drobniewski FA, Wilson SM. The rapid diagnosis of isoniazid and rifampicin resistance in Mycobacterium tuberculosis — a molecular story. J Med Microbiol. 1998; 47 (3): 189–96.
  2. Heifets LB. Antimycobacterial drugs. Semin Respir Infect. 1994; 9 (2): 84–103.
  3. TB Drug Resistance Mutation Database. Available from: https://tbdreamdb.ki.se/Data/MutationDetail.aspx?AreaId=RIF&GeneID=Rv0667.
  4. Mokrousov I, Otten T, Vyshnevskiy B, Narvskaya O. Allele-specific rpoB PCR assays for detection of rifampin-resistant Mycobacterium tuberculosis in sputum smears. Antimicrob Agents Chemother. 2003; 47 (7): 2231–5.
  5. Filipenko ML, Dymova MA, Hrapov EA, Bojarskih, UA, Petrenko TI, Cherednichenko AG i dr. Sposob vyjavlenija ustojchivyh k rifampicinu izoljatov. Vestnik NGU. 2012; 10 (2): 101–6.
  6. Gill P, Ghaemi A. Nucleic acid isothermal amplification technologies: a review. Nucleosides Nucleotides Nucleic Acids. 2008; 27 (3): 224–43.
  7. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000; 28 (12): E63.
  8. Francois P, Tangomo M, Hibbs J, Bonetti E-J, Boehme CC, Notomi T et. al. Robustness of a loop-mediated isothermal amplification reaction for diagnostic applications. FEMS Immunol Med Microbiol. 2011; 62 (1): 41–8.
  9. Mori Y, Nagamine K, Tomita N, Notomi T. Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochem Biophys Res Commun. 2001; 289 (1): 150–4.
  10. Kouguchi Y, Fujiwara T, Teramoto M, Kuramoto M. Homogenous, real-time duplex loop-mediated isothermal amplification using a single fluorophore-labeled primer and an intercalator dye: Its application to the simultaneous detection of Shiga toxin genes 1 and 2 in Shiga toxigenic Escherichia coli isolates. Mol Cell Probes. 2010; 24 (4): 190–5.
  11. Liu W, Huang S, Liu N, Dong D, Yang Z, Tang Y et al. Establishment of an accurate and fast detection method using molecular beacons in loop-mediated isothermal amplification assay. Sci Rep. 2017; (7): 40125.
  12. Goto M, Honda E, Ogura A, Nomoto A, Hanaki K-I. Colorimetric detection of loop-mediated isothermal amplification reaction by using hydroxy naphthol blue. Biotechniques. 2009; 46 (3): 167–72.
  13. Nagai K, Horita N, Yamamoto M, Tsukahara T, Nagakura H, Tashiro K et al. Diagnostic test accuracy of loop-mediated isothermal amplification assay for Mycobacterium tuberculosis: systematic review and meta-analysis. Sci Rep. 2016; (6): 39090.
  14. World Health Organization, editors. Global Tuberculosis Programme The use of loop-mediated isothermal amplification (TB-LAMP) for the diagnosis of pulmonary tuberculosis: policy guidance. 2016.
  15. Oscorbin IP, Boyarskikh UA, Filipenko ML. Large fragment of DNA polymerase I from Geobacillus sp. 777: cloning and comparison with DNA polymerases I in practical applications. Mol Biotechnol. 2015; 57 (10): 947–59.
  16. Oscorbin IP, Belousova EA, Zakabunin AI, Boyarskikh UA, Filipenko ML. Comparison of fluorescent intercalating dyes for quantitative loop-mediated isothermal amplification (qLAMP). Biotechniques. 2016; 61 (1): 20–5.
  17. Badolo A, Bando H, Traoré A, Ko-ketsu M, Guelbeogo WM, Kanuka H et al. Detection of G119S ace-1 R mutation in field-collected Anopheles gambiae mosquitoes using allele-specific loop-mediated isothermal amplification (AS-LAMP) method. Malar J. 2015; (14): 477.
  18. Carlos FF, Veigas B, Matias AS, Doria G, Flores O, Baptista PV. Allele specific LAMP-gold nanoparticle for characterization of single nucleotide polymorphisms. Biotechnol Reports. 2017; (16): 21–5.
  19. Chakrabarti R, Schutt CE. The enhancement of PCR amplification by low molecular-weight sulfones. Gene. 2001; 274 (1–2): 293–8.
  20. Jiang YS, Bhadra S, Li B, Wu YR, Milligan JN, Ellington AD. Robust strand exchange reactions for the sequence-specific, real-time detection of nucleic acid amplicons. Anal Chem. 87 (6): 3314–20.
  21. Nakamura N, Ito K, Takahashi M, Hashimoto K, Kawamoto M, Yamanaka M et al. Detection of six single-nucleotide polymorphisms associated with rheumatoid arthritis by a loop-mediated isothermal amplification method and an electrochemical DNA chip. Anal Chem. 2007; 79 (12): 9484–93.
  22. Yongkiettrakul S, Kampeera J, Chareanchim W, Rattanajak R, Pornthanakasem W, Kiatpathomchai W et al. Simple detection of single nucleotide polymorphism in Plasmodium falciparum by SNP-LAMP assay combined with lateral flow dipstick. Parasitol Int. 2017; 66 (1): 964–71.
  23. Zhang L, Zhang Y, Wang C, Feng Q, Fan F, Zhang G, et al. Integrated microcapillary for sample-to-answer nucleic acid pretreatment, amplification, and detection. Anal Chem. 2014; 86 (20): 10461–6.
  24. Itonaga M, Matsuzaki I, Warigaya K, Tamura T, Shimizu Y, Fujimoto M, et al. Novel methodology for rapid detection of KRAS mutation using PNA-LNA mediated loop-mediated isothermal amplification. PLoS One. 2016; (11): e0151654.
  25. Newton CR, Graham A, Heptinstall LE, Powell SJ, Summers C, Kalsheker N, et al. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 1989; 17 (7): 2503–16.
  26. Li B, Kadura I, Fu D-J, Watson DE. Genotyping with TaqMAMA. Genomics. 2004; 83 (2): 311–20.
  27. Nagai Y, Iwade Y, Nakano M, Akachi S, Kobayashi T, Nishinaka T. Rapid and simple identification of Beijing genotype strain of Mycobacterium tuberculosis using a loop-mediated isothermal amplification assay. Microbiol Immunol. 2016; 60 (7): 459–67.