An efficient alternative marker for specific identification of Mycobacterium tuberculosis

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• 作者：Jianing Zhao (1)
  Yiwei Wang (2)
  Dairong Li (3)
  Jiawen Liu (4)
  Xuemei Zhang (1)
  Yujuan He (1)
  Hong Wang (1)
  Ju Cao (3)
  Yibing Yin (1) (5)
  Wenchun Xu (1)
  
• 关键词：Molecular marker ; Mycobacterium tuberculosis ; PCR ; Real ; time PCR
• 刊名：World Journal of Microbiology and Biotechnology
• 出版年：2014
• 出版时间：August 2014
• 年：2014
• 卷：30
• 期：8
• 页码：2189-2197
• 全文大小：448 KB
• 参考文献：1. Bouakaze C, Keyser C, De Martino S, Sougakoff W, Veziris N, Dabernat H, Ludes B (2010) Identification and genotyping of / Mycobacterium tuberculosis complex species by use of a SNaPshot minisequencing-based assay. J Clin Microbiol 48(5):1758-766 CrossRef
  2. Brosch R, Gordon SV, Marmiesse M, Brodin P, Buchrieser C, Eiglmeier K, Garnier T, Gutierrez C, Hewinson G, Kremer K (2002) A new evolutionary scenario for the / Mycobacterium tuberculosis complex. Proc Natl Acad Sci USA 99(6):3684-689 CrossRef
  3. Das S, Paramasivan C, Lowrie D, Prabhakar R, Narayanan P (1995) IS / 6110?restriction fragment length polymorphism typing of clinical isolates of / Mycobacterium tuberculosis from patients with pulmonary tuberculosis in Madras. South India. Tuber Lung Dis 76(6):550-54 CrossRef
  4. Del Portillo P, Murillo LA, Patarroyo ME (1991) Amplification of a species-specific DNA fragment of / Mycobacterium tuberculosis and its possible use in diagnosis. J Clin Microbiol 29(10):2163-168
  5. Frothingham R, Hills HG, Wilson KH (1994) Extensive DNA sequence conservation throughout the / Mycobacterium tuberculosis complex. J Clin Microbiol 32(7):1639-643
  6. Giampaglia C, Martins M, Inumaru V, Butuem I, Telles M (2005) Evaluation of a rapid differentiation test for the / Mycobacterium tuberculosis complex by selective inhibition with rho-nitrobenzoic acid and thiophene-2-carboxylic acid hydrazide. Int J Tuberc Lung Dis 9(2):206-09
  7. Hellyer TJ, DesJardin LE, Assaf MK, Bates JH, Cave MD, Eisenach KD (1996) Specificity of IS / 6110-based amplification assays for / Mycobacterium tuberculosis complex. J Clin Microbiol 34(11):2843-846
  8. Ho C–C, Lau CC, Martelli P, Chan S-Y, Cindy W, Wu AK, Yuen K-Y, Lau SK, Woo PC (2011a) Novel pan-genomic analysis approach in target selection for multiplex PCR identification and detection of / Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia cepacia complex species: a proof-of-concept study. J Clin Microbiol 49(3):814-21 CrossRef
  9. Ho C–C, Yuen K-Y, Lau SK, Woo PC (2011b) Rapid identification and validation of specific molecular targets for detection of Escherichia coli O104: H4 outbreak strain by use of high-throughput sequencing data from nine genomes. J Clin Microbiol 49(10):3714-716 CrossRef
  10. Ho C–C, Wu AK, Cindy W, Yuen K-Y, Lau SK, Woo PC (2012) Automated pangenomic analysis in target selection for PCR detection and identification of bacteria by use of ssGeneFinder Webserver and its application to / Salmonella enterica serovar Typhi. J Clin Microbiol 50(6):1905-911 CrossRef
  11. Huard RC, de Oliveira Lazzarini LC, Butler WR, van Soolingen D, Ho JL (2003) PCR-based method to differentiate the subspecies of the / Mycobacterium tuberculosis complex on the basis of genomic deletions. J Clin Microbiol 41(4):1637-650 CrossRef
  12. Jordan JA, Durso MB (2005) Real-time polymerase chain reaction for detecting bacterial DNA directly from blood of neonates being evaluated for sepsis. J Mol Diagn 7(5):575-81 CrossRef
  13. Kirschner P, Springer B, Vogel U, Meier A, Wrede A, Kiekenbeck M, Bange F, B?ttger E (1993) Genotypic identification of mycobacteria by nucleic acid sequence determination: report of a 2-year experience in a clinical laboratory. J Clin Microbiol 31(11):2882-889
  14. Kox L, Van Leeuwen J, Knijper S, Jansen H, Kolk A (1995) PCR assay based on DNA coding for 16S rRNA for detection and identification of mycobacteria in clinical samples. J Clin Microbiol 33(12):3225-233
  15. Liébana E, Aranaz A, Francis B, Cousins D (1996) Assessment of genetic markers for species differentiation within the / Mycobacterium tuberculosis complex. J Clin Microbiol 34(4):933-38
  16. Maurya A, Kant S, Nag V, Kushwaha R, Dhole T (2012) Detection of 123?bp fragment of insertion element IS6110 / Mycobacterium tuberculosis for diagnosis of extrapulmonary tuberculosis. Indian J Med Microbiol 30(2):182 CrossRef
  17. Muldrew KL, Simpson JF, Stratton CW, Tang Y-W (2005) Molecular diagnosis of necrotizing fasciitis by 16S rRNA gene sequencing and superantigen gene detection. J Mol Diagn 7(5):641-45 CrossRef
  18. Neonakis I, Gitti Z, Petinaki E, Maraki S, Spandidos D (2007) Evaluation of the GenoType MTBC assay for differentiating 120 clinical / Mycobacterium tuberculosis complex isolates. Eur J Clin Microbiol Infect Dis 26(2):151-52 CrossRef
  19. Niemann S, Harmsen D, Rüsch-Gerdes S, Richter E (2000) Differentiation of clinical / Mycobacterium tuberculosis complex isolates by gyrB DNA sequence polymorphism analysis. J Clin Microbiol 38(9):3231-234
  20. Niesters HG (2001) Quantitation of viral load using real-time amplification techniques. Methods 25(4):419-29 CrossRef
  21. Parsons LM, Brosch R, Cole ST, Somosk?vi á, Loder A, Bretzel G, Van Soolingen D, Hale YM, Salfinger M (2002) Rapid and simple approach for identification of / Mycobacterium tuberculosis complex isolates by PCR-based genomic deletion analysis. J Clin Microbiol 40(7):2339-345 CrossRef
  22. Pinsky BA, Banaei N (2008) Multiplex real-time PCR assay for rapid identification of / Mycobacterium tuberculosis complex members to the species level. J Clin Microbiol 46(7):2241-246 CrossRef
  23. Qian Q, Tang Y-W, Kolbert CP, Torgerson CA, Hughes JG, Vetter EA, Harmsen WS, Montgomery SO, Cockerill FR, Persing DH (2001) Direct identification of bacteria from positive blood cultures by amplification and sequencing of the 16S rRNA gene: evaluation of BACTEC 9240 instrument true-positive and false-positive results. J Clin Microbiol 39(10):3578-582 CrossRef
  24. Qin L, Zheng R, Fan C, Cai J, Liu Z, Wang J, Lu J, Jin R, Yang H, Cui Z (2010) Identification and evaluation of a new nucleic acid amplification test target for specific detection of / Mycobacterium tuberculosis. Clin Chem Lab Med 48(10):1501-505 CrossRef
  25. Richter E, Weizenegger M, Rüsch-Gerdes S, Niemann S (2003) Evaluation of genotype MTBC assay for differentiation of clinical / Mycobacterium tuberculosis complex isolates. J Clin Microbiol 41(6):2672-675 CrossRef
  26. Roth A, Fischer M, Hamid ME, Michalke S, Ludwig W, Mauch H (1998) Differentiation of phylogenetically related slowly growing mycobacteria based on 16S-23S rRNA gene internal transcribed spacer sequences. J Clin Microbiol 36(1):139-47
  27. Somoskovi A, Dormandy J, Rivenburg J, Pedrosa M, McBride M, Salfinger M (2008) Direct comparison of the genotype MTBC and genomic deletion assays in terms of ability to distinguish between members of the / Mycobacterium tuberculosis complex in clinical isolates and in clinical specimens. J Clin Microbiol 46(5):1854-857 CrossRef
  28. Sreevatsan S, Pan X, Stockbauer KE, Connell ND, Kreiswirth BN, Whittam TS, Musser JM (1997) Restricted structural gene polymorphism in the / Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci USA 94(18):9869-874 CrossRef
  29. Stránská R, Schuurman R, de Vos M, van Loon AM (2004) Routine use of a highly automated and internally controlled real-time PCR assay for the diagnosis of herpes simplex and varicella-zoster virus infections. J Clin Virol 30(1):39-4 CrossRef
  30. Talbot EA, Williams DL, Frothingham R (1997) PCR identification of Mycobacterium bovis BCG. J Clin Microbiol 35(3):566-69
  31. Tang Y-W, Meng S, Li H, Stratton CW, Koyamatsu T, Zheng X (2004) PCR enhances acid-fast bacillus stain-based rapid detection of / Mycobacterium tuberculosis. J Clin Microbiol 42(4):1849-850 CrossRef
  32. van Soolingen D, van der Zanden AG, de Haas PE, Noordhoek GT, Kiers A, Foudraine NA, Portaels F, Kolk AH, Kremer K, van Embden JD (1998) Diagnosis of / Mycobacterium microtiinfections among humans by using novel genetic markers. J Clin Microbiol 36(7):1840-845
  33. Viana-Niero C, De Haas P, Van Soolingen D, Leao S (2004) Analysis of genetic polymorphisms affecting the four phospholipase C (plc) genes in / Mycobacterium tuberculosis complex clinical isolates. Microbiology 150(4):967-78 CrossRef
  34. Yam W-C, Yuen K-Y, Kam S-Y, Yiu L-S, Chan K-S, Leung C–C, Tam C-M, Ho P-O, Yew W–W, Seto W-H (2006) Diagnostic application of genotypic identification of mycobacteria. J Med Microbiol 55(5):529-36 CrossRef
  35. Yang S, Rothman RE (2004) PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings. Lancet Infect Dis 4(6):337-48 CrossRef
  
• 作者单位：Jianing Zhao (1)
  Yiwei Wang (2)
  Dairong Li (3)
  Jiawen Liu (4)
  Xuemei Zhang (1)
  Yujuan He (1)
  Hong Wang (1)
  Ju Cao (3)
  Yibing Yin (1) (5)
  Wenchun Xu (1)
  
  1. Department of Laboratory Medicine, College of Laboratory Medicine, Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People’s Republic of China
  2. Department of Clinical Laboratory, Chongqing Pulmonary Hospital, Chongqing, People’s Republic of China
  3. Department of Pneumatology, The First Affiliated Hospital, Chongqing Medical University, Chongqing, People’s Republic of China
  4. Department of Clinical Laboratory, Beijing Geriatric Hospital, Beijing, People’s Republic of China
  5. Department of Clinical Laboratory, Children’s Hospital, Chongqing Medical University, Chongqing, People’s Republic of China
  
• ISSN：1573-0972

文摘

Rapid and accurate identification of mycobacteria to the species level is important to provide epidemiological information and to guide the appropriate treatment, especially identification of the Mycobacterium tuberculosis (MTB) which is the leading pathogen causing tuberculosis. The genetic marker named as Mycobacterium tuberculosis specific sequence 90 (mtss90) was screened by a bioinformatics software and verified by a series of experiments. To test its specificity, 266 strains of microorganisms and human cells were used for the mtss90 conventional PCR method. Moreover, the efficiency of mtss90 was evaluated by comparing 16S rDNA (Mycobacterium genus-specific), IS6110 (specific identification of MTB complex), mtp40 (MTB-specific) and PNB/TCH method (traditional bacteriology testing) in Mycobacterium strains. All MTB isolates were mtss90 positive. No amplification was observed from any other tested strains with M. microti as an exception. Compared with the traditional PNB/TCH method, the coincidence?rate was 99.1?% (233/235). All of the mtss90 positive strains were IS6110 and 16S rDNA positive, indicating a 100?% coincidence rate (216/216) between mtss90 and these two genetic markers. Additionally, mtss90 had a better specificity than mtp40 in the identification of MTB. Lastly, a real-time PCR diagnostic assay was developed for the rapid identification of MTB. In conclusion, mtss90 may be an efficient alternative marker for species-specific identification of MTB and could be used for the diagnosis of tuberculosis combined with other genetic markers.