Simple multiplex PCR assay for identification of Beijing family Mycobacterium tuberculosis isolates with a lineage-specific mutation in Rv0679c

Journal of Clinical Microbiology

Volumn 51, Issue 7, 2013, Pages 2025-2032

  Nakajima, Chie ^a   Tamaru, Aki ^b   Rahim, Zeaur ^c   Poudel, Ajay ^a   Maharjan, Bhagwan ^d   Aye, Khin Saw ^e   Ling, Hong ^f   Hattori, Toshio ^g   Iwamoto, Tomotada ^h   Fukushima, Yukari ^a   Suzuki, Haruka ^a   Suzuki, Yasuhiko ^a,i   Matsuba, Takashi ^j  

^a HOKKAIDO UNIVERSITY   (Japan)

^b OSAKA PREFECTURAL INSTITUTE OF PUBLIC HEALTH   (Japan)

^c INTERNATIONAL CENTRE FOR DIARRHOEAL DISEASE RESEARCH   (Bangladesh)

^d German Nepal Tuberculosis Project (GENETUP)   (Nepal)

^e Ministry of Health   (Myanmar)

^f HARBIN MEDICAL UNIVERSITY   (China)

^g TOHOKU UNIVERSITY   (Japan)

^h KOBE INSTITUTE OF HEALTH   (Japan)

ⁱ JAPAN INTERNATIONAL COOPERATION AGENCY   (Japan)

^j TOTTORI UNIVERSITY   (Japan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; MUTANT PROTEIN; OUTER MEMBRANE PROTEIN;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CHINA; CLADISTICS; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; EPIDEMIOLOGICAL MONITORING; GENE MUTATION; GENE SEQUENCE; GENETIC LINE; GENOTYPE; MOLECULAR CLONING; MULTIPLEX POLYMERASE CHAIN REACTION; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PREVALENCE; PRIORITY JOURNAL; RV0679C GENE; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TUBERCULOSIS CONTROL; CLASSIFICATION; EVALUATION STUDY; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR DIAGNOSIS; MOLECULAR TYPING; PROCEDURES; TUBERCULOSIS;

MYCOBACTERIUM TUBERCULOSIS;

BACTERIAL OUTER MEMBRANE PROTEINS; GENOTYPE; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; MOLECULAR TYPING; MULTIPLEX POLYMERASE CHAIN REACTION; MUTANT PROTEINS; MYCOBACTERIUM TUBERCULOSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; TUBERCULOSIS;

EID: 84879441608     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.03404-12     Document Type: Article

References (39)

1. van Soolingen D, Qian L, de Haas PE, Douglas JT, Traore H, Portaels F, Qing HZ, Enkhsaikan D, Nymadawa P, van Embden JD. 1995. Predominance of a single genotype of Mycobacterium tuberculosis in countries of east Asia. J. Clin. Microbiol. 33:3234-3238.
2. Bifani PJ, Mathema B, Kurepina NE, Kreiswirth BN. 2002. Global dissemination of the Mycobacterium tuberculosis W-Beijing family strains. Trends Microbiol. 10:45-52.
3. Brudey K, Driscoll JR, Rigouts L, Prodinger WM, Gori A, Al-Hajoj SA, Allix C, Aristimuño L, Arora J, Baumanis V, Binder L, Cafrune P, Cataldi A, Cheong S, Diel R, Ellermeier C, Evans JT, Fauville-Dufaux M, Ferdinand S, Garcia de Viedma D, Garzelli C, Gazzola L, Gomes HM, Guttierez MC, Hawkey PM, van Helden PD, Kadival GV, Kreiswirth BN, Kremer K, Kubin M, Kulkarni SP, Liens B, Lillebaek T, Ho ML, Martin C, Martin C, Mokrousov I, Narvskaïa O, Ngeow YF, Naumann L, Niemann S, Parwati I, Rahim Z, Rasolofo-Razanamparany V, Rasolonavalona T, Rossetti ML, Rüsch-Gerdes S, Sajduda A, Samper S, Shemyakin IG, et al. 2006. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol. 6:23. doi:10.1186/1471-2180-6-23.
4. Hanekom M, Gey van Pittius NC, McEvoy C, Victor TC, Van Helden PD, Warren RM. 2011. Mycobacterium tuberculosis Beijing genotype: a template for success. Tuberculosis (Edinb.) 91:510-523.
5. Colditz GA, Brewer TF, Berkey CS, Wilson ME, Burdick E, Fineberg HV, Mosteller F. 1994. Efficacy of BCG vaccine in the prevention of tuberculosis. Meta-analysis of the published literature. JAMA 271:698-702.
6. de Steenwinkel JE, ten Kate MT, de Knegt GJ, Kremer K, Aarnoutse RE, Boeree MJ, Verbrugh HA, van Soolingen D, Bakker-Woudenberg IAJM. 2012. Drug susceptibility of Mycobacterium tuberculosis Beijing genotype and association with MDR TB. Emerg. Infect. Dis. 18:660-663.
7. Parwati I, van Crevel R, van Soolingen D. 2010. Possible underlying mechanisms for successful emergence of the Mycobacterium tuberculosis Beijing genotype strains. Lancet Infect. Dis. 10:103-111.
8. López B, Aguilar D, Orozco H, Burger M, Espitia C, Ritacco V, Barrera L, Kremer K, Hernandez-Pando R, Huygen K, van Soolingen D. 2003. A marked difference in pathogenesis and immune response induced by different Mycobacterium tuberculosis genotypes. Clin. Exp. Immunol. 133: 30-37.
9. Reed MB, Domenech P, Manca C, Su H, Barczak AK, Kreiswirth BN, Kaplan G, Barry CE, III. 2004. A glycolipid of hypervirulent tuberculosis strains that inhibits the innate immune response. Nature 431:84-87.
10. Chuang PC, Chen HY, Jou R. 2010. Single-nucleotide polymorphism in the fadD28 gene as a genetic marker for east Asia lineage Mycobacterium tuberculosis. J. Clin. Microbiol. 48:4245-4247.
11. Mokrousov I, Ly HM, Otten T, Lan NN, Vyshnevskyi B, Hoffner S, Narvskaya O. 2005. Origin and primary dispersal of the Mycobacterium tuberculosis Beijing genotype: clues from human phylogeography. Genome Res. 15:1357-1364.
12. Wada T, Iwamoto T, Maeda S. 2009. Genetic diversity of the Mycobacterium tuberculosis Beijing family in east Asia revealed through refined population structure analysis. FEMS Microbiol. Lett. 291:35-43.
13. Wang J, Liu Y, Zhang CL, Ji BY, Zhang LZ, Shao YZ, Jiang SL, Suzuki Y, Nakajima C, Fan CL, Ma YP, Tian GW, Hattori T, Ling H. 2011. Genotypes and characteristics of clustering and drug susceptibility of Mycobacterium tuberculosis isolates collected in Heilongjiang Province, China. J. Clin. Microbiol. 49:1354-1362.
14. Cowley D, Govender D, February B, Wolfe M, Steyn L, Evans J, Wilkinson RJ, Nicol MP. 2008. Recent and rapid emergence of W-Beijing strains of Mycobacterium tuberculosis in Cape Town, South Africa. Clin. Infect. Dis. 47:1252-1259.
15. Plikaytis BB, Marden JL, Crawford JT, Woodley CL, Butler WR, Shinnick TM. 1994. Multiplex PCR assay specific for the multidrug-resistant strainWof Mycobacterium tuberculosis. J. Clin. Microbiol. 32:1542-1546.
16. Iwamoto T, Yoshida S, Suzuki K, Wada T. 2008. Population structure analysis of the Mycobacterium tuberculosis Beijing family indicates an association between certain sublineages and multidrug resistance. Antimicrob. Agents Chemother. 52:3805-3809.
17. Kato-Maeda M, Shanley CA, Ackart D, Jarlsberg LG, Shang S, Obregon-Henao A, Harton M, Basaraba RJ, Henao-Tamayo M, Barrozo JC, Rose J, Kawamura LM, Coscolla M, Fofanov VY, Koshinsky H, Gagneux S, Hopewell PC, Ordway DJ, Orme IM. 2012. Beijing sublineages of Mycobacterium tuberculosis differ in pathogenicity in the guinea pig. Clin. Vaccine Immunol. 19:1227-1237.
18. Beggs ML, Eisenach KD, Cave MD. 2000. Mapping of IS6110 insertion sites in two epidemic strains of Mycobacterium tuberculosis. J. Clin. Microbiol. 38:2923-2928.
19. Kremer K, Glynn JR, Lillebaek T, Niemann S, Kurepina NE, Kreiswirth BN, Bifani PJ, van Soolingen D. 2004. Definition of the Beijing/W lineage of Mycobacterium tuberculosis on the basis of genetic markers. J. Clin. Microbiol. 42:4040-4049.
20. Hillemann D, Warren R, Kubica T, Rüsch-Gerdes S, Niemann S. 2006. Rapid detection of Mycobacterium tuberculosis Beijing genotype strains by real-time PCR. J. Clin. Microbiol. 44:302-306.
21. Sun JR, Lee SY, Dou HY, Lu JJ. 2009. Using a multiplex polymerase chain reaction for the identification of Beijing strains of Mycobacterium tuberculosis. Eur. J. Clin. Microbiol. Infect. Dis. 28:105-107.
22. Warren RM, Victor TC, Streicher EM, Richardson M, Beyers N, Gey van Pittius NC, van Helden PD. 2004. Patients with active tuberculosis often have different strains in the same sputum specimen. Am. J. Respir. Crit. Care Med. 169:610-614.
23. Tsolaki AG, Gagneux S, Pym AS, Goguet de la Salmoniere YOL, Kreiswirth BN, Van Soolingen D, Small PM. 2005. Genomic deletions classify the Beijing/W strains as a distinct genetic lineage of Mycobacterium tuberculosis. J. Clin. Microbiol. 43:3185-3191.
24. Stucki D, Malla B, Hostettler S, Huna T, Feldmann J, Yeboah-Manu D, Borrell S, Fenner L, Comas I, Coscollà M, Gagneux S. 2012. Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages. PLoS One 7:e41253. doi:10.1371/journal.pone.0041253.
25. Huard RC, Fabre M, de Haas P, Lazzarini LC, van Soolingen D, Cousins D, Ho JL. 2006. Novel genetic polymorphisms that further delineate the phylogeny of the Mycobacterium tuberculosis complex. J. Bacteriol. 188:4271-4287.
26. Filliol I, Motiwala AS, Cavatore M, Qi W, Hazbón MH, Bobadilla del Valle M, Fyfe J, García-García L, Rastogi N, Sola C, Zozio T, Guerrero MI, León CI, Crabtree J, Angiuoli S, Eisenach KD, Durmaz R, Joloba ML, Rendón A, Sifuentes-Osornio J, Ponce de León A, Cave MD, Fleischmann R, Whittam TS, Alland D. 2006. Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set. J. Bacteriol. 188:759-772.
27. Cifuentes DP, Ocampo M, Curtidor H, Vanegas M, Forero M, Patarroyo ME, Patarroyo MA. 2010. Mycobacterium tuberculosis Rv0679c protein sequences involved in host-cell infection: potential TB vaccine candidate antigen. BMC Microbiol. 10:109. doi:10.1186/1471-2180-10-109.
28. Matsuba T, Suzuki Y, Tanaka Y. 2007. Association of the Rv0679c protein with lipids and carbohydrates in Mycobacterium tuberculosis/Mycobacterium bovis BCG. Arch. Microbiol. 187:297-311.
29. Poudel A, Nakajima C, Fukushima Y, Suzuki H, Pandey BD, Maharjan B, Suzuki Y. 2012. Molecular characterization of multidrug-resistant Mycobacterium tuberculosis isolated in Nepal. Antimicrob. Agents Chemother. 56:2831-2836.
30. Rahim Z, Nakajima C, Raqib R, Zaman K, Endtz HP, van der Zanden AG, Suzuki Y. 2012. Molecular mechanism of rifampicin and isoniazid resistance in Mycobacterium tuberculosis from Bangladesh. Tuberculosis (Edinb.) 92:529-534.
31. Tamaru A, Nakajima C, Wada T, Wang Y, Inoue M, Kawahara R, Maekura R, Ozeki Y, Ogura H, Kobayashi K, Suzuki Y, Matsumoto S. 2012. Dominant incidence of multidrug and extensively drug-resistant specific Mycobacterium tuberculosis clones in Osaka Prefecture, Japan. PLoS One 7:e42505. doi:10.1371/journal.pone. 0042505.
32. Reddy TB, Riley R, Wymore F, Montgomery P, DeCaprio D, Engels R, Gellesch M, Hubble J, Jen D, Jin H, Koehrsen M, Larson L, Mao M, Nitzberg M, Sisk P, Stolte C, Weiner B, White J, Zachariah ZK, Sherlock G, Galagan JE, Ball CA, Schoolnik GK. 2009. TB database: an integrated platform for tuberculosis research. Nucleic Acids Res. 37(Database issue):D499-D508. doi:10.1093/nar/ gkn652.
33. Kamerbeek J, Schouls L, Kolk L, van Agterveld M, van Soolingen D, Kuijper S, Bunschoten A, Molhuizen H, Shaw R, Goyal M, van Embden J. 1997. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J. Clin. Microbiol. 35: 907-914.
34. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE, III, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, Quail MA, Rajandream MA, Rogers J, Rutter S, Seeger K, Skelton J, Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537-544.
35. Fenner L, Malla B, Ninet B, Dubuis O, Stucki D, Borrell S, Huna T, Bodmer T, Egger M, Gagneux S. 2011. "Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis. PLoS One 6:e24737. doi:10.1371/journal.pone.0024737.
36. 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. U. S. A. 94:9869-9874.
37. Lazzarini LC, Rosenfeld J, Huard RC, Hill V, Lapa e Silva JR, DeSalle R, Rastogi N, Ho JL. 2012. Mycobacterium tuberculosis spoligotypes that may derive from mixed strain infections are revealed by a novel computational approach. Infect. Genet. Evol. 12:798-806.
38. Supply P, Mazars E, Lesjean S, Vincent V, Gicquel B, Locht C. 2000. Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome. Mol. Microbiol. 36:762-771.
39. Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, Homolka S, Roach JC, Kremer K, Petrov DA, Feldman MW, Gagneux S. 2008. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol. 6:e311. doi:10.1371/journal.pbio.0060311.