"Spoligoriftyping," a dual-priming-oligonucleotide-based direct-hybridization assay for tuberculosis control with a multianalyte microbead-based hybridization system

Journal of Clinical Microbiology

Volumn 50, Issue 10, 2012, Pages 3172-3179

  Gomgnimbou, Michel Kiréopori ^a,b   Abadia, Edgar ^c   Zhang, Jian ^a   Refrégier, Guislaine ^a   Panaiotov, Stefan ^d   Bachiyska, Elizabeta ^d   Sola, Christophe ^a  

^a CNRS   (France)

^b CENTRE MURAZ   (Burkina Faso)

^c Instituto Venezolano de Investigaciones Cientificas Centro de Microbiologia y Biologia Celular   (Venezuela)

^d NATIONAL CENTER OF INFECTIOUS AND PARASITIC DISEASES   (Bulgaria)

Author keywords

[No Author keywords available]

Indexed keywords

KATG PROTEIN; OLIGONUCLEOTIDE; PALINDROMIC DNA; REPETITIVE DNA; RIFAMPICIN; RNA POLYMERASE BETA SUBUNIT;

ANALYZER; ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL GENE; BULGARIA; DNA EXTRACTION; EMBB GENE; GENE AMPLIFICATION; GENE LOCUS; GENE MUTATION; GENE SEQUENCE; GENOTYPE; GERMANY; HIGH THROUGHPUT SCREENING; HUMAN; INHA GENE; KATG GENE; MOLECULAR TYPING; MULTIANALYTE MICROBEAD BASED HYBRIDIZATION SYSTEM; MULTIDRUG RESISTANT TUBERCULOSIS; MUTATIONAL ANALYSIS; MYCOBACTERIUM TUBERCULOSIS; NIGERIA; NONHUMAN; NUCLEIC ACID HYBRIDIZATION; PHENOTYPE; PNCA GENE; PRIORITY JOURNAL; PROCESS DEVELOPMENT; RIFOLIGOTYPING ASSAY; RPOB GENE; RPSL GENE; RRS GENE; SENSITIVITY AND SPECIFICITY; SPOLIGORIFTYPING ASSAY; SPOLIGOTYPING ASSAY; TUBERCULOSIS CONTROL;

ANTITUBERCULAR AGENTS; BULGARIA; DNA-DIRECTED RNA POLYMERASES; DRUG RESISTANCE, BACTERIAL; GENOTYPE; GERMANY; HUMANS; MICROBIAL SENSITIVITY TESTS; MICROSPHERES; MOLECULAR TYPING; MYCOBACTERIUM TUBERCULOSIS; NIGERIA; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDES; RIFAMPIN; TUBERCULOSIS, MULTIDRUG-RESISTANT;

MYCOBACTERIUM TUBERCULOSIS;

EID: 84866463018     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.00976-12     Document Type: Article

References (43)

1. Abadia E, et al. 2011. The use of microbead-based spoligotyping for Mycobacterium tuberculosis complex to evaluate the quality of the conventional membrane-based method: providing guidelines for quality control issues when working on membranes. BMC Infect. Dis. 11:110.
2. Arnold C, et al. 2005. Single-nucleotide polymorphism-based differentiation and drug resistance detection in Mycobacterium tuberculosis from isolates or directly from sputum. Clin. Microbiol. Infect. 11:122-130. (Pubitemid 40253816)
3. Bergval IL, et al. 2008. Development of multiplex assay for rapid characterization of Mycobacterium tuberculosis. J. Clin. Microbiol. 46:689-699. (Pubitemid 351231319)
4. Bergval I, et al. Combined species identification genotyping and drug resistance detection of Mycobacterium tuberculosis cultures by MLPA on a bead-based array. PLoS One, in press.
5. Boehme CC, et al. 2010. Rapid molecular detection of tuberculosis and rifampin resistance. N. Engl. J. Med. 363:1005-1015.
6. Brudey K, 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.
7. CDC. 2011. Report of expert consultations on rapid molecular testing to detect drug-resistant tuberculosis in the United States. CDC, Atlanta, GA. http://www.cdc.gov/tb/topic/laboratory/rapidmoleculartesting/default.htm.
8. Choi GE, et al. 2010. High-resolution melting curve analysis for rapid detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis clinical isolates. J. Clin. Microbiol. 48:3893-3898.
9. Chun JY, et al. 2007. Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene. Nucleic Acids Res. 35:e40. doi:10.1093/nar/gkm051.
10. Corpet F. 1988. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16:10881-10890.
11. Cowan LS, Diem L, Brake MC, Crawford JT. 2004. Transfer of a Mycobacterium tuberculosis genotyping method, spoligotyping, from a reverse line-blot hybridization, membrane-based assay to the Luminex multianalyte profiling system. J. Clin. Microbiol. 42:474-477. (Pubitemid 38082775)
12. Deshpande A, et al. 2009. A rapid multiplex assay for nucleic acid-based diagnostics. J. Microbiol. Methods 80:155-163.
13. Dubois Cauwelaert N, Ramarokoto H, Ravololonandriana P, Richard V, Rasolofo V. 2011. DNA extracted from stained sputum smears can be used in the MTBDRplus assay. J. Clin. Microbiol. 49:3600-3603.
14. Dunbar SA. 2006. Applications of Luminex® xMAP technology for rapid, high-throughput multiplexed nucleic acid detection. Clin. Chim. Acta 363:71-82. (Pubitemid 41745226)
15. Evans CA. 2011. GeneXpert - a game-changer for tuberculosis control? PLoS Med. 8:e1001064. doi:10.1371/journal.pmed.1001064.
16. Hardenbol P, et al. 2003. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat. Biotechnol. 21:673-678. (Pubitemid 36638095)
17. Heep M, et al. 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. (Pubitemid 32059577)
18. Helb D, et al. 2010. Rapid detection of Mycobacterium tuberculosis and rifampin resistance by use of on-demand, near-patient technology. J. Clin. Microbiol. 48:229-237.
19. Hernandez-Neuta I, et al. 2010. Rifampin-isoniazid oligonucleotide typing: an alternative format for rapid detection of multidrug-resistant Mycobacterium tuberculosis. J. Clin. Microbiol. 48:4386-4391.
20. Herrera L, Jimenez S, Valverde A, Garcia-Aranda MA, Saez-Nieto JA. 2003. Molecular analysis of rifampicin-resistant Mycobacterium tuberculosis isolated in Spain (1996-2001). Description of new mutations in the rpoB gene and review of the literature. Int. J. Antimicrob. Agents 21:403-408. (Pubitemid 36506631)
21. Hillemann D, Rusch-Gerdes S, Richter E. 2007. Evaluation of the Geno-Type MTBDRplus assay for rifampin and isoniazid susceptibility testing of Mycobacterium tuberculosis strains and clinical specimens. J. Clin. Microbiol. 45:2635-2640. (Pubitemid 47295497)
22. Kamerbeek J, et al. 1997. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J. Clin. Microbiol. 35:907-914. (Pubitemid 27146535)
23. Lawson L, et al. 2012. A molecular epidemiological and genetic diversity study of tuberculosis in Ibadan, Nnewi and Abuja, Nigeria. PLoS One 7:e38409. doi:10.1371/journal.pone.0038409.
24. Lin A, et al. 2011. Rapid O serogroup identification of the ten most clinically relevant STECs by Luminex® microbead-based suspension array. J. Microbiol. Methods 87:105-110.
25. Mlambo CK, et al. 2008. Genotypic diversity of extensively drug-resistant tuberculosis (XDR-TB) in South Africa. Int. J. Tuberc. Lung Dis. 12:99-104.
26. Morcillo N, et al. 2002. A low cost, home-made, reverse-line blot hybridisation assay for rapid detection of rifampicin resistance in Mycobacterium tuberculosis. Int. J. Tuberc. Lung Dis. 6:959-965. (Pubitemid 35408181)
27. Mori T. 2007. MDR-TB-its characteristics and control in Asia-Pacific rim symposium in USJCMSP 10th international conference on emerging infectious diseases in the Pacific rim. Tuberculosis (Edinb.) 87(Suppl 1): S5-S9. (Pubitemid 47223834)
28. Nikolayevskyy V, et al. 2009. Performance of the Genotype MTBDRPlus assay in the diagnosis of tuberculosis and drug resistance in Samara, Russian Federation. BMC Clin. Pathol. 9:2.
29. Novais RC, Borsuk S, Dellagostin OA, Thorstenson YR. 2008. Molecular inversion probes for sensitive detection of Mycobacterium tuberculosis. J. Microbiol. Methods 72:60-66. (Pubitemid 350309684)
30. Schouten J, et al. 2002. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res. 30:e57. doi:10.1093/nar/gnf056.
31. Shen Z, et al. 2010. MPprimer: a program for reliable multiplex PCR primer design. BMC Bioinformatics 11:143.
32. Song Y, et al. 2010. A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A. J. Antimicrob. Chemother. 65:1631-1641.
33. Supply P, et al. 2006. Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J. Clin. Microbiol. 44:4498-4510. (Pubitemid 44937085)
34. Tafaj S, et al. 2009. First insight into genetic diversity of the Mycobacterium tuberculosis complex in Albania obtained by multilocus variablenumber tandem-repeat analysis and spoligotyping reveals the presence of Beijing multidrug-resistant isolates. J. Clin. Microbiol. 47:1581-1584.
35. Telenti A, et al. 1993. Detection of rifampicin-resistance mutations in Mycobacterium tuberculosis. Lancet 341:647-650. (Pubitemid 23083244)
36. Van Der Zanden AG, Te Koppele-Vije EM, Vijaya Bhanu N, Van Soolingen D, Schouls LM. 2003. Use of DNA extracts from Ziehl- Neelsen-stained slides for molecular detection of rifampin resistance and spoligotyping of Mycobacterium tuberculosis. J. Clin. Microbiol. 41:1101-1108. (Pubitemid 36307113)
37. van Soolingen D, Hermans PWM, de Haas PEW, Sool DR, Embden JDA. 1991. The occurrence and stability of insertion sequences in Mycobacterium tuberculosis complex strains: evaluation of an insertion sequence-dependent DNA polymorphism as a tool in the epidemiology of tuberculosis. J. Clin. Microbiol. 29:2578-2586.
38. Wada T, et al. 2004. Dual-probe assay for rapid detection of drugresistant Mycobacterium tuberculosis by real-time PCR. J. Clin. Microbiol. 42:5277-5285. (Pubitemid 39506241)
39. Wallengren K, et al. 2011. Drug-resistant tuberculosis, KwaZulu-Natal, South Africa, 2001-2007. Emerg. Infect. Dis. 17:1913-1916.
40. Weile J, Knabbe C. 2009. Current applications and future trends of molecular diagnostics in clinical bacteriology. Anal. Bioanal. Chem. 394: 731-742.
41. Wright A, et al. 2009. Epidemiology of antituberculosis drug resistance 2002-07: an updated analysis of the Global Project on Anti-Tuberculosis Drug Resistance Surveillance. Lancet 373:1861-1873.
42. Yao C, et al. 2010. Detection of rpoB, katG and inhA gene mutations in Mycobacterium tuberculosis clinical isolates from Chongqing as determined by microarray. Clin. Microbiol. Infect. 16:1639-1643.
43. Zhang J, et al. 2010. Mycobacterium tuberculosis complex CRISPR genotyping: improving efficiency, throughput and discriminative power of 'spoligotyping' with new spacers and a microbead-based hybridization assay. J. Med. Microbiol. 59:285-294.