Rapid detection of Mycobacterium tuberculosis by recombinase polymerase amplification

PLoS ONE

Volumn 9, Issue 8, 2014, Pages

  Boyle, David S ^a   McNerney, Ruth ^b   Teng Low, Hwee ^b   Leader, Brandon Troy ^a   Pérez Osorio, Ailyn C ^c   Meyer, Jessica C ^d   O'Sullivan, Denise M ^b   Brooks, David G ^d   Piepenburg, Olaf ^d   Forrest, Matthew S ^d  

^a Program for Appropriate Technology in Health   (United States)

^b LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

^c WASHINGTON STATE DEPARTMENT OF HEALTH   (United States)

^d TWISTDX LIMITED   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

CHEMISTRY; EVALUATION STUDY; GENETICS; HUMAN; MYCOBACTERIUM TUBERCULOSIS; POLYMERASE CHAIN REACTION; PROCEDURES; SENSITIVITY AND SPECIFICITY; TUBERCULOSIS;

DNA, BACTERIAL; HUMANS; MYCOBACTERIUM TUBERCULOSIS; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; TUBERCULOSIS;

EID: 84905913871     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0103091     Document Type: Article

References (44)

1. World Health Organization (2013) Global Tuberculosis Report.
2. World Health Organization (2009) Global Tuberculosis Report.
3. McNerney R, Daley P (2011) Towards a point-of-care test for active tuberculosis: obstacles and opportunities. Nat Rev Microbiol 9: 204-213.
4. WHO (2010) The global plan to stop TB 2011-2015: transforming the fight towards elimination of tuberculosis.
5. World Health Organisation (2010) Strategic and Technical Advisory Group for Tuberculosis Report of 10th Meeting. Geneva.
6. Lawn SD, Nicol MP (2011) Xpert(R) MTB/RIF assay: development, evaluation and implementation of a new rapid molecular diagnostic for tuberculosis and rifampicin resistance. Future Microbiol 6: 1067-1082.
7. Denkinger CM, Nicolau I, Ramsay A, Chedore P, Pai M (2013) Are peripheral microscopy centres ready for next generation molecular tuberculosis diagnostics? Eur Respir J 42: 544-547.
8. 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.
9. Niemz A, Boyle DS (2012) Nucleic acid testing for TB at the point-of-care in high burden countries. Exp Rev Mol Diagn 12: 687-701.
10. Pai NP, Pai M (2012) Point-of-care diagnostics for HIV and tuberculosis: landscape, pipeline, and unmet needs. Discov Med 13: 35-45.
11. Castan P, de Pablo A, Fernandez-Romero N, Rubio JM, Cobb BD, et al. (2014) Point-of-Care System for Detection of Mycobacterium tuberculosis and Rifampin Resistance in Sputum Samples. J Clin Microbiol 52: 502-507.
12. Fang R, Li X, Hu L, You Q, Li J, et al. (2009) Cross-priming amplification for rapid detection of Mycobacterium tuberculosis in sputum specimens. J Clin Microbiol 47: 845-847.
13. Mitarai S, Okumura M, Toyota E, Yoshiyama T, Aono A, et al. (2011) Evaluation of a simple loop-mediated isothermal amplification test kit for the diagnosis of tuberculosis. Int J Tuberc Lung Dis 15: 1211-1217.
14. Nikam C, Jagannath M, Narayanan MM, Ramanabhiraman V, Kazi M, et al. (2013) Rapid diagnosis of Mycobacterium tuberculosis with Truenat MTB: a near-care approach. PLoS One 8: e51121.
15. UNITAID (2012) Tuberculosis diagnostics technology & market landscape - semi-annual update.
16. Ao W, Aldous S, Woodruff E, Hicke B, Rea L, et al. (2012) Rapid detection of rpoB gene mutations conferring rifampin resistance in Mycobacterium tuberculosis. J Clin Microbiol 50: 2433-2440.
17. Boehme CC, Nabeta P, Henostroza G, Raqib R, Rahim Z, et al. (2007) Operational feasibility of using loop-mediated isothermal amplification for diagnosis of pulmonary tuberculosis in microscopy centers of developing countries. J Clin Microbiol 45: 1936-1940. (Pubitemid 46933929)
18. LaBarre P, Hawkins KR, Gerlach J, Wilmoth J, Beddoe A, et al. (2011) A simple, inexpensive device for nucleic acid amplification without electricity-toward instrument-free molecular diagnostics in low-resource settings. PLoS One 6: e19738.
19. Mori Y, Nagamine K, Tomita N, Notomi T (2001) Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochem Biophys Res Commun 289: 150-154. (Pubitemid 33108807)
20. Niemz A, Ferguson TM, Boyle DS (2011) Point-of-care nucleic acid testing for infectious diseases. Trends Biotechnol 29: 240-250.
21. Piepenburg O, Williams CH, Stemple DL, Armes NA (2006) DNA detection using recombination proteins. PLoS Biol 4: e204.
22. Boyle DS, Lehman DA, Lillis L, Peterson D, Singhal M, et al. (2013) Rapid detection of HIV-1 proviral DNA for early infant diagnosis using recombinase polymerase amplification. MBio 4.
23. Abd El Wahed A, El-Deeb A, El-Tholoth M, Abd El Wahed KH, Ahmed A, et al. (2013) A portable reverse transcription recombinase polymerase amplification assay for rapid detection of foot-and-mouth disease virus. PLoS One 8: e71642.
24. Abd El Wahed A, Patel P, Heidenreich D, Hufert FT, Weidmann M (2013) Reverse transcription recombinase polymerase amplification assay for the detection of middle East respiratory syndrome coronavirus. PLoS Curr 5.
25. van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, et al. (1993) Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol 31: 406-409. (Pubitemid 23028649)
26. Seki M, Honda I, Fujita I, Yano I, Yamamoto S, et al. (2009) Whole genome sequence analysis of Mycobacterium bovis bacillus Calmette-Guerin (BCG) Tokyo 172: a comparative study of BCG vaccine substrains. Vaccine 27: 1710-1716.
27. Perez-Osorio AC, Boyle DS, Ingham ZK, Ostash A, Gautom RK, et al. (2012) Rapid identification of mycobacteria and drug-resistant Mycobacterium tuberculosis by use of a single multiplex PCR and DNA sequencing. J Clin Microbiol 50: 326-336.
28. CLSI (2008) Laboratory detection and identification of mycobacteria: Approved guideline. CLSI document M48-A. Clinical and Laboratory Standards Institute, Wayne, PA.
29. Eisenach KD, Cave MD, Bates JH, Crawford JT (1990) Polymerase chain reaction amplification of a repetitive DNA sequence specific for Mycobacterium tuberculosis. J Infect Dis 161: 977-981. (Pubitemid 20148335)
30. Thierry D, Brisson-Noel A, Vincent-Levy-Frebault V, Nguyen S, Guesdon JL, et al. (1990) Characterization of a Mycobacterium tuberculosis insertion sequence, IS6110, and its application in diagnosis. J Clin Microbiol 28: 2668-2673.
31. Flores LL, Pai M, Colford JM Jr, Riley LW (2005) In-house nucleic acid amplification tests for the detection of Mycobacterium tuberculosis in sputum specimens: meta-analysis and meta-regression. BMC Microbiol 5: 55.
32. Savelkoul PH, Catsburg A, Mulder S, Oostendorp L, Schirm J, et al.(2006) Detection of Mycobacterium tuberculosis complex with Real Time PCR: comparison of different primer-probe sets based on the IS6110 element. J Microbiol Methods 66: 177-180. (Pubitemid 43767522)
33. Alonso H, Samper S, Martin C, Otal I (2013) Mapping IS6110 in high-copy number Mycobacterium tuberculosis strains shows specific insertion points in the Beijing genotype. BMC Genomics 14: 422.
34. Huyen MN, Tiemersma EW, Kremer K, de Hass P, Lan NT, et al. (2013) Characterisation of Mycobacterium tuberculosis isolates lacking IS6110 in Viet Nam. Int J Tuberc Lung Dis 17: 1479-1485.
35. Fomukong NG, Tang TH, al-Maamary S, Ibrahim WA, Ramayah S, et al. (1994) Insertion sequence typing of Mycobacterium tuberculosis: characterization of a widespread subtype with a single copy of IS6110. Tuber Lung Dis 75: 435-440.
36. Behr MA, Warren SA, Salamon H, Hopewell PC, Ponce de LA, et al. (1999) Transmission of Mycobacterium tuberculosis from patients smear-negative for acid-fast bacilli. Lancet 353: 444-449. (Pubitemid 29067335)
37. van Soolingen D., Hermans PW, de Haas PE, van Embden JD (1992) Insertion element IS1081-associated restriction fragment length polymorphisms in Mycobacterium tuberculosis complex species: a reliable tool for recognizing Mycobacterium bovis BCG. J Clin Microbiol 30: 1772-1777.
38. Collins DM, Stephens DM (1991) Identification of an insertion sequence, IS1081, in Mycobacterium bovis. FEMS Microbiol Lett 67: 11-15.
39. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, et al. (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537-544. (Pubitemid 28319235)
40. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
41. Van Deun A., Salim AH, Cooreman E, Daru P, Das AP, et al. (2004) Scanty AFB smears: what's in a name? Int J Tuberc Lung Dis 8: 816-823. (Pubitemid 38937597)
42. Miller DN, Bryant JE, Madsen EL, Ghiorse WC (1999) Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol 65: 4715-4724.
43. Drain PK, Hyle EP, Noubary F, Freedberg KA, Wilson D, et al. (2013) Diagnostic point-of-care tests in resource-limited settings. Lancet Infect Dis.
44. Denkinger CM, Pai M (2011) Point-of-care tuberculosis diagnosis: are we there yet? Lancet Infect Dis.