Hybridization-based detection of Helicobacter pylori at human body temperature using advanced Locked Nucleic Acid (LNA) probes

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Fontenete, Sílvia ^a,b   Guimarães, Nuno ^a,b   Leite, Marina ^a   Figueiredo, Céu ^a,c   Wengel, Jesper ^b   Azevedo, Nuno Filipe ^a  

^a UNIVERSITY OF PORTO   (Portugal)

^b UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^c University of Porto   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

2' O METHYL RNA; LOCKED NUCLEIC ACID; PHOSPHATE; PHOSPHOROTHIOIC ACID; RNA; UNCLASSIFIED DRUG; NUCLEIC ACID PROBE;

ACCURACY; ANIMAL CELL; ARTICLE; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM DETECTION; BODY TEMPERATURE; CONTROLLED STUDY; FLUORESCENCE IN SITU HYBRIDIZATION; FLUORESCENCE IN VIVO HYBRIDIZATION; HELICOBACTER PYLORI; HUMAN; HUMAN TISSUE; HYBRIDIZATION; IN VIVO STUDY; MELTING POINT; MOLECULAR IMAGING; NONHUMAN; NUCLEIC ACID PROBE; PROTEIN ANALYSIS; SENSITIVITY AND SPECIFICITY; STOMACH BIOPSY; FLOW CYTOMETRY; FLUORESCENCE MICROSCOPY; GENETICS; HELICOBACTER INFECTIONS; MICROBIOLOGY; NUCLEIC ACID HYBRIDIZATION; PROCEDURES; STOMACH;

FLOW CYTOMETRY; HELICOBACTER INFECTIONS; HELICOBACTER PYLORI; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MICROSCOPY, FLUORESCENCE; NUCLEIC ACID HYBRIDIZATION; NUCLEIC ACID PROBES; STOMACH;

EID: 84896723935     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0081230     Document Type: Article

References (57)

1. Woese CR (1987) Bacterial evolution. Microbiol Rev 51: 221-271. PubMed: 2439888.
2. Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA et al. (2006) Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci U S A 103: 732-737. doi:10.1073/pnas.0506655103. PubMed: 16407106. (Pubitemid 43153094)
3. Thèves C, Senescau A, Vanin S, Keyser C, Ricaut FX et al. (2011) Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects. PLOS ONE 6: e21733. doi:10.1371/journal.pone.0021733. PubMed: 21765907.
4. Robertson KL, Vora GJ (2012) Locked nucleic acid flow cytometry-fluorescence in situ hybridization (LNA flow-FISH): a method for bacterial small RNA detection. J Vis Exp: e3655. PubMed: 22258228.
5. Malic S, Hill KE, Hayes A, Percival SL, Thomas DW et al. (2009) Detection and identification of specific bacteria in wound biofilms using peptide nucleic acid fluorescent in situ hybridization (PNA FISH). Microbiology 155: 2603-2611. doi:10.1099/mic.0.028712-0. PubMed: 19477903.
6. McNulty CA, Lehours P, Mégraud F (2011) Diagnosis of Helicobacter pylori Infection. Helicobacter 16 Suppl 1: 10-18. doi:10.1111/j.1523-5378.2011. 00875.x. PubMed: 21896080.
7. Miller SJ, Joshi BP, Feng Y, Gaustad A, Fearon ER et al. (2011) In vivo fluorescence-based endoscopic detection of colon dysplasia in the mouse using a novel peptide probe. PLOS ONE 6: e17384. doi:10.1371/journal.pone.0017384. PubMed: 21408169.
8. Ji R, Li YQ, Gu XM, Yu T, Zuo XL et al. (2010) Confocal laser endomicroscopy for diagnosis of Helicobacter pylori infection: a prospective study. J Gastroenterol Hepatol 25: 700-705. doi:10.1111/j.1440-1746.2009.06197. x. PubMed: 20492325.
9. Polglase AL, McLaren WJ, Skinner SA, Kiesslich R, Neurath MF et al. (2005) A fluorescence confocal endomicroscope for in vivo microscopy of the upper- and the lower-GI tract. Gastrointest Endosc 62: 686-695. doi:10.1016/j.gie.2005.05.021. PubMed: 16246680. (Pubitemid 41502992)
10. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59: 143-169. PubMed: 7535888.
11. Silahtaroglu AN, Tommerup N, Vissing H (2003) FISHing with locked nucleic acids (LNA): evaluation of different LNA/DNA mixmers. Mol Cell Probes 17: 165-169. doi:10.1016/S0890-8508(03)00048-3. PubMed: 12944118. (Pubitemid 36999813)
12. Kubota K, Ohashi A, Imachi H, Harada H (2006) Improved in situ hybridization efficiency with locked-nucleic-acid-incorporated DNA probes. Appl Environ Microbiol 72: 5311-5317. doi:10.1128/AEM.03039-05. PubMed: 16885281.
13. Silahtaroglu A, Pfundheller H, Koshkin A, Tommerup N, Kauppinen S (2004) LNA-modified oligonucleotides are highly efficient as FISH probes. Cytogenet Genome Res 107: 32-37. doi:10.1159/000079569. PubMed: 15305054. (Pubitemid 39140343)
14. Robertson KL, Thach DC (2009) LNA flow-FISH: a flow cytometry- fluorescence in situ hybridization method to detect messenger RNA using locked nucleic acid probes. Anal Biochem 390: 109-114. doi:10.1016/j.ab.2009.04.026. PubMed: 19393610.
15. Maruo R, Yamada H, Watanabe M, Hidaka Y, Iwatani Y et al. (2011) mRNA quantification after fluorescence activated cell sorting using locked nucleic acid probes. Mol Biotechnol 49: 42-47. doi:10.1007/s12033-011-9375-9. PubMed: 21246309.
16. Veedu RN, Wengel J (2009) Locked nucleic acid as a novel class of therapeutic agents. RNA Biol 6: 321-323. doi:10.4161/rna.6.3.8807. PubMed: 19458498.
17. Singh Skkaa, Wengel J, Nielsen P (1998) LNA (locked nucleic acids): synthesis and high-affinity nucleic acid recognition. Chem Commun: 455-456.
18. Koshkin AA, Singh SK, Nielsen P, Rajwanshi VK, Kumar R, et al. (1998) LNA (Locked Nucleic Acids): Synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron: 3607-3630. (Pubitemid 28108183)
19. Søe MJ, Møller T, Dufva M, Holmstrøm K (2011) A sensitive alternative for microRNA in situ hybridizations using probes of 2′-O-methyl RNA + LNA. J Histochem Cytochem 59: 661-672. doi:10.1369/0022155411409411. PubMed: 21525189.
20. Molenaar C, Marras SA, Slats JC, Truffert JC, Lemaître M et al. (2001) Linear 2′ O-Methyl RNA probes for the visualization of RNA in living cells. Nucleic Acids Res 29: E89-E89. doi:10.1093/nar/29.17.e89. PubMed: 11522845.
21. Aronica E, Fluiter K, Iyer A, Zurolo E, Vreijling J et al. (2010) Expression pattern of miR-146a, an inflammation-associated microRNA, in experimental and human temporal lobe epilepsy. Eur J Neurosci 31: 1100-1107. doi:10.1111/j.1460-9568.2010.07122.x. PubMed: 20214679.
22. Majlessi M, Nelson NC, Becker MM (1998) Advantages of 2′-O-methyl oligoribonucleotide probes for detecting RNA targets. Nucleic Acids Res 26: 2224-2229. doi:10.1093/nar/26.9.2224. PubMed: 9547284. (Pubitemid 28291770)
23. Kierzek E, Ciesielska A, Pasternak K, Mathews DH, Turner DH et al. (2005) The influence of locked nucleic acid residues on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes. Nucleic Acids Res 33: 5082-5093. doi:10.1093/nar/gki789. PubMed: 16155181. (Pubitemid 41487816)
24. Matsukura M, Koike K, Zon G (1995) Antisense phosphorothioates as antivirals against human immunodeficiency virus (HIV) and hepatitis B virus (HBV). Toxicol Lett 82-83: 435-438. doi:10.1016/0378-4274(95)03574-5. PubMed: 8597090. (Pubitemid 26054732)
25. Dias N, Stein CA (2002) Antisense oligonucleotides: basic concepts and mechanisms. Mol Cancer Ther 1: 347-355. PubMed: 12489851.
26. Guga P, Koziołkiewicz M (2011) Phosphorothioate nucleotides and oligonucleotides - recent progress in synthesis and application. Chem Biodivers 8: 1642-1681. doi:10.1002/cbdv.201100130. PubMed: 21922655.
27. Hoke GD, Draper K, Freier SM, Gonzalez C, Driver VB et al. (1991) Effects of phosphorothioate capping on antisense oligonucleotide stability, hybridization and antiviral efficacy versus herpes simplex virus infection. Nucleic Acids Res 19: 5743-5748. doi:10.1093/nar/19.20.5743. PubMed: 1658742. (Pubitemid 21912983)
28. Stein CA, Mori K, Loke SL, Subasinghe C, Shinozuka K et al. (1988) Phosphorothioate and normal oligodeoxyribonucleotides with 5′-linked acridine: characterization and preliminary kinetics of cellular uptake. Gene 72: 333-341. doi:10.1016/0378-1119(88)90160-6. PubMed: 2854090. (Pubitemid 19032254)
29. Woolf TM, Jennings CG, Rebagliati M, Melton DA (1990) The stability, toxicity and effectiveness of unmodified and phosphorothioate antisense oligodeoxynucleotides in Xenopus oocytes and embryos. Nucleic Acids Res 18: 1763-1769. doi:10.1093/nar/18.7.1763. PubMed: 1692405.
30. Belair C, Darfeuille F, Staedel C (2009) Helicobacter pylori and gastric cancer: possible role of microRNAs in this intimate relationship. Clin Microbiol Infect 15: 806-812. doi:10.1111/j.1469-0691.2009.02960.x. PubMed: 19702585.
31. Resende C, Thiel A, Machado JC, Ristimäki A (2011) Gastric cancer: basic aspects. Helicobacter 16 Suppl 1: 38-44. doi:10.1111/j.1523-5378.2011. 00879.x. PubMed: 21896084.
32. Guimarães N, Azevedo NF, Figueiredo C, Keevil CW, Vieira MJ (2007) Development and application of a novel peptide nucleic acid probe for the specific detection of Helicobacter pylori in gastric biopsy specimens. J Clin Microbiol 45: 3089-3094. doi:10.1128/JCM.00858-07. PubMed: 17609326.
33. Kumar R, Singh SK, Koshkin AA, Rajwanshi VK, Meldgaard M et al. (1998) The first analogues of LNA (locked nucleic acids): phosphorothioate-LNA and 2′-thio-LNA. Bioorg Med Chem Lett 8: 2219-2222. doi:10.1016/S0960-894X(98) 00366-7. PubMed: 9873516.
34. You Y, Moreira BG, Behlke MA, Owczarzy R (2006) Design of LNA probes that improve mismatch discrimination. Nucleic Acids Res 34: e60. doi:10.1093/nar/gkl175. PubMed: 16670427.
35. Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA et al. (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33: D294-D296. PubMed: 15608200. (Pubitemid 40207881)
36. Azevedo N, Vieira MJ, Keevil CW (2003) Development of peptide nucleic acid probes to detect Helicobacter pylori in diverse species potable water biofilms. In: McBain A, Alison D, Brading M, Rickard A, Verran J, et al. editors. Biofilm Communities: Order from Chaos?: BioLine. pp. 105-112
37. Almeida C, Azevedo NF, Fernandes RM, Keevil CW, Vieira MJ (2010) Fluorescence in situ hybridization method using a peptide nucleic acid probe for identification of Salmonella spp. in a broad spectrum of samples. Appl Environ Microbiol 76: 4476-4485. doi:10.1128/AEM.01678-09. PubMed: 20453122.
38. Simard C, Lemieux R, Côté S (2001) Urea substitutes toxic formamide as destabilizing agent in nucleic acid hybridizations with RNA probes. Electrophoresis 22: 2679-2683. doi:10.1002/1522-2683(200108)22:13. PubMed: 11545392. (Pubitemid 32798931)
39. Huang E, Talukder S, Hughes TR, Curk T, Zupan B et al. (2011) BzpF is a CREB-like transcription factor that regulates spore maturation and stability in Dictyostelium. Dev Biol 358: 137-146. doi:10.1016/j.ydbio.2011.07.017. PubMed: 21810415.
40. Dewald GW, Smyrk TC, Thorland EC, McWilliams RR, Van Dyke DL et al. (2009) Fluorescence in situ hybridization to visualize genetic abnormalities in interphase cells of acinar cell carcinoma, ductal adenocarcinoma, and islet cell carcinoma of the pancreas. Mayo Clin Proc 84: 801-810. doi:10.4065/84.9.801. PubMed: 19720778.
41. Garcia-Hernandez J, Moreno Y, Amorocho CM, Hernandez M (2012) A combination of direct viable count and fluorescence in situ hybridization for specific enumeration of viable Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus. Lett Appl Microbiol.
42. Wiegant J, Brouwer AK, Tanke HJ, Dirks RW (2010) Visualizing nucleic acids in living cells by fluorescence in vivo hybridization. Methods Mol Biol 659: 239-246. doi:10.1007/978-1-60761-789-1-17. PubMed: 20809316.
43. Neumann H, Kiesslich R, Wallace MB, Neurath MF (2010) Confocal laser endomicroscopy: technical advances and clinical applications. Gastroenterology 139: 388-392, e381-382
44. Neumann H, Neurath MF, Mudter J (2011) New endoscopic approaches in IBD. World J Gastroenterol 17: 63-68. doi:10.3748/wjg.v17.i1.63. PubMed: 21218085.
45. Shukla R, Abidi WM, Richards-Kortum R, Anandasabapathy S (2011) Endoscopic imaging: How far are we from real-time histology? World J Gastrointest Endosc 3: 183-194. doi:10.4253/wjge.v3.i10.183. PubMed: 22013499.
46. Krauss E, Agaimy A, Douplik A, Albrecht H, Neumann H, et al. (2012) Normalized autofluorescence imaging diagnostics in upper GI tract: a new method to improve specificity in neoplasia detection. Int J Clin Exp Pathol 5: 956-964
47. Szöllösi J, Lockett SJ, Balázs M, Waldman FM (1995) Autofluorescence correction for fluorescence in situ hybridization. Cytometry 20: 356-361. doi:10.1002/cyto.990200412. PubMed: 7587724.
48. Bingham E, Hyvärinen A (2000) A fast fixed-point algorithm for independent component analysis of complex valued signals. Int J Neural Syst 10: 1-8. doi:10.1016/S0129-0657(00)00002-8. PubMed: 10798706.
49. Borisova EVB, Avramov L (2008) 5-ALAMediated Fluorescence Detection of Gastrointestinal Tumors. Advances in Optical Technologies.
50. Flexner C, Barditch-Crovo PA, Kornhauser DM, Farzadegan H, Nerhood LJ et al. (1991) Pharmacokinetics, toxicity, and activity of intravenous dextran sulfate in human immunodeficiency virus infection. Antimicrob Agents Chemother 35: 2544-2550. doi:10.1128/AAC.35.12.2544. PubMed: 1810188.
51. Koley D, Bard AJ (2010) Triton X-100 concentration effects on membrane permeability of a single HeLa cell by scanning electrochemical microscopy (SECM). Proc Natl Acad Sci U S A 107: 16783-16787. doi:10.1073/pnas.1011614107. PubMed: 20837548.
52. Ha Englert (2001) Nucleic Acid Hybridization. In: A.S. G, editor. Molecular Biology Problem Solver: A Laboratory Guide: John Wiley and Sons.
53. Matthiesen SH, Hansen CM (2012) Fast and non-toxic in situ hybridization without blocking of repetitive sequences. PLOS ONE 7: e40675. doi:10.1371/journal.pone.0040675. PubMed: 22911704.
54. Kiesslich R, Goetz M, Burg J, Stolte M, Siegel E et al. (2005) Diagnosing Helicobacter pylori in vivo by confocal laser endoscopy. Gastroenterology 128: 2119-2123. doi:10.1053/j.gastro.2004.12.035. PubMed: 15940642. (Pubitemid 40824718)
55. Cerqueira L, Fernandes RM, Ferreira RM, Carneiro F, Dinis-Ribeiro M et al. (2011) PNA-FISH as a new diagnostic method for the determination of clarithromycin resistance of Helicobacter pylori. BMC Microbiol 11: 101. doi:10.1186/1471-2180-11-101. PubMed: 21569555.
56. Ngo JT, Parkins MD, Gregson DB, Pitout JD, Ross T et al. (2013) Population-based assessment of the incidence, risk factors, and outcomes of anaerobic bloodstream infections. Infection 41: 41-48. doi:10.1007/s15010-012- 0389-4. PubMed: 23292663.
57. Erdem I, Ozgultekin A, Inan AS, Ozturk Engin D, Senbayrak Akcay S et al. (2009) Bloodstream infections in a medical-surgical intensive care unit: incidence, aetiology, antimicrobial resistance patterns of Gram-positive and Gram-negative bacteria. Clin Microbiol Infect 15: 943-946. doi:10.1111/j.1469- 0691.2009.02863.x. PubMed: 19548920.