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Selection of aptamers against pathogenic bacteria and their diagnostics application


Aptamers are short nucleotide sequences which can specifically bind to a variety of targets with high affinity. They are identified and selected via systematic evolution of ligands by exponential enrichment (SELEX). Compared to antibodies, aptamers offer several advantages including easy labeling, high stability and lower cost. Those advantages make it possible to be a potential for use as a recognition probe to replace antibody in the diagnostic field. This article is intended to provide a comprehensive review, which is focused on systemizing recent advancements concerning SELEX procedures, with special emphasis on the key steps in SELEX procedures. The principles of various aptamer-based detections of pathogenic bacteria and their application are discussed in detail, including colorimetric detection, fluorescence detection, electrochemical detection, lateral flow strip test, mass sensitive detection and PCR-based aptasensor. By discussing recent research and future trends based on many excellent publications and reviews, we attempt to give the readers a comprehensive view in the field of aptamer selection against pathogenic bacteria and their diagnostics application. Authors hope that this review will promote lively and valuable discussions in order to generate new ideas and approaches towards the development of aptamer-based methods for application in pathogenic bacteria diagnosis.

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  1. Abbaspour A, Norouz-Sarvestani F, Noori A et al (2015) Aptamer-conjugated silver nanoparticles for electrochemical dual-aptamer-based sandwich detection of Staphylococcus aureus. Biosens Bioelectron 68:149–155

  2. Bagheryan Z, Raoof JB, Golabi M et al (2016) Diazonium-based impedimetric aptasensor for the rapid label-free detection of Salmonella typhimurium in food sample. Biosens Bioelectron 80:566–573

  3. Bayraç C, Eyidoğan F, Avni ÖH (2017) DNA aptamer-based colorimetric detection platform for Salmonella enteritidis. Biosens Bioelectron 98:22–28

  4. Bruno JG (2014) Application of DNA aptamers and quantum dots to lateral flow test strips for detection of foodborne pathogens with improved sensitivity versus colloidal gold. Pathogens 3:341–355

  5. Cao X, Li S, Chen L et al (2009) Combining use of a panel of ssDNA aptamers in the detection of Staphylococcus aureus. Nucleic Acids Res 37:4621–4628

  6. Chang T, Wang L, Zhao K et al (2016) Duplex identification of Staphylococcus aureus by aptamer and gold nanoparticles. J Nanosci Nanotechnol 16:5513–5519

  7. Demirkol DO, Timur S (2016) A sandwich-type assay based on quantum dot/aptamer bioconjugates for analysis of E. coli O157:H7 in microtiter plate format. Int J Polym Mater 65:85–90

  8. Duan N, Wu S, Zhu C et al (2012) Dual-color upconversion fluorescence and aptamer-functionalized magnetic nanoparticles-based bioassay for the simultaneous detection of Salmonella typhimurium and Staphylococcus aureus. Anal Chim Acta 723:1–6

  9. Duan N, Ding X, He L et al (2013a) Selection, identification and application of a DNA aptamer against Listeria monocytogenes. Food Control 33:239–243

  10. Duan N, Ding X, Wu S et al (2013b) In vitro selection of a DNA aptamer targeted against Shigella dysenteriae. J Microbiol Methods 94:170–174

  11. Duan N, Wu S, Chen X et al (2013c) Selection and characterization of aptamers against Salmonella typhimurium using whole-bacterium systemic evolution of ligands by exponential enrichment (SELEX). J Agric Food Chem 61:3229–3234

  12. Duan N, Wu S, Yu Y et al (2013d) A dual-color flow cytometry protocol for the simultaneous detection of Vibrio parahaemolyticus and Salmonella typhimurium using aptamer conjugated quantum dots as labels. Anal Chim Acta 804:151–158

  13. Duan YF, Ning Y, Song Y et al (2014) Fluorescent aptasensor for the determination of Salmonella typhimurium based on a graphene oxide platform. Microchim Acta 181:647–653

  14. Duan N, Wu S, Dai S et al (2015) Simultaneous detection of pathogenic bacteria using an aptamer based biosensor and dual fluorescence resonance energy transfer from quantum dots to carbon nanoparticles. Microchem Acta 182:917–923

  15. Duan N, Xu B, Wu S et al (2016) Magnetic nanoparticles-based aptasensor using gold nanoparticles as colorimetric probes for the detection of Salmonella typhimurium. Anal Sci 32:431–436

  16. Fang Z, Wu W, Lu X et al (2014) Lateral flow biosensor for DNA extraction-free detection of Salmonella based on aptamer mediated strand displacement amplification. Biosens Bioelectron 56:192–197

  17. Gong W, Duan N, Wu S et al (2015) Selection, identification, and application of dual DNA aptamers against Shigella sonnei. Anal Methods-UK 7:3625–3631

  18. Guo Y, Wang Y, Liu S et al (2016) Label-free and highly sensitive electrochemical detection of E. coli based on rolling circle amplifications coupled peroxidase-mimicking DNAzyme amplification. Biosens Bioelectron 75:315–319

  19. Ikanovic M, Rudzinski WE, Bruno JG et al (2007) Fluorescence assay based on aptamer-quantum dot binding to Bacillus thuringiensis spores. J Fluoresc 17:193–199

  20. Jia F, Duan N, Wu S et al (2014) Impedimetric aptasensor for Staphylococcus aureus based on nanocomposite prepared from reduced graphene oxide and gold nanoparticles. Microchim Acta 181:967–974

  21. Jin B, Wang S, Lin M et al (2017) Upconversion nanoparticles based FRET aptasensor for rapid and ultrasenstive bacteria detection. Biosens Bioelectron 90:525–533

  22. Kaur H, Shorie M, Sharma M et al (2017) Bridged Rebar Graphene functionalized aptasensor for pathogenic E. coli O78:K80:H11 detection. Biosens Bioelectron 98:486–493

  23. Kim YS, Chung J, Song MY et al (2014) Aptamer cocktails: enhancement of sensing signals compared to single use of aptamers for detection of bacteria. Biosens Bioelectron 54:195–198

  24. Kim YS, Raston NHA, Gu MB (2016) Aptamer-based nanobiosensors. Biosens Bioelectron 76:2–19

  25. Kim H, Kim Y, Chon J et al (2017) Two-stage label-free aptasensing platform for rapid detection of Cronobacter sakazakii in powdered infant formula. Sens Actuators B 239:94–99

  26. Kurt H, Yüce M, Hussain B et al (2016) Dual-excitation upconverting nanoparticle and quantum dot aptasensor for multiplexed food pathogen detection. Biosens Bioelectron 81:280–286

  27. Lavu PSR, Mondal B, Ramlal S et al (2016) Selection and characterization of aptamers using a modified whole cell bacterium SELEX for the detection of Salmonella enterica Serovar typhimurium. ACS Comb Sci 18:292–301

  28. Lee HJ, Kim BC, Kim KW et al (2009) A sensitive method to detect Escherichia coli based on immunomagnetic separation and real-time PCR amplification of aptamers. Biosens Bioelectron 24:3550–3555

  29. Lee SH, Ahn JY, Lee KA et al (2015) Analytical bioconjugates, aptamers, enable specific quantitative detection of Listeria monocytogenes. Biosens Bioelectron 68:272–280

  30. Li H, Ding X, Peng Z et al (2011) Aptamer selection for the detection of Escherichia coli K88. Can J Microbiol 57:453–459

  31. Lian Y, He F, Wang H et al (2015) A new aptamer/graphene interdigitated gold electrode piezoelectric sensor for rapid and specific detection of Staphylococcus aureus. Biosens Bioelectron 65:314–319

  32. Luo C, Lei Y, Yan L et al (2012) A rapid and sensitive aptamer-based electrochemical biosensor for direct detection of Escherichia coli O111. Electroanalysis 24:1186–1191

  33. Luo Z, Zhou H, Jiang H et al (2015) Development of a fraction collection approach in capillary electrophoresis SELEX for aptamer selection. Analyst 140:2664–2670

  34. Ma X, Jiang Y, Jia F et al (2014) An aptamer-based electrochemical biosensor for the detection of Salmonella. J Microbiol Methods 98:94–98

  35. Moon J, Kim G, Park S (2014) Development of ssDNA aptamers for the capture and detection of Salmonella typhimurium. Anal Methods-UK 6:7442–7448

  36. Muniandy S, Dinshaw IJ, Teh SJ et al (2017) Graphene-based label-free electrochemical aptasensor for rapid and sensitive detection of foodborne pathogen. Anal Bioanal Chem 409:1–13

  37. Ozalp VC, Bayramoglu G, Erdem Z et al (2015) Pathogen detection in complex samples by quartz crystal microbalance sensor coupled to aptamer functionalized core–shell type magnetic separation. Anal Chim Acta 853:533–540

  38. Park JY, Jeong HY, Kim MI et al (2015) Colorimetric detection system for Salmonella typhimurium based on peroxidase-Like activity of magnetic nanoparticles with DNA aptamers. J Nanomater 2015

  39. Queirós RB, de-Los-Santos-Álvarez N, Noronha J et al (2013) A label-free DNA aptamer-based impedance biosensor for the detection of E. coli outer membrane proteins. Sens Actuators B 181:766–772

  40. Savory N, Lednor D, Tsukakoshi K et al (2013) In silico maturation of binding-specificity of DNA aptamers against Proteus mirabilis. Biotechnol Bioeng 110:2573–2580

  41. Shao K, Ding W, Wang F et al (2011) Emulsion PCR: a high efficient way of PCR amplification of random DNA libraries in aptamer selection. PloS ONE 6:e24910

  42. Song S, Wang L, Li J et al (2008) Aptamer-based biosensors. Trend Anal Chem 27:108–117

  43. Teng J, Yuan F, Ye Y et al (2016) Aptamer-based technologies in foodborne pathogen detection. Front Microbiol 7:1426

  44. Toh SY, Citartan M, Gopinath SC et al (2015) Aptamers as a replacement for antibodies in enzyme-linked immunosorbent assay. Biosens Bioelectron 64:392–403

  45. Tolle F, Wilke J, Wengel J et al (2014) By-Product formation in repetitive PCR amplification of DNA libraries during SELEX. PloS One 9:e114693

  46. Verma MS, Rogowski JL, Jones L et al (2015) Colorimetric biosensing of pathogens using gold nanoparticles. Biotechnol Adv 33:666–680

  47. Wang R, Xu Y, Zhang T et al (2015) Rapid and sensitive detection of Salmonella typhimurium using aptamer-conjugated carbon dots as fluorescence probe. Anal Methods-UK 7:1701–1706

  48. Wang L, Wang R, Chen F et al (2017a) QCM-based aptamer selection and detection of Salmonella typhimurium. Food Chem 221:776–782

  49. Wang L, Wang R, Wang H et al (2017b) An aptamer-based PCR method coupled with magnetic immunoseparation for sensitive detection of Salmonella typhimurium in ground turkey. Anal Biochem 533:34–40

  50. Wu W, Li M, Wang Y et al (2012) Aptasensors for rapid detection of Escherichia coli O157:H7 and Salmonella typhimurium. Nanoscale Res Lett 7:1–7

  51. Wu S, Wang Y, Duan N et al (2015) Colorimetric aptasensor based on enzyme for the detection of Vibrio parahemolyticus. J Agric Food Chem 63:7849–7854

  52. Wu S, Duan N, Qiu Y et al (2017) Colorimetric aptasensor for the detection of Salmonella enterica serovar typhimurium using ZnFe2O4-reduced graphene oxide nanostructures as an effective peroxidase mimetics. Int J Food Microbiol 261:42–48

  53. Xu L, Callaway ZT, Wang R et al (2015) A fluorescent aptasensor coupled with nanobead-based immunomagnetic separation for simultaneous detection of four foodborne pathogenic bacteria. Trans ASABE 58:891–906

  54. Yoo SM, Kim D-K, Lee SY (2015) Aptamer-functionalized localized surface plasmon resonance sensor for the multiplexed detection of different bacterial species. Talanta 132:112–117

  55. Yu X, Chen F, Wang R et al (2017) Whole-bacterium SELEX of DNA aptamers for rapid detection of E. coli O157:H7 using a QCM sensor. J Biotechnol 266:39–49

  56. Yuan J, Tao Z, Yu Y et al (2014a) A visual detection method for Salmonella typhimurium based on aptamer recognition and nanogold labeling. Food Control 37:188–192

  57. Yuan J, Wu S, Duan N et al (2014b) A sensitive gold nanoparticle-based colorimetric aptasensor for Staphylococcus aureus. Talanta 127:163–168

  58. Zhu CQ, Hong Y, Xiao Z et al (2016) Colorimetric determination of Salmonella typhimurium based on aptamer recognition. Anal Methods-UK 8:6560–6565

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This research was supported in part by Open Research Subject of Key Laboratory of Xihua University (szjj2017-115), Walmart Foundation and Walmart Food Safety Collaboration Center. The authors thank Lisa Kelso for English edition and correction.

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Correspondence to Yanbin Li.

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Wang, L., Wang, R., Wei, H. et al. Selection of aptamers against pathogenic bacteria and their diagnostics application. World J Microbiol Biotechnol 34, 149 (2018).

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  • Aptamer
  • Diagnostic detection
  • Pathogenic bacteria
  • Recognition elements