Springer Principles Of Bacterial Detection Biosensors Recognition Receptors And Microsystems Sep 2008 ISBN 0387751122 pdf
Principles of Bacterial Detection:
Biosensors, Recognition Receptors
and Microsystems
Principles of Bacterial Detection:
Biosensors, Recognition Receptors and Microsystems Edited by MOHAMMED ZOUROB Biophage Pharma Inc.Montreal, Canada SOUNA ELWARY Consultant to Biophage Pharma Inc.
Montreal, Canada
ANTHONY TURNER
Cranfield University Bedfordshire, UK
Editors Mohammed Zourob Souna Elwary Biophage Pharma Inc. Consultant to Biophage Pharma Inc. Montreal Montreal Canada Canada m.zourob@biophagepharma.net selwary@yahoo.com Anthony Turner Cranfield University Bedfordshire UK a.p.turner@cranfield.ac.uk
ISBN: 978-0-387-75112-2 e-ISBN: 978-0-387-75113-9 Library of Congress Control Number: 2007941938 © 2008 Springer Science+Business Media, LLC
All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the
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developed is forbidden.The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified
as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights.Preface
Bacterial contamination of food and water resources, as well as the increasing incidence of nosocomial infections, has us on our toes, looking for ways of recognizing these elements. In addition, the recent and growing threats to personal and territorial securities make this task even more urgent. Therefore, accurate assessment of the state of current technologies is a prerequisite for undertaking any course of action towards future improvements. In particular, development of new detection and identification technologies for the plethora of bacterial agents has become increasingly important to scientists and to regulatory agencies. In recent years, there has been much progress in the field of bacterial agents detection, resulting in the development of more accurate, fast, analyte-specific, robust, and cost effective techniques by incorporating emerging technologies from various disciplines.
Principles of Bacterial Detection: Biosensors, Recognition Receptors and Microsystems presents a significant and up-to-date review of various integrated approaches for bacterial detection by distinguished engineers and scientists. This work is a comprehensive approach to bacterial detection, presenting a thorough knowledge of the subject and an effective integration of disciplines in order to appropriately convey the state-of the-art fundamentals and applications of the most innovative approaches.
The book consists of four parts. The first part (Chapters 1–4) is an introduction to pathogenic bacteria and sampling techniques and provides an overview of the rapid microbio- logical methods. The second part (Chapters 5–20) describes the different transducers used for bacterial detection. It covers the theory behind each technique and delivers a detailed state- of-the-art review for all the new technologies used. The third part (Chapters 21–29) covers the different recognition receptors used in the latest methods for the detection of bacteria. It describes in detail the use of immunoassays, nucleic acids, oligonucleotide microarrays, carbohydrates, aptamers, protein microarrays, bacteriophage, phage display, and molecular imprinted polymers as recognition elements. The fourth part (Chapters 30–36) covers the different microsystems used for detection/identification and bacterial manipulations, mainly bacteria lysis in microfluidics, PCR in microfluidics, dielectrophoresis, ultrasonic manipulation techniques, and mass spectrometry.
We anticipate that the book will be helpful to academicians, practitioners, and professionals working in various fields, including biomedical sciences, physical sciences, microsystems engineering, nanotechnology, veterinary science and medicine, food QA, bioter- rorism and security as well as allied health, healthcare and surveillance. Since the fundamentals are also reviewed, we believe that the book will appeal to advanced undergraduate and graduate students who study in areas related to bacterial detection.
We gratefully acknowledge all authors for their participation and contributions, which made this book a reality. We give many thanks to Olivier Laczka and Joseph Piliero for the book cover design.
Contents
Part I Introduction
1. Introduction to Pathogenic Bacteria
Tracey Elizabeth Love and Barbara Jones 1. Pathogenic Microorganisms...............................................................................................................
3
1.1. Toxins .........................................................................................................................................
4
1.2. Adherence ...................................................................................................................................
4
1.3. Invasion.......................................................................................................................................
7
1.4. Evasion of the Host Immune Response .....................................................................................
7
1.5. Iron Acquisition ..........................................................................................................................
8
1.6. Regulation of Virulence Factors ................................................................................................
8 2. Sources and Routes of Infection........................................................................................................
9
2.1. Natural Infection.........................................................................................................................
9
2.2. Food and Water ..........................................................................................................................
9
2.3. Hospital Acquired Infections......................................................................................................
10
2.4. Intentional Infection—Biological Warfare.................................................................................
10 3. Detection of Pathogenic Microorganisms..........................................................................................
11 4. Conclusions ........................................................................................................................................
12 References...........................................................................................................................................
12
2. Sample Preparation: An Essential Prerequisite for High-Quality Bacteria Detection
Jan W. Kretzer, Manfred Biebl and Stefan Miller 1. Introduction ........................................................................................................................................
15 2. The Sample.........................................................................................................................................
16 3. Sampling.............................................................................................................................................
17
3.1. Sample drawing ..........................................................................................................................
17 4. Microbiological Examination of Foods .............................................................................................
17 5. Microbiological Examination of Surfaces .........................................................................................
17 6. Microbiological Examination of Air..................................................................................................
18 7. Sample Handling ................................................................................................................................
20 8. Sample Preparation ............................................................................................................................
21 9. Sample Preparation for Detection of Intact Bacterial Cells..............................................................
21 10. Sample Preparation for Detection of Bacterial Nucleic Acids .........................................................
23 11. Conclusions and Future Perspectives ................................................................................................
27 References...........................................................................................................................................
28
3. Detection of Bacterial Pathogens in Different Matrices: Current Practices and Challenges
viii Contents
50 3. Types of Microbial Testing Performed .............................................................................................
44
7.3. Which Traits to Analyze, and How Many Tests are Needed for Identifying a Bacterial
Pathogen? ....................................................................................................................................
45
7.4. Real-Time Detection...................................................................................................................
46 References...........................................................................................................................................
46
4. Overview of Rapid Microbiological Methods
Jeanne Moldenhauer 1. Introduction ........................................................................................................................................
49
2. A History of Rapid Microbiological Methods: Industry Reluctance to Accept
These Methods ..................................................................................................................................
50 4. Types of Rapid Microbiological Methods.........................................................................................
44
7.1. Pathogen Quantification Problems .............................................................................................
50
4.1. Growth-Based Technologies.......................................................................................................
50
4.2. Viability-Based Technologies.....................................................................................................
50
4.3. Cellular Component or Artifact-Based Technologies................................................................
51
4.4. Nucleic Acid-Based Technologies .............................................................................................
51
4.5. Automated Methods....................................................................................................................
51
4.6. Combination Methods.................................................................................................................
51 5. Overview of Rapid Technologies and How They Work ..................................................................
51
5.1. Adenosine Tri-Phosphate (ATP) Bioluminescence ...................................................................
51
5.2. Adenylate Kinase........................................................................................................................
52
5.3. Autofluorescence ........................................................................................................................
44
7.2. Can a Small Bacterial Population be Detected Rapidly and Reliably?.....................................
44 7. Challenges to Current Detection Methods.........................................................................................
3. Defining the Terms ............................................................................................................................
39
6.2. Sample Preparation .....................................................................................................................
32 4. Matrix Complexity and Pathogen Detection .....................................................................................
32 5. Techniques Currently Used in Pathogen Detection Methods ...........................................................
33
5.1. Culture Techniques .....................................................................................................................
33
5.2. Enzyme-Linked Immunoassay....................................................................................................
35
5.3. Polymerase Chain Reaction (PCR) ............................................................................................
36 6. Basics of Pathogen Detection ............................................................................................................
36
6.1. Sampling .....................................................................................................................................
37
6.1.1. Air Sampling.....................................................................................................................
37
6.1.2. Surfaces Sampling ............................................................................................................
37
6.1.3. Bulk Sampling ..................................................................................................................
39
6.3. Pathogen Amplification ..............................................................................................................
44
6.7. Testing for Specific Traits ..........................................................................................................
39
6.4. Selection and Screening..............................................................................................................
40
6.5. Identification ...............................................................................................................................
40
6.5.1. Morphological Characteristics..........................................................................................
41
6.5.2. Biochemical and Physiological Traits..............................................................................
41
6.5.3. Serological Properties.......................................................................................................
42
6.5.4. Genetic Characteristics .....................................................................................................
42
6.6. Pathogenicity Testing..................................................................................................................
43
6.6.1. Koch’s Postulates..............................................................................................................
43
6.6.2. Mammalian Cell Culture (Tissue Culture).......................................................................
43
6.6.3. Virulence Genes and Gene Expression Products.............................................................
52
Contents ix
75 References...........................................................................................................................................
61 5.33. Ribotyping/Molecular Typing ....................................................................................................
61 5.34. Solid Phase Laser Scanning Cytometry.....................................................................................
61 5.35. Southern Blotting/Restriction Fragment Length Polymorphism ...............................................
62 5.36. Spiral Plating ..............................................................................................................................
62 5.37. Turbidimetry ...............................................................................................................................
62 6. Potential Areas of Application of Rapid Microbiological Methods .................................................
62 7. Disclaimer...........................................................................................................................................
75 8. Conclusions ........................................................................................................................................
75 Part II Biosensors
60 5.31. Rep-PCR .....................................................................................................................................
5. Surface Plasmon Resonance (SPR) Sensors for the Detection of Bacterial Pathogens
Allen D. Taylor, Jon Ladd, Jiˇrí Homola and Shaoyi Jiang 1. Introduction ........................................................................................................................................
83 2. Fundamentals of Surface Plasmon Resonance Biosensing ...............................................................
83 3. SPR Sensor Instrumentation ..............................................................................................................
85 4. Surface Chemistries and Molecular Recognition Elements ..............................................................
88 5. Detection Formats ..............................................................................................................................
90 6. Quantification of Bacteria Cells ........................................................................................................
91
6.1. Challenges for the Detection of Whole Bacteria by SPR..........................................................
91
6.2. Effect of Bacteria Sample Treatment .........................................................................................
60 5.32. Raman Spectroscopy ..................................................................................................................
59 5.30. Polymerase Chain Reaction (PCR) ............................................................................................
5.8. Colorimetric Detection of Carbon Dioxide Production.............................................................
56 5.18. Gram Stains (Rapid Method) .....................................................................................................
53
5.9. Concentric Arcs of Photovoltaic Detectors with Laser Scanning.............................................
54 5.10. Direct Epifluorescent Filter Technique (DEFT)........................................................................
54 5.11. DNA Sequencing........................................................................................................................
54 5.12. Endospore Detection ..................................................................................................................
55 5.13. Enzyme Linked Immunosorbent Assay (ELISA)......................................................................
55 5.14. Flow Cytometry..........................................................................................................................
55 5.15. Fluorescent Probe Detection ......................................................................................................
55 5.16. Fatty Acid Profiles (Fatty Acid Methyl Esters, FAMEs)..........................................................
56 5.17. Fourier Transformed Infrared Spectroscopy (FTIR) .................................................................
56 5.19. Impedance...................................................................................................................................
59 5.29. Optical Particle Detection ..........................................................................................................
57 5.20. Immunological Methods.............................................................................................................
57 5.21. Lab-on-a-Chip (LOC), Arrays, Microarrays and Microchips ...................................................
57 5.22. Limulus Amebocyte Lysate (LAL) Endotoxin Testing.............................................................
58 5.23. Mass Spectrometry (Matrix-Assisted Laser Desorption-Time of Flight (MALTI-TOF))........
58 5.24. Microcalorimetry ........................................................................................................................
58 5.25. Micro-Electro-Mechanical Systems (MEMS) ...........................................................................
59 5.26. Nanotechnology..........................................................................................................................
59 5.27. Near Infrared Spectroscopy (NIRS)...........................................................................................
59 5.28. Nucleic Acid Probes...................................................................................................................
92
x Contents
6.3.4. Other Bacteria ..................................................................................................................
98
6.3.5. Detection of Multiple Bacteria ........................................................................................
99
7. Genetic Markers ................................................................................................................................. 101
8. Antibody Biomarkers ......................................................................................................................... 103
9. Conclusions and Future Perspectives ................................................................................................ 103
References........................................................................................................................................... 1046. Bacterial Detection Using Evanescent Wave-Based Fluorescent Biosensors
Kim E. Sapsford and Lisa C. Shriver-Lake
1. Introduction ........................................................................................................................................ 109
2. Current State of Bacterial Fluorescent TIRF Biosensors.................................................................. 112
2.1. Non-Planar Substrates................................................................................................................. 112
2.1.1. Fiber Optics ...................................................................................................................... 112
2.1.2. Capillaries......................................................................................................................... 112
2.2. Planar Substrates......................................................................................................................... 112
2.2.1. NRL Array Biosensor ...................................................................................................... 113
2.2.2. Other Optical Waveguides ............................................................................................... 115
2.2.3. TIRF-Microscopy ............................................................................................................. 116
3. Future Aspects of Bacterial Fluorescent TIRF Biosensors ............................................................... 117
4. Conclusions ........................................................................................................................................ 119
References........................................................................................................................................... 1207. Fiber Optic Biosensors for Bacterial Detection
Ryan B. Hayman
1. Fiber Optic Biosensors....................................................................................................................... 125
1.1. Whole-Cell Detection ................................................................................................................. 126
1.1.1. Evanescent-Field Sensing ................................................................................................ 126
1.1.2. Sandwich Immunoassays ................................................................................................. 127
1.2. Bead-Based Arrays ..................................................................................................................... 128
1.3. Nucleic Acid Sandwich Assays.................................................................................................. 129
1.4. Nucleic Acid Direct Hybridization............................................................................................. 131
1.5. Extension Reactions.................................................................................................................... 134
2. Conclusions and Future Perspectives ................................................................................................ 134
References........................................................................................................................................... 1358. Integrated Deep-Probe Optical Waveguides for Label Free Bacterial Detection
Mohammed Zourob, Nina Skivesen, Robert Horvath, Stephan Mohr, Martin B. McDonnell
and Nicholas J. Goddard
1. Introduction ........................................................................................................................................ 139
1.1. Planar Optical Waveguides......................................................................................................... 141
1.2. Total Internal Reflection and Evanescent Waves ...................................................................... 141
1.3. Waveguide Modes ...................................................................................................................... 143
1.4. Frustrated Total Internal Reflection, Leaky Modes ................................................................... 144
Contents xi
2. The Bacterial (lux) Luminescent System for Direct Pathogen Detection........................................ 215
7. Sample Collection Systems................................................................................................................ 198
8. Interferometric Applications for Whole-Cell Detection.................................................................... 199
9. Advantages and Limitations............................................................................................................... 206
10. Potential for Improving Current Performance................................................................................... 206
References........................................................................................................................................... 20810. Luminescence Techniques for the Detection of Bacterial Pathogens
Leigh Farris, Mussie Y. Habteselassie, Lynda Perry, S. Yanyun Chen, Ronald Turco,
Brad Reuhs and Bruce Applegate
1. Beyond Robert Boyle’s Chicken....................................................................................................... 214
3. The Firefly (luc) Luminescent System for Direct Pathogen Detection............................................ 219
5. Other Interferometric Methods and Designs ..................................................................................... 196
4. The Use of Alternative Luciferases in Pathogen Detection ............................................................. 222
5. Luminescent-Based Immunoassays................................................................................................... 222
6. Chemiluminescence Detection Methods ........................................................................................... 222
7. Conclusions and Future Perspectives ................................................................................................ 225
References.......................................................................................................................................... 22611. Porous and Planar Silicon Sensors
Charles R. Mace and Benjamin L. Miller
1. Introduction........................................................................................................................................ 231
1.1. Porous Silicon: A Three-Dimensional Matrix for Biosensing .................................................. 232
6. Surface Functionalization................................................................................................................... 197
4. Surface Plasmon Interferometry ........................................................................................................ 195
2.2. Waveguide Designs Based on Low-Index Substrates................................................................ 150
9. Interferometric Biosensors
2.2.1. Bacteria Detection Using Reverse Symmetry Waveguides ............................................ 151
2.3. Waveguide Designs Based on Metal- and Dye-Clad Substrates—Leaky Modes..................... 152
2.3.1. Results .............................................................................................................................. 156
3. Integrated Deep-Probe Optical Waveguides Systems ....................................................................... 160
3.1. Integration with Electric Field.................................................................................................... 161
3.2. Integration with Ultrasound Standing Waves (USW)................................................................ 163
4. Conclusions and Future Perspectives ................................................................................................ 166
References........................................................................................................................................... 166Daniel P. Campbell
3. Interferometric Array Sensors............................................................................................................ 192
1. Principles of Optical Interferometry .................................................................................................. 169
1.1. Optical Waveguides .................................................................................................................... 171
1.2. Planar Waveguide Operation...................................................................................................... 172
1.3. Types of Waveguides ................................................................................................................. 175
2. Light Coupling Methods .................................................................................................................... 178
2.1. Interferometers ............................................................................................................................ 180
2.2. Collinear or Single Channel Interferometers ............................................................................. 183
2.3. Two-Channel Interferometers..................................................................................................... 186
1.2. Effect of PSi Immobilization on Probe Viability: Experiments with GST .............................. 233
xii Contents
13. Amperometric Biosensors for Pathogenic Bacteria Detection
3.5.3. Combined Langmuir-Blodgett/Molecular Assembling Method ..................................... 272
3.5.4. Solvent-Free Purified Monolayers................................................................................... 275
3.5.5. Immobilization of Monolayers of Phage Coat Proteins ................................................. 276
3.5.6. Immobilization of Molecular Probes onto Porous Substrates ........................................ 281
4. Problem of “Negative Mass”............................................................................................................. 282
5. Coupled Oscillators Model................................................................................................................ 286
6. Conclusions........................................................................................................................................ 290
References.......................................................................................................................................... 291Ilaria Palchetti and Marco Mascini
3.5.1. Physical Adsorption......................................................................................................... 271
1. Introduction........................................................................................................................................ 299
2. Amperometric Biosensors.................................................................................................................. 300
2.1. Microbial Metabolism-Based Biosensors .................................................................................. 302
2.2. Immunosensors ........................................................................................................................... 303
2.3. DNA-Based Biosensors.............................................................................................................. 306
3. Conclusion and Future Perspectives.................................................................................................. 310
References.......................................................................................................................................... 31014. Microbial Genetic Analysis Based on Field Effect Transistors
Yuji Miyahara, Toshiya Sakata and Akira Matsumoto
3.5.2. Other Coupling Methods ................................................................................................. 272
3.5. Immobilization of Probes onto Sensor Surface ......................................................................... 269
2.1.1. Physical Rationale............................................................................................................ 236
12. Acoustic Wave (TSM) Biosensors: Weighing Bacteria
2.1.2. Substrate Design .............................................................................................................. 237
2.1.3. Mathematical Model ........................................................................................................ 238
2.1.4. Monitoring the Null Reflectance Condition.................................................................... 240
2.2. Applications of AIR Biosensing ................................................................................................ 242
2.2.1. Limitations ....................................................................................................................... 242
2.2.2. Probe Immobilization ...................................................................................................... 244
2.2.3. Pathogen Detection .......................................................................................................... 246
3. Conclusions and Future Perspectives ................................................................................................ 250
References.......................................................................................................................................... 251Eric Olsen, Arnold Vainrub and Vitaly Vodyanoy
3.4. Commercial TSM Microbalances .............................................................................................. 267
1. Introduction........................................................................................................................................ 255
2. Historical Perspective, Theory and Background............................................................................... 256
2.1. Piezoelectricity and Acoustic Waves......................................................................................... 256
2.2. Acoustic Wave Devices ............................................................................................................. 256
3. TSM Biosensors................................................................................................................................. 259
3.1. Detection of Microorganisms..................................................................................................... 261
3.2. Measurement in Liquid .............................................................................................................. 263
3.3. TSM Biosensor Characteristics.................................................................................................. 264
1. Introduction........................................................................................................................................ 313
Contents xiii
3.1.4. Other Recognition Strategies........................................................................................... 356
2.2.2. Faradaic Parameters......................................................................................................... 347
2.3. Measuring at Impedimetric Biosensors...................................................................................... 350
2.3.1. Measurement Modes........................................................................................................ 350
2.4. Bacterial Parasitizing Effect on Electrode Surface.................................................................... 353
3. Development of an Immunosensor.................................................................................................... 354
3.1. Biological Recognition Elements in Biosensors for Pathogen Detection................................. 354
3.1.1. Antibodies ........................................................................................................................ 355
3.1.2. Nucleic Acids................................................................................................................... 355
3.1.3. Aptamers .......................................................................................................................... 356
3.2. Surface Modification Methods................................................................................................... 357
2.2. Data Analysis: Interpretation ..................................................................................................... 344
3.2.1. Adsorption........................................................................................................................ 357
3.2.2. Self-assembled Monolayers............................................................................................. 358
3.2.3. Silanisation....................................................................................................................... 359
3.2.4. Protein A and Protein G .................................................................................................. 360
3.2.5. The Biotin-(Strept)Avidin System................................................................................... 360
3.2.6. Chemical Conjugation ..................................................................................................... 361
3.2.7. Entrapment ....................................................................................................................... 362
3.2.8. Microencapsulation.......................................................................................................... 362
3.3. Blocking...................................................................................................................................... 362
2.2.1. Non-Faradaic Parameters................................................................................................. 345
2.1. Data Analysis: Plotting............................................................................................................... 344
3. Fundamentals of Genetic Analysis.................................................................................................... 317
5.1. Fundamental Characteristics of Genetic Field Effect Devices.................................................. 322
3.1. DNA............................................................................................................................................ 317
3.2. Genetic Analysis......................................................................................................................... 317
3.3. DNA Chip / DNA Microarray ................................................................................................... 318