Current and emerging technologies for the diagnosis of microbial infections:
Gespeichert in:
Weitere Verfasser: | , |
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Format: | Buch |
Sprache: | English |
Veröffentlicht: |
Amsterdam ; Boston ; Heidelberg ; London ; New York ; Oxford ; Paris ; San Diego ; San Francisco ; Singapore ; Sydney ; Tokyo
Elsevier, AP
2015
|
Ausgabe: | First edition |
Schriftenreihe: | Methods in microbiology
volume 42 |
Schlagworte: | |
Online-Zugang: | Inhaltsverzeichnis |
Beschreibung: | Literaturangaben |
Beschreibung: | xix, 613, [24] Seiten Illustrationen 24 cm |
ISBN: | 9780128032978 |
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245 | 1 | 0 | |a Current and emerging technologies for the diagnosis of microbial infections |c edited by Andrew Sails (Public Health England Newcastle Laboratory, National Infection Service, The Medical Scool, Royal Victory Infirmary, Newcastle, UK), Yi-Wei Tang (Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, and Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, USA) |
250 | |a First edition | ||
264 | 1 | |a Amsterdam ; Boston ; Heidelberg ; London ; New York ; Oxford ; Paris ; San Diego ; San Francisco ; Singapore ; Sydney ; Tokyo |b Elsevier, AP |c 2015 | |
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Datensatz im Suchindex
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adam_text | Contents
Contributors.............................................................xv
Preface............................................................*.....xix
CHAPTER 1 Total Laboratory Automation in Ciinicai
Bacteriology........................................... i
Susan M. Novak-Weekley, Elizabeth M. Marlowe
1. Clinical Bacteriology and Automation; Background.......... I
2. Specimen Collection: Liquid Microbiology..................4
3. Pre-analytical Automation.................................6
4. Pre-analytical Bacteriology Specimen Plating instruments..7
4.1. Isoplater .......................................... 7
4.2. Innova.............................................. 9
4.3. BD Kiestra™ InoqulA+™............................. .Î2
4.4. Previ K/ isola................................... 14
4.5. Copan WASP* ..................................... 16
4.6. Prelude: i2a..................................... 20
4.7. deltalab AUTOPLAK....................................21
5. Digital Plate Reading.................................. 23
6. TLA Systems..............................................27
6.1. BD Kiestra....................................... 27
6.2. Copan WASPLab™................................. 30
6.3. i2a: ECITALS™.................................... 32
7. Change Management: A Holistic Approach to Automation
in Bacteriology...........................................33
References......................................... .....34
CHAPTER 2 MALDI-TOF Mass Spectrometry for Microorganism
Identification............................................37
Lori Bourassa, Susan M. Butler-Wu
1. introduction........................................... 37
LL MALDI-TOF MS: Principles and Processes.................37
1.2. Commercially Available MALDI-TOF MS Platforms........39
1.3. Factors Influencing the Performance
of MALDI-TOF MS........................ .............43
2. Microbial Identification by MALDI-TOF MS............... 44
2.1. Comparison of MALDI-TOF MS and Conventional
Methods for the Identification of Routine Isolates...45
V
Contents
2.2. Comparison of Commercially Available
MALDI-TOF MS Systems.....................................46
2.3. Laboratory Cost Savings Associated with Using
MALDI-TOF MS for Isolate Identification..................46
3. Performance of MALDI-TOF MS for the Identification
of Routine Clinical Isolates..................................47
3.1. Identification of Gram-Positive Bacteria.................51
3.2. Identification of Gram-Negative Bacteria.................53
3.3. Identification of Anaerobes..............................55
3.4. Identification of Mycobacteria...........................56
3.5. Identification of Yeast..................................58
3.6. Identification of Filamentous Fungi......................59
3.7. Identification of Select Agents..........................61
4. Direct Identification from Clinicai Specimens................62
4.1. Identification of Microorganisms Directly from
Positive Blood Cultures..................................62
4.2. Identification of Bacteria Directly from
Urine Specimens..........................................64
4.3. Identification of Bacteria Directly from
Cerebrospinal Fluid......................................65
Limitations and Conclusions...................................66
References....................................................68
CHAPTER 3 POC Tests in Microbial Diagnostics:
Current Status................................................87
Luc Bissonnette, Michel G. Bergeron
1. Introduction..................................................87
2. The Current Utilisation of Infectious Diseases
POC Testing...................................................90
2.1. Viral Respiratory Infections.............................94
2.2. HIV/AIDS, Tuberculosis, Sexually Transmitted
Infections...............................................94
2.3. Diarrhoea and Gastrointestinal Diseases..................95
2.4. Surveillance, Prevention, and Diagnosis of
Healthcare-Acquired Infections...........................96
2.5. Anticipated POC Testing Advances Through
Biomarkers or Improved Technologies......................96
2.6. Patient Empowerment Is Key for Any POC Test..............97
3. The Road to POC Molecular Diagnostics Is Paved
with Good Intentions and Technologies.........................98
3.1. Near-POC Testing.........................................99
Contents vil
3.2. Isothermal Amplification Technologies...............99
3.3. Integrated Molecular Diagnostics Platforms.........100
Conclusions.............................................102
Acknowledgements........................................103
References..............................................104
CHAPTER 4 Molecular Diagnostics in the Diagnosis
of Parasitic Infection..................................ill
Bobbi s. Pritt
1. Introduction............................................Ill
2. Blood Parasites........................................114
2.1. Plasmodium Species (Malaria).......................114
2.2. Babesia Species (Babesiosis).......................119
2.3. Trypanosoma brucei (Human African
Trypanosomiasis)....................................121
2.4. Tiypanosoma cruzi (Chagas Disease).................123
2.5. Filariasis.........................................126
3. Tissue Parasites.......................................128
3.1. Leishmania Species (Leishmaniasis).................128
3.2. Toxoplasma gondii (Toxoplasmosis)..................130
3.3. Free-Living Amoebae: Naegleria fowleri,
Acanthamoeba Species and Balamuthia
mandrillaris........................................132
4. Intestinal Protozoa and Microsporidia..................135
4.1. Background.........................................135
4.2. Diagnostic Modalities..............................135
4.3. Design and Performance of Molecular Tests..........136
4.4. Clinical Implementation of Molecular Tests.........137
5. Intestinal Helminths...................................138
5.1. Background.........................................138
5.2. Diagnostic Modalities..............................139
5.3. Design and Performance of Molecular Tests..........139
5.4. Clinical Implementation of Molecular Tests.........140
6- Trichomonas vaginalis..................................140
6.1. Background....................................... 140
6.2. Diagnostic Modalities..............................141
6.3. Design and Performance of Molecular Tests..........142
6.4. Clinical Implementation of Molecular Tests.........143
7. Summary................................................143
References............................................ 144
viii Contents
CHAPTER 5 Clinical Applications of Quantitative Real-Time
PCR in Virology.........................................161
Julia Engstrom-Melnyk, Pedro L Rodriguez,
Olivier Peraud, Raymond C. Hein
1. Introduction...........................................161
1.1. Quantitative Real-Time PCR..........................162
1.2. Co-evolution of Real-Time PCR and Diagnostics.......164
2. Applications in the Continuum of Care...................167
2.1. Screening...........................................167
2.2. Diagnosis...........................................168
2.3. Treatment Decision..................................171
2.4. Monitoring..........................................175
2.5. Test of Cure........................................179
3. Expanding Applications..................................181
3.1. PCR-Based Laboratory-Developed Tests................181
3.2. Emerging/Re-emerging Infectious Diseases............182
3.3. Real-Time PCR and Point-of֊Care Testing.............183
4. Discussion............................................ 184
References...............................................185
CHAPTER 6 Low-Density TaqMan® Array Cards for the
Detection of Pathogens...................................199
Jude Heaney, Kathryn Rolfe, Nicholas S. Gleadall,
Jane S. Greatorex, Martin D. Curran
1- Introduction............................................199
2. TaqMan® Array Cards.....................................200
3. Developing a TAC Based on In-House Real-Time
PCR Assays...............................................206
4. Syndromic TAC...........................................208
4.1. Respiratory TACs....................................208
4.2. Gastrointestinal TACs...............................209
4.3. Other Syndromic TACs................................212
Conclusions..............................................215
Acknowledgements.........................................216
References...............................................216
CHAPTER 7 Invasive Fungal Infections and Approaches
to Their Diagnosis.......................................219
Michael A. Pfaller
1. Introduction............................................219
2. Spectrum of Opportunistic Pathogens.....................221
Contents
IX
3. Clinical Recognition of Fungal Infection................224
4. Laboratory Diagnosis....................................225
4.1. Stains and Direct Examination.......................225
4.2. Culture.............................................230
4.3. Identifying Characteristics of Fungi................235
4.4. Immunologic, Biochemical, and Nucleic Acid-Based
Methods of Diagnosis................................241
5. Antifungal Susceptibility Testing.......................257
Summary and Conclusions..................................263
References...............................................264
CHAPTER 8 Technical and Software Advances in Bacterial
Pathogen Typing..........................................289
Linda Chui, Vincent Li
1. Introduction............................................289
2. Pulsed-Field Gel Electrophoresis........................290
3. Serotyping for Salmonella...............................292
4. Sequencing-Based Molecular Typing.......................296
4.1. spa Typing..........................................296
4.2. emm Typing..........................................297
4.3. Serotyping for Shiga Toxin-Producing E. coli........299
4.4. Multilocus Sequence Typing..........................300
4.5. Variable Number of Tandem Repeat Typing............301
5. Comparative Genomic Fingerprinting......................302
8. Tools for Pathogen Surveillance and Reporting...........305
6.1. PulseNet............................................305
6.2. Exposure Investigation System.......................307
6.3. Data Integration for Alberta Laboratories Tool......309
7. Geographic Informations Systems.........................310
8. Whole-Genome Sequencing.................................312
9. Discussion..............................................313
Acknowledgements.........................................314
References...............................................314
CHAPTER 9 Molecular Strain Typing and Characterisation
of Toxigenic Clostridium difficile.......................329
Tanis C. Dingle, Duncan R. MacCannell
1. Introduction............................................329
2. Methods for Molecular Strain Typing.....................330
2.1. Restriction Fragment Methods........................330
2.2. PCR Amplification Methods...........................333
X
Contents
2.3. Sequence-Based Methods.............................337
2.4. Genomic and Metagenomic Applications...............341
3. Comparison of Molecular Typing Methods..................341
4. Impact and Applications of Molecular Strain Typing.....344
5. Standardisation Efforts................................346
6. Future Directions......................................347
Conclusion.............................................348
References..............................................348
CHAPTER 10 Accurate Whole-Genome Sequencing-Based
Epidemiological Surveillance of Mycobacterium
tuberculosis............................................359
Hannes Pouseele, Philip Supply
1. Introduction............................................359
1.1. The Need for Powerful, Standardised
Molecular-Guided TB Epidemiological Surveillance...359
1.2. Constraints Imposed by Biological Specificities
of the Pathogen.....................................361
2. Classical Molecular Typing for Molecular-Guided
Investigation...........................................361
2.1. IS6110 RFLP........................................361
2.2. Spoligotyping......................................362
2.3. MIRU-VNTR Typing...................................364
2.4. Epidemiological Inferences Based on Classical Typing ...366
3. Whole-Genome-Based Typing for Molecular-Guided
Investigation...........................................368
3.1. DNA Extraction, and Fragmentation and Construction
of DNA Libraries....................................369
3.2. Massive Parallel Sequencing........................370
3.3. Analysis of Sequencing Results.....................371
3.4. Alternative Analysis Methods.......................380
3.5. Epidemiological Inferences Based on WGS..383
Concluding Remarks......................................386
Acknowledgements........................................386
References..............................................386
CHAPTER 11 Solid and Suspension Microarrays for Microbial
Diagnostics.............................................395
Steve Miller, Ulas Karaoz, Eoin Brodie, Sherry Dunbar
1. Introduction............................................395
2. Solid-State Microarrays.................................397
2.1. Printed Microarrays................................397
Contents
XI
2.2. In S/ta-Synthesised Microarrays........................398
2.3. Electronic Microarrays.................................403
3. Suspension Bead Arrays.....................................404
3.1. Direct Hybridisation...................................404
3.2. Competitive Hybridisation..............................407
3.3. Enzymatic Chemistries with Universal Capture Probes....407
4. Clinical Applications of Microarray Testing................407
4.1. Pathogen Detection.....................................408
4.2. Pathogen Genotyping....................................414
4.3. Antimicrobial Resistance Gene Detection................415
Conclusions.................................................418
References..................................................418
CHAPTER 12 Gene Amplification and Sequencing for Bacterial
Identification..............................................433
Susanna K.P. Lau, Jade L.L. Teng, Chi-Chun Ho,
Patrick C.Y. Woo
1. Importance of Accurate Identification of Bacteria...........433
2. Evolution of Bacterial Identification Methods..............434
2.1. Traditional Phenotypic Methods.........................434
2.2. Gas Chromatography~~Mass Spectrometry..................434
2.3. Gene Sequencing........................................434
2.4. Matrix-Assisted Laser Desorption lonisation-
Time-of-Flight Mass Spectrometry.......................435
3. 16S rRNA Gene Sequencing...................................435
3.1. 16S rRNA Gene Sequencing for Identification
of Bacterial Isolates..................................436
3.2. 16S rRNA Gene Sequencing for Direct Detection
of Bacteria from Clinical Specimens.................. 440
3.3. 16S rRNA Gene Sequencing for Bacterial Discovery......441
3.4. Performing 16S rRNA Gene Sequencing and Analysis ....441
3.5. Databases for Bacterial Identification.................442
4. Sequencing of Other Gene Targets for Bacterial
Identification..............................................442
5. Bacterial Identification by Multilocus and Genome
Sequence Analysis...........................................443
6. Comparison of Gene Sequencing and MALDI-TOE MS
for Bacterial Identification.............................. 444
7. Identification by Species-Specific Gene Amplification......445
Conclusion.............................................. 450
References..................................................450
xii Contents
CHAPTER 13 Host-Based Diagnostics for Detection and
Prognosis of Infectious Diseases.......................465
William E. Yang, Christopher W. Woods,
Ephraim L. Tsalik
1. Introduction..........................................465
2. Techniques and Markers................................466
2.1. Transcriptomics...................................466
2.2. Proteomics and Metabolomics.......................470
2.3. Synthesising and Interpreting Big Data............477
3. Diseases..............................................479
3.1. Diagnostic Approach...............................479
3.2. Bacterial Pathogens...............................480
3.3. Viral Pathogens...................................483
3.4. Fungal Pathogens..................................487
3.5. Parasitic Pathogens...............................489
Conclusions............................................490
References.............................................491
CHAPTER 14 MALDI-TOF Mass Spectrometry in the Clinical
Microbiology Laboratory; Beyond Identification........501
Soren Schubert, Markus Kostrzewa
1- MALDI-TOF MS for Microbial Strain Typing and
Epidemiology...........................................501
1.1. Introduction......................................501
1.2. Strain Typing of Gram-Positive Bacteria Using
MALDI-TOF MS......................................504
1.3. Strain Typing of Gram-Negative Bacteria Using
MALDI-TOF MS......................................506
1.4. Strain Typing of Fungi Using MALDI-TOF MS.........508
2. Resistance Testing by MALDI-TOF MS....................508
2.1. Introduction......................................508
2.2. MALDI-TOF Typing for Resistance Detection.........509
2.3. Mass Profile Changes Induced by Antibiotic
Drugs.............................................511
2.4. Detection of Drug Resistance Mechanisms:
The Beta-Lactamase Assay..........................512
2.5. Stable Isotope-Based Resistance Detection.........515
2.6. Growth Monitoring by MALDf-TOF-MS.................516
Concluding Remarks.....................................518
References.............................................518
Contents
CHAPTER 15 Next-Generation Sequencing for Pathogen
Detection and Identification..............................525
Kenneth G. Frey, Kimberly A. Bishop-Lilly
1. Introduction to Next-Generation Sequencing...............525
2. Metagenomic Sequencing...................................528
3. NGS for Research Diagnostic Applications.................530
3.1. Advantages of NGS for Infectious Disease
Diagnostics..........................................530
3.2. Disadvantages of NGS for Microbial Diagnostics.......534
4. Challenges Going Forth and Successful Implementation.....539
4.1. Discussion: Limitations and Common
Misconceptions.......................................542
4.2. When NGS Adds Value..................................543
4.3. Where Future Efforts Should Focus....................545
References................................................546
CHAPTER 16 Virology: The Next Generation from Digital
PCR to Single Virion Genomics.............................555
Richard Allen White III, Jessica N. Brazelton de Cardenas,
Randall T. Hayden
1. Introduction.............................................555
2. Digital PCR..............................................556
3. Viral Load Testing.......................................560
4. Single Virion Genomics...................................561
Conclusions...............................................562
References................................................562
CHAPTER 17 Artificial Nucleic Acid Probes and Their
Applications in Clinical Microbiology.....................569
Alon Singer, Yi-Wei Tang
1. Introduction........................................... 569
2. Artificial Nucleic Acids: The Unmet Need Drives
Innovation................................................570
3. The Many Flavours of Artificial Nucleic Acids;
Different Structures, Internal Modifications,
and Characteristics.......................................574
4. Artificial NAs in Use: Versatile, Flexible,
and Outperforming DNA/RNA............................... 578
4.1. Microarrays..........................................578
4.2. In Situ Hybridisation................................580
Contents
4.3. PCR.................................................582
4.4. Novel Approaches....................................585
5. Artificial Probes and Diagnostic Clinical Microbiology..587
Conclusion...............................................589
References...............................................590
Index...................................................................597
|
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author2 | Sails, Andrew Tang, Yi-Wei |
author2_role | edt edt |
author2_variant | a s as y w t ywt |
author_GND | (DE-588)1080545220 (DE-588)173852300 |
author_facet | Sails, Andrew Tang, Yi-Wei |
building | Verbundindex |
bvnumber | BV043279034 |
classification_rvk | WC 5700 XD 1611 |
ctrlnum | (OCoLC)932422806 (DE-599)GBV844207950 |
discipline | Biologie Medizin |
edition | First edition |
format | Book |
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illustrated | Illustrated |
indexdate | 2024-07-10T07:22:07Z |
institution | BVB |
isbn | 9780128032978 |
language | English |
oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-028700475 |
oclc_num | 932422806 |
open_access_boolean | |
owner | DE-19 DE-BY-UBM DE-355 DE-BY-UBR |
owner_facet | DE-19 DE-BY-UBM DE-355 DE-BY-UBR |
physical | xix, 613, [24] Seiten Illustrationen 24 cm |
publishDate | 2015 |
publishDateSearch | 2015 |
publishDateSort | 2015 |
publisher | Elsevier, AP |
record_format | marc |
series | Methods in microbiology |
series2 | Methods in microbiology |
spelling | Current and emerging technologies for the diagnosis of microbial infections edited by Andrew Sails (Public Health England Newcastle Laboratory, National Infection Service, The Medical Scool, Royal Victory Infirmary, Newcastle, UK), Yi-Wei Tang (Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, and Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, USA) First edition Amsterdam ; Boston ; Heidelberg ; London ; New York ; Oxford ; Paris ; San Diego ; San Francisco ; Singapore ; Sydney ; Tokyo Elsevier, AP 2015 xix, 613, [24] Seiten Illustrationen 24 cm txt rdacontent n rdamedia nc rdacarrier Methods in microbiology volume 42 Literaturangaben Infektionskrankheit (DE-588)4026879-2 gnd rswk-swf Diagnose (DE-588)4012040-5 gnd rswk-swf Methode (DE-588)4038971-6 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Infektionskrankheit (DE-588)4026879-2 s Diagnose (DE-588)4012040-5 s Methode (DE-588)4038971-6 s b DE-604 Sails, Andrew (DE-588)1080545220 edt Tang, Yi-Wei (DE-588)173852300 edt Methods in microbiology volume 42 (DE-604)BV000899780 42 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028700475&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
spellingShingle | Current and emerging technologies for the diagnosis of microbial infections Methods in microbiology Infektionskrankheit (DE-588)4026879-2 gnd Diagnose (DE-588)4012040-5 gnd Methode (DE-588)4038971-6 gnd |
subject_GND | (DE-588)4026879-2 (DE-588)4012040-5 (DE-588)4038971-6 (DE-588)4143413-4 |
title | Current and emerging technologies for the diagnosis of microbial infections |
title_auth | Current and emerging technologies for the diagnosis of microbial infections |
title_exact_search | Current and emerging technologies for the diagnosis of microbial infections |
title_full | Current and emerging technologies for the diagnosis of microbial infections edited by Andrew Sails (Public Health England Newcastle Laboratory, National Infection Service, The Medical Scool, Royal Victory Infirmary, Newcastle, UK), Yi-Wei Tang (Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, and Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, USA) |
title_fullStr | Current and emerging technologies for the diagnosis of microbial infections edited by Andrew Sails (Public Health England Newcastle Laboratory, National Infection Service, The Medical Scool, Royal Victory Infirmary, Newcastle, UK), Yi-Wei Tang (Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, and Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, USA) |
title_full_unstemmed | Current and emerging technologies for the diagnosis of microbial infections edited by Andrew Sails (Public Health England Newcastle Laboratory, National Infection Service, The Medical Scool, Royal Victory Infirmary, Newcastle, UK), Yi-Wei Tang (Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, and Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, USA) |
title_short | Current and emerging technologies for the diagnosis of microbial infections |
title_sort | current and emerging technologies for the diagnosis of microbial infections |
topic | Infektionskrankheit (DE-588)4026879-2 gnd Diagnose (DE-588)4012040-5 gnd Methode (DE-588)4038971-6 gnd |
topic_facet | Infektionskrankheit Diagnose Methode Aufsatzsammlung |
url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028700475&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
volume_link | (DE-604)BV000899780 |
work_keys_str_mv | AT sailsandrew currentandemergingtechnologiesforthediagnosisofmicrobialinfections AT tangyiwei currentandemergingtechnologiesforthediagnosisofmicrobialinfections |