Details

Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry


Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry

Industrial and Environmental Applications
1. Aufl.

von: Haroun N. Shah, Saheer E. Gharbia, Ajit J. Shah, Erika Y. Tranfield, K. Clive Thompson

142,99 €

Verlag: Wiley
Format: EPUB
Veröffentl.: 29.03.2023
ISBN/EAN: 9781119814078
Sprache: englisch
Anzahl Seiten: 560

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Beschreibungen

<b>Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry</b> <p><b>Detailed resource presenting the capabilities of MALDI mass spectrometry (MS) to industrially and environmentally significant areas in the biosciences</b> <p><i>Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry </i>fulfills a need to bring the key analytical technique of MALDI mass spectrometric analysis into routine practice by specialists and non-specialists, and technicians. It informs and educates established researchers on the development of techniques as applied to industrially significant areas within the biosciences. Throughout the text, the reader is presented with recognized and emerging techniques of this powerful and continually advancing field of analytical science to key areas of importance. <p>While many scientific papers are reporting new applications of MS-based analysis in specific foci, this book is unique in that it draws together an incredibly diverse range of applications that are pushing the boundaries of MS across the broad field of biosciences. <p>Contributed to by recognized experts in the field of MALDI MS who have been key players in promoting the advancement and dissemination of authoritative information in this field, <i>Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry </i>covers sample topics such as: <ul><li> Oil microbiology, marine and freshwater ecosystems, agricultural and food microbiology, and industrial waste microbiology</li> <li> Bioremediation and landfill sites microbiology, microbiology of inhospitable sites (e.g. Arctic and Antarctic, and alkaline and acidic sites, and hot temperatures)</li> <li> Veterinary, poultry and animals, viral applications of MS, and antibiotic resistance using tandem MS methods</li> <li> Recent developments which are set to transform the use of MS from its success in clinical microbiology to a wide range of commercial and environmental uses</li></ul> <p>Bridging the gap between measurement and key applications, this text is an ideal resource for industrial and environmental analytical scientists, including technologists in the food industry, pharmaceuticals, and agriculture, as well as biomedical scientists, researchers, clinicians and academics and scientists in bio-resource centers.
<p>List of Contributors xix</p> <p>Preface xxiii</p> <p><b>1 Progress in the Microbiological Applications of Mass Spectrometry: from Electron Impact to Soft Ionization Techniques, MALDI- TOF MS and Beyond 1<br /> </b><i>Emmanuel Raptakis, Ajit J. Shah, Saheer E. Gharbia, Laila M.N. Shah, Simona Francese, Erika Y. Tranfield, Louise Duncan, and Haroun N. Shah</i></p> <p>1.1 Introduction 1</p> <p>1.1.1 Algorithms Based upon Traditional Carbohydrate Fermentation Tests 1</p> <p>1.1.2 Dynamic Changes in the Chemotaxonomic Era (c. 1970–1985) through the Lens of the Genus Bacteroides 2</p> <p>1.1.3 Microbial Lipids as Diagnostic Biomarkers; Resurgence of Interest in MALDI- TOF MS with Advances in Lipidomics 3</p> <p>1.2 The Dawn of MALDI- TOF MS: Establishing Proof of Concept for Diagnostic Microbiology 7</p> <p>1.2.1 Development of a MALDI- TOF MS Database for Human Infectious Diseases 10</p> <p>1.2.2 The Dilemma with Clostridium difficile: from Intact Cells to Intracellular Proteins, MALDI- TOF MS Enters a New Phase 13</p> <p>1.3 Linear/Reflectron MALDI- TOF MS to Tandem Mass Spectrometry 15</p> <p>1.3.1 Tandem MALDI- TOF Mass Spectrometry 17</p> <p>1.3.2 Electrospray- based Mass Analysers 18</p> <p>1.3.3 Tandem Mass Spectrometry 18</p> <p>1.3.4 Mass Spectrometry- based Proteomics 19</p> <p>1.3.5 Case Study: LC- MS/MS of Biothreat Agents, Proteomes of Pathogens and Strain- level Tying Using Bottom- up and Top- down Proteomics 19</p> <p>1.3.6 Discovery Proteomics 21</p> <p>1.3.7 Targeted Proteomics 22</p> <p>1.3.8 Top- down Proteomics 23</p> <p>1.3.9 Targeted Protein Quantitation 24</p> <p>1.4 The Application of MALDI- MS Profiling and Imaging in Microbial Forensics: Perspectives 25</p> <p>1.4.1 MALDI- MSP of Microorganisms and their Products 26</p> <p>1.5 Hydrogen/Deuterium Exchange Mass Spectrometry in Microbiology 27</p> <p>1.6 The Omnitrap, a Novel MS Instrument that Combines Many Applications of Mass Spectrometry 29</p> <p>References 35</p> <p><b>2 Machine Learning in Analysis of Complex Flora Using Mass Spectrometry 45<br /> </b><i>Luis Mancera, Manuel J. Arroyo, Gema Méndez, Omar Belgacem, Belén Rodríguez-Sánchez, and Marina Oviaño</i></p> <p>2.1 Introduction 45</p> <p>2.2 An Improved MALDI- TOF MS Data Analysis Pipeline for the Identification of Carbapenemase- producing Klebsiella pneumoniae 47</p> <p>2.2.1 Motivation 47</p> <p>2.2.2 Materials and Methods 47</p> <p>2.2.3 Spectra Acquisition 50</p> <p>2.2.4 Results 51</p> <p>2.2.5 Discussion 54</p> <p>2.3 Detection of Vancomycin- Resistant Enterococcus faecium 55</p> <p>2.3.1 Motivation 55</p> <p>2.3.2 Materials and Methods 56</p> <p>2.3.3 Results and Discussion 59</p> <p>2.4 Detection of Azole Resistance in Aspergillus fumigatus Complex Isolates 59</p> <p>2.4.1 Introduction 59</p> <p>2.4.2 Material and Methods 60</p> <p>2.4.3 Results 60</p> <p>2.4.4 Discussion 64</p> <p>2.5 Peak Analysis for Discrimination of Cryptococcus neoformans Species Complex and their Interspecies Hybrids 64</p> <p>2.5.1 Motivation 64</p> <p>2.5.2 Material and Methods 65</p> <p>2.5.3 Results and Discussion 65</p> <p>2.6 Conclusions 66</p> <p>References 67</p> <p><b>3 Top- down Identification of Shiga Toxin (and Other Virulence Factors and Biomarkers) from Pathogenic E. coli using MALDI- TOF/TOF Tandem Mass Spectrometry 71<br /> </b><i>Clifton K. Fagerquist</i></p> <p>3.1 Introduction 71</p> <p>3.2 Decay of Metastable Peptide and Protein Ions by the Aspartic Acid Effect 72</p> <p>3.3 Energy Deposition during Desorption/Ionization by MALDI 75</p> <p>3.4 Protein Denaturation and Fragmentation Efficiency of PSD 76</p> <p>3.5 Arginine and its Effect on Fragment Ion Detection and MS/MS Spectral Complexity 79</p> <p>3.6 Inducing Gene Expression in Wild- type Bacteria for Identification by Top- Down Proteomic Analysis 82</p> <p>3.7 Top- down Proteomic Identification of B- Subunit of Shiga Toxin from STEC Strains 83</p> <p>3.8 Furin- digested Shiga Toxin and Middle- down Proteomics 85</p> <p>3.9 Top- down Identification of an Immunity Cognate of a Bactericidal Protein Produced from a STEC Strain 87</p> <p>3.10 Lc- Maldi- Tof/tof 88</p> <p>3.11 Conclusions 89</p> <p>References 94</p> <p><b>4 Liquid Atmospheric Pressure (LAP) – MALDI MS(/MS) Biomolecular Profiling for Large- scale Detection of Animal Disease and Food Adulteration and Bacterial Identification 97<br /> </b><i>Cristian Piras and Rainer Cramer</i></p> <p>4.1 Introduction 97</p> <p>4.2 Background to LAP- MALDI MS 98</p> <p>4.3 Bacterial Identification by LAP- MALDI MS 102</p> <p>4.4 Food Adulteration and Milk Quality Analysis by LAP- MALDI MS 105</p> <p>4.5 Animal Disease Detection by LAP- MALDI MS 108</p> <p>4.6 Antibiotic Resistance Detection of Microbial Consortia by Lap- Maldi Ms 110</p> <p>4.7 Future Directions for LAP- MALDI MS Applications 113</p> <p>References 114</p> <p><b>5 Development of a MALDI- TOF Mass Spectrometry Test for Viruses 117<br /> </b><i>Ray K. Iles, Jason K. Iles, and Raminta Zmuidinaite</i></p> <p>5.1 Introduction 117</p> <p>5.2 Understanding the Systems Biology of the Virus and Viral Infections 120</p> <p>5.3 Understanding the Nature of Viral Proteins and Molecular Biology 121</p> <p>5.4 Virion Protein Solubilization and Extraction 123</p> <p>5.5 Sampling and Virion Enrichment 123</p> <p>5.6 Peak Identification: Quantification and Bioinformatics 125</p> <p>5.7 Promise and Pitfalls of Machine Learning Bioinformatics 126</p> <p>5.8 Accelerating MALDI- TOF Assay Protocol Development Using Pseudotypes/ pseudoviruses 128</p> <p>5.9 Understanding the Operational Parameters of your MALDI- TOF MS 130</p> <p>5.10 Understanding the Operational Requirements of the Clinical Testing Laboratory: Validation and International Accreditation 131</p> <p>5.10.1 Limitation and Advantages of CLIA LDTs 131</p> <p>5.11 MALDI- TOF MS Screening Test for SARS- CoV- 2s 132</p> <p>5.11.1 Prepare Positive Control 132</p> <p>5.11.2 Prepare Gargle- saliva Samples 132</p> <p>5.11.3 Viral Particle Enrichment 132</p> <p>5.11.4 Dissolution of Virions and Solubilization of Viral Proteins 133</p> <p>5.11.5 Maldi- Tof Ms 133</p> <p>5.12 CLIA LDT Validation of a MALDI- TOF MS Test for SARS- CoV- 2 133</p> <p>5.12.1 Limit of Detection 134</p> <p>5.12.2 Interfering Substances and Specificity 134</p> <p>5.12.3 Clinical Performance Evaluation 136</p> <p>5.12.3.1 Establishing Operational Cut- off Values 137</p> <p>5.12.3.2 Direct comparison with an RT- PCR SARS- CoV- 2 test 138</p> <p>5.12.3.3 Internal Sampling Quality Control 138</p> <p>5.12.3.4 Daily System Quality Control 138</p> <p>5.12.4 Reproducibility 139</p> <p>5.12.5 Stability 139</p> <p>5.12.6 Validation Disposition 141</p> <p>5.12.6.1 Global Biosecurity 141</p> <p>References 142</p> <p><b>6 A MALDI- TOF MS Proteotyping Approach for Environmental, Agricultural and Food Microbiology 147<br /> </b><i>Hiroto Tamura</i></p> <p>6.1 Introduction 147</p> <p>6.2 Serotyping of Salmonella enterica Subspecies enterica 151</p> <p>6.3 Discrimination of the Lineages of Listeria monocytogenes and Species of</p> <p>Listeria 161</p> <p>6.4 Discrimination of the Bacillus cereus Group and Identification of Cereulide 167</p> <p>6.5 Identification of Alkylphenol Polyethoxylate- degrading Bacteria in the Environment 171</p> <p>6.6 Conclusions and Future Perspectives 173</p> <p>References 175</p> <p><b>7 Diversity, Transmission and Selective Pressure on the Proteome of Pseudomonas aeruginosa 183<br /> </b><i>Louise Duncan, Ajit J. Shah, Malcolm Ward, Radhey S. Gupta, Bashudev Rudra, Alvin Han, Ken Bruce, and Haroun N. Shah</i></p> <p>7.1 Introduction: Diversity 183</p> <p>7.1.1 P. aeruginosa: from ‘Atypical’ to Diverse 183</p> <p>7.1.2 Phenotypical Diversity in Isolates from Different Environments 183</p> <p>7.1.2.1 Clinical Isolates 183</p> <p>7.1.2.2 Environmental Isolates 184</p> <p>7.1.2.3 Veterinary Isolates 184</p> <p>7.1.2.4 Comparing P. aeruginosa Phenotypical Profiles from Different Environments 184</p> <p>7.1.2.5 Antibiotic Resistance in P. aeruginosa from Different Environments 186</p> <p>7.1.3 The Relationship Between Phenotypical and Proteomic Diversity 186</p> <p>7.1.4 Techniques and Practical Considerations for Studying Proteomic Diversity 186</p> <p>7.1.5 Proteomic Diversity and MS Applications 189</p> <p>7.2 Transmission 189</p> <p>7.2.1 The History of P. aeruginosa Transmission 189</p> <p>7.2.2 Proteomics and P. aeruginosa Transmission 191</p> <p>7.2.3 The Impact of Proteomic Diversity on Transmission 191</p> <p>7.3 Selective Pressures on the Proteome 192</p> <p>7.3.1 Tandem MS Systems for Studying Selected Proteomes 192</p> <p>7.3.2 Microenvironment Selection 192</p> <p>7.3.2.1 The Human Body and CF Lung 192</p> <p>7.3.2.2 The Natural Environment 192</p> <p>7.3.3 Antimicrobial Selection 193</p> <p>7.4 Conclusions on Studies of the Proteome 193</p> <p>7.5 Genomic Studies on Pseudomonas aeruginosa Strains Revealing the Presence of Two Distinct Clades 195</p> <p>7.5.1 Phylogenomic Analysis Reveals the Presence of Two Distinct Clades Within</p> <p>P. aeruginosa 196</p> <p>7.5.2 Identification of Molecular Markers Distinguishing the Two P. aeruginosa</p> <p>Clades 198</p> <p>7.6 Final Conclusions 201</p> <p>References 201</p> <p><b>8 Characterization of Biodegradable Polymers by MALDI- TOF MS 211<br /> </b><i>Hiroaki Sato</i></p> <p>8.1 Introduction 211</p> <p>8.2 Structural Characterization of Poly(ε- caprolactone) Using Maldi- Tof Ms 212</p> <p>8.3 Biodegradation Profiles of a Terminal- modified PCL Observed by Maldi- Tof Ms 216</p> <p>8.4 Bacterial Biodegradation Mechanisms of Non- ionic Surfactants 218</p> <p>8.5 Advanced Molecular Characterization by High- resolution MALDI- TOF MS Combined with KMD Analysis 221</p> <p>8.6 Structural Characterization of High- molecular- weight Biocopolyesters by High- resolution MALDI- TOF MS Combined with KMD Analysis 225</p> <p>References 228</p> <p><b>9 Phytoconstituents and Antimicrobiological Activity 231<br /> </b><i>Philip L. Poole and Giulia T.M. Getti</i></p> <p>9.1 Introduction to Phytochemicals 231</p> <p>9.2 An Application to Bacteriology 233</p> <p>9.2.1 Allicin Leads to a Breakdown of the Cell Wall of Staphylococcus aureus 234</p> <p>9.3 Applications to Parasitology 239</p> <p>9.3.1 Drug Discovery 239</p> <p>9.3.2 Parasite Characterization 240</p> <p>9.4 A Proteomic Approach: Leishmania Invasion of Macrophages 240</p> <p>9.5 Intracellular Leishmania Amastigote Spreading between Macrophages 243</p> <p>9.6 Potential Virus Applications 244</p> <p>Acknowledgements 246</p> <p>References 246</p> <p><b>10 Application of MALDI- TOF MS in Bioremediation and Environmental Research 255<br /> </b><i>Cristina Russo and Diane Purchase</i></p> <p>10.1 Introduction 255</p> <p>10.2 Microbial Identification: Molecular Methods and MALDI- TOF MS 257</p> <p>10.2.1 PCR- based Methods 258</p> <p>10.2.2 Maldi- Tof Ms 260</p> <p>10.3 Combination of MALDI- TOF MS with Other Methods for the Identification of Microorganisms 261</p> <p>10.4 Application of MALDI- TOF MS in Environmental and Bioremediation Studies 263</p> <p>10.4.1 The Atmospheric Environment 263</p> <p>10.4.2 The Aquatic Environment 263</p> <p>10.4.3 The Terrestrial Environment 265</p> <p>10.4.4 Bioremediation Research Applications 266</p> <p>10.5 Microbial Products and Metabolite Activity 268</p> <p>10.6 Challenges of Environmental Applications 270</p> <p>10.7 Opportunities and Future Outlook 271</p> <p>10.8 Conclusions 272</p> <p>References 273</p> <p><b>11 From Genomics to MALDI- TOF MS: Diagnostic Identification and Typing of Bacteria in Veterinary Clinical Laboratories 283<br /> </b><i>John Dustin Loy and Michael L. Clawson</i></p> <p>11.1 Introduction 283</p> <p>11.2 Genomics 284</p> <p>11.3 Defining Bacterial Species Through Genomics 286</p> <p>11.4 Maldi- Tof Ms 287</p> <p>11.5 Combining Genomics with MALDI- TOF MS to Classify Bacteria at the Subspecies Level 290</p> <p>11.6 Data Exploration with MALDI- TOF MS 292</p> <p>11.7 Validation of Typing Strategies 294</p> <p>11.8 Future Directions 294</p> <p>References 295</p> <p><b>12 MALDI- TOF MS Analysis for Identification of Veterinary Pathogens from Companion Animals and Livestock Species 303<br /> </b><i>Dorina Timofte, Gudrun Overesch, and Joachim Spergser</i></p> <p>12.1 Veterinary Diagnostic Laboratories and the MALDI- TOF Clinical Microbiology Revolution 303</p> <p>12.1.1 MALDI- TOF MS: Reshaping the Workflow in Clinical Microbiology 304</p> <p>12.1.2 Identification of Bacterial Pathogens Directly from Clinical Specimens 305</p> <p>12.1.3 Prediction of Antimicrobial Resistance 307</p> <p>12.1.4 Impact in Veterinary Hospital Biosecurity and Epidemiological Surveillance 308</p> <p>12.2 Identification of Campylobacter spp. and Salmonella spp. in Routine Clinical Microbiology Laboratories 309</p> <p>12.2.1 General Aspects on the Importance of Species/Subspecies and Serovar Identification of Campylobacter spp. and Salmonella spp. 309</p> <p>12.2.2 General Aspects on Influence of Media/Culture Environment on Bacterial Species Identification by MALDI- TOF MS 311</p> <p>12.2.3 Possibilities and Limits of Identification of Campylobacter spp. by Maldi- Tof Ms 312</p> <p>12.2.3.1 Thermophilic Campylobacter spp. 312</p> <p>12.2.3.2 Human- hosted Campylobacter Species 313</p> <p>12.2.3.3 Campylobacter spp. of Veterinary Importance 313</p> <p>12.2.4 Possibilities and Limits of Identification of Salmonella spp. by Maldi- Tof Ms 314</p> <p>12.3 Identification and Differentiation of Mycoplasmas Isolated from Animals 316</p> <p>12.3.1 Animal Mycoplasmas at a Glance 316</p> <p>12.3.2 Laboratory Diagnosis of Animal Mycoplasmas 317</p> <p>12.3.3 MALDI- TOF MS for the Identification of Animal Mycoplasmas 318</p> <p>References 322</p> <p><b>13 MALDI- TOF MS: from Microbiology to Drug Discovery 333<br /> </b><i>Ruth Walker, Maria E. Dueñas, Alan Ward, and Kaveh Emami</i></p> <p>13.1 Introduction 333</p> <p>13.2 Microbial Fingerprinting 334</p> <p>13.2.1 Environmental 335</p> <p>13.2.1.1 Actinobacteria 335</p> <p>13.2.1.2 Aquatic Microorganisms 335</p> <p>13.2.2 Terrestrial Microbiology 337</p> <p>13.2.3 Food and Food Safety 338</p> <p>13.2.3.1 Food Storage Effect on Identification 338</p> <p>13.2.3.2 Insects 339</p> <p>13.3 Mammalian Cell Fingerprinting 339</p> <p>13.3.1 Differentiation of Cell Lines and Response to Stimuli 339</p> <p>13.3.2 Cancer Diagnostics 341</p> <p>13.3.3 Biomarkers 342</p> <p>13.4 Drug Discovery Using MALDI- TOF 342</p> <p>13.4.1 Enzymatic Assays 343</p> <p>13.4.1.1 Targeting Antibiotic Resistance Using MALDI- TOF MS Enzymatic Assays 343</p> <p>13.4.2 Cellular- based Assays for Drug Discovery 344</p> <p>13.4.3 Automation in Drug Discovery 345</p> <p>13.4.4 Assay Multiplexing 345</p> <p>13.4.5 MS Imaging in Drug Discovery 346</p> <p>13.4.6 Maldi- 2 346</p> <p>13.5 Limitations/Challenges, Future Outlook, and Conclusions 347</p> <p>13.5.1 Sample Preparation Limitations 347</p> <p>13.5.1.1 Matrix 347</p> <p>13.5.1.2 Interference from Low- molecular- mass Matrix Clusters 348</p> <p>13.5.1.3 Buffer Compatibility 348</p> <p>13.5.1.4 TOF Mass Resolution Limitations 348</p> <p>13.5.2 Data Analysis and Application of Machine Learning 348</p> <p>13.6 Future Outlook/Conclusions 349</p> <p>References 350</p> <p><b>14 Rapid Pathogen Identification in a Routine Food Laboratory Using High- throughput MALDI- TOF Mass Spectrometry 359<br /> </b><i>Andrew Tomlin</i></p> <p>14.1 Introduction 359</p> <p>14.2 MALDI- TOF MS in Food Microbiology 359</p> <p>14.3 Review of Existing Confirmation Techniques and Comparison to Maldi- Tof Ms 362</p> <p>14.4 Strain Typing Using MALDI- TOF MS 364</p> <p>14.5 Verification Trial 365</p> <p>14.6 Limitations of MALDI- TOF MS Strain Typing and Future Studies 369</p> <p>14.7 Listeria Detection by MALDI- TOF MS 370</p> <p>14.8 Trial Sample Preparation Procedure 370</p> <p>14.9 Initial Trial 374</p> <p>14.10 Limit of Detection Trial 375</p> <p>14.11 Method Optimization, Further Prospects, and Conclusions 376</p> <p>References 379</p> <p><b>15 Detection of Lipids in the MALDI Negative Ion Mode for Diagnostics, Food Quality Control, and Antimicrobial Resistance 381<br /> </b><i>Yi Liu, Jade Pizzato, and Gerald Larrouy-Maumus</i></p> <p>15.1 Introduction 381</p> <p>15.2 Applications of Lipids in Clinical Microbiology Diagnostics 382</p> <p>15.2.1 Use of Cell Envelope Lipids for Bacterial Identification 382</p> <p>15.2.2 Detection of Cell Envelope Lipids and their Modifications to Determine Bacterial Drug Susceptibility 384</p> <p>15.2.3 Detection of Lipids in MALDI Negative Ion Mode for Fungal Identification 387</p> <p>15.2.4 Detection of Lipids in MALDI Negative Ion Mode for Parasite Identification 387</p> <p>15.2.5 Detection of Lipids in MALDI Negative Ion Mode for Virus Identification 388</p> <p>15.3 Applications of the Detection of Lipids in Negative Ion Mode MALDI- MS in Cancer Studies 388</p> <p>15.3.1 Lipids and MALDI Negative Ion Mode for Diagnosis of Lung Cancer 389</p> <p>15.3.2 Lipids and MALDI Negative Ion Mode for the Diagnosis of Breast Cancer 390</p> <p>15.3.3 Lipids and MALDI Negative Ion Mode for Diagnosis of Other Cancers 391</p> <p>15.3.4 Lipids and MALDI Negative Ion Mode for Drug–Cell Interactions and Prognosis 392</p> <p>15.4 Applications of the Detection of Lipids and MALDI- MS in Alzheimer’s Disease Studies 392</p> <p>15.5 Applications of MALDI in Negative Ion Mode and the Detection of Lipids in Toxicology 393</p> <p>15.6 Lipids and MALDI Negative Ion Mode for Food Fraud Detection 394</p> <p>15.7 Conclusions and Future Development of Lipids and their Detection in MALDI in Negative Ion Mode 395</p> <p>Acknowledgments 395</p> <p>References 397</p> <p><b>16 Use of MALDI- TOF MS in Water Testing Laboratories 405<br /> </b><i>Matthew Jones, Nadia Darwich, Rachel Chalmers, K. Clive Thompson, and Bjorn Nielsen</i></p> <p>16.1 Introduction 405</p> <p>16.2 Application in a Drinking Water Laboratory 408</p> <p>16.2.1 Introduction 408</p> <p>16.2.2 Method Validation 409</p> <p>16.2.2.1 Reference Database Validation 410</p> <p>16.2.2.2 Method Comparison 411</p> <p>16.2.2.3 Agar Assessment 412</p> <p>16.2.3 Application Within Drinking Water Laboratory 412</p> <p>16.3 Application in Water Hygiene and Environmental Laboratory Testing 413</p> <p>16.3.1 Introduction 413</p> <p>16.3.2 Legionella Testing 414</p> <p>16.3.3 Wastewater and Sewage Sludge Microbiology 415</p> <p>16.3.4 Healthcare Water Testing 416</p> <p>16.3.5 Investigative Analysis 417</p> <p>16.3.6 Method Validation 417</p> <p>16.3.6.1 Characterization of Intended Use 417</p> <p>16.3.6.2 Library Assessment 418</p> <p>16.3.6.3 Assessment of Variables 418</p> <p>16.3.6.4 Comparison Assessment 419</p> <p>16.3.6.5 Ongoing Verification 420</p> <p>16.3.7 Conclusion on Suitability for Use in an Environmental Testing Laboratory 422</p> <p>16.4 Potential Application for Cryptosporidium Identification 423</p> <p>References 425</p> <p><b>17 A New MALDI- TOF Database Based on MS Profiles of Isolates in Icelandic Seawaters for Rapid Identification of Marine Strains 431<br /> </b><i>Sibylle Lebert, Viggó Þór Marteinsson, and Pauline Vannier</i></p> <p>17.1 Introduction 431</p> <p>17.2 Selection and Cultivation of the Strains 432</p> <p>17.3 Genotypic Identification 433</p> <p>17.4 MALDI- TOF MS Data Acquisition and Database Creation 438</p> <p>17.5 Verification of the Accuracy of the Home- made Database 441</p> <p>17.6 Conclusions 448</p> <p>Funding 448</p> <p>References 449</p> <p><b>18 MALDI- TOF MS Implementation Strategy for a Pharma Company Based upon a Network Microbial Identification Perspective 453<br /> </b><i>Lynn Johnson, Christoph Hansy, and Hilary Chan</i></p> <p>18.1 Introduction 453</p> <p>18.1.1 Microbial Identifications from a Pharmaceutical Industry Perspective 453</p> <p>18.1.2 Historical Evolution 453</p> <p>18.2 Regulatory Requirements/Guidance for Microbial Identification 455</p> <p>18.3 Strategic Approaches to MALDI- TOF Implementation Within the Modern Microbial Methods Framework 455</p> <p>18.3.1 Incorporation of MALDI- TOF into a Technical Evaluation Roadmap 455</p> <p>18.3.2 Initial Implementation Planning Stage 456</p> <p>18.3.2.1 Roles and Responsibilities (Global/Local, Partners/IT, Stakeholders) 456</p> <p>18.3.2.2 Considerations When Selecting a Vendor/Model 457</p> <p>18.3.2.3 Overall Identification Process Flow and MALDI- TOF as the Defined Application 458</p> <p>18.3.2.4 Benefits of an In- house System for Pharmaceutical Companies Compared with Outsourcing 458</p> <p>18.3.2.5 The Center of Excellence (CoE) Approach 460</p> <p>18.3.2.6 Building a Business Case for the MALDI- TOF as a Network Strategy 461</p> <p>18.3.3 Implementation Strategy – From Feasibility Studies to Global Deployment 463</p> <p>18.3.3.1 Pilot Trials/Feasibility 463</p> <p>18.3.3.2 Risk Assessment/Risk- based Validation Approach 463</p> <p>18.3.3.3 Network Validation Approach 464</p> <p>18.4 Conclusions 467</p> <p>18.a Appendix 468</p> <p>References 470</p> <p><b>19 MALDI- TOF MS – Microbial Identification as Part of a Contamination Control Strategy for Regulated Industries 473<br /> </b><i>Christine E. Farrance and Prasanna D. Khot</i></p> <p>19.1 Industry Perspective 473</p> <p>19.1.1 Introduction to Regulated Industries 473</p> <p>19.1.2 Contamination Control Strategy 474</p> <p>19.1.3 Tracking and Trending EM Data 474</p> <p>19.1.4 Drivers for Microbial Identification 476</p> <p>19.1.5 Level of Resolution of an Identification 476</p> <p>19.1.6 Global Harmonization 477</p> <p>19.1.7 Validation Requirements for Regulated Industries 477</p> <p>19.1.8 Summary 478</p> <p>19.2 Technical Perspective 478</p> <p>19.2.1 Identification Technologies 478</p> <p>19.2.2 Phenotypic Systems 479</p> <p>19.2.3 Proteotypic Systems 479</p> <p>19.2.4 Genotypic Systems 479</p> <p>19.2.5 The Importance of the Reference Database 480</p> <p>19.2.6 MALDI- TOF in Regulated Industries 480</p> <p>19.2.7 Outsourcing 480</p> <p>19.2.8 Summary 481</p> <p>19.3 MALDI- TOF MS Microbial Identification Workflow at a High- throughput Laboratory 481</p> <p>19.3.1 MALDI- TOF MS Principles for Microbial Identification 481</p> <p>19.3.2 Organism Cultivation for Microbial Identification with MALDI- TOF MS 482</p> <p>19.3.3 Sample Preparation for Microbial Identification with MALDI- TOF MS 482</p> <p>19.3.4 Sample Processing Workflow for Microbial Identification 482</p> <p>19.3.5 Data Interpretation 483</p> <p>19.3.6 Importance of a Sequence- based Secondary (or Fall- through) Identification System 484</p> <p>19.4 MALDI- TOF MS Library Development and Coverage 485</p> <p>19.4.1 Importance of Library Development Under a Quality System 485</p> <p>19.4.2 Targeted Library Development for Gram- positive Bacteria and Water Organisms 488</p> <p>19.4.2.1 Case Study 1: Impact of MALDI- TOF MS Library Coverage for Organisms of the Family Bacillaceae 488</p> <p>19.4.2.2 Case Study 2: Impact of MALDI- TOF MS Library Coverage for Organisms Recovered from Water Systems 489</p> <p>19.4.3 Supplemental and Custom MALDI- TOF MS Libraries 489</p> <p>19.5 Comparison of MALDI- TOF MS with Other Microbial Identification Methods 490</p> <p>19.6 Future Perspectives 490</p> <p>References 491</p> <p><b>20 Identification of Mold Species and Species Complex from the Food Environment Using MALDI- TOF MS 497<br /> </b><i>Victoria Girard, Valérie Monnin, Nolwenn Rolland, Jérôme Mounier, and Jean-Luc Jany</i></p> <p>20.1 Fungal Taxonomy 497</p> <p>20.1.1 Defining What Is a Fungal Species 497</p> <p>20.1.2 Fungal Speciation within a Food Context 498</p> <p>20.1.3 Delimiting Species 498</p> <p>20.1.4 Foodborne Fungi within the Fungal Tree of Life 499</p> <p>20.2 Impact of Molds in Food 500</p> <p>20.2.1 Filamentous Fungi in Fermented Foods 500</p> <p>20.2.2 Filamentous Fungi with Undesirable Impacts on Food Quality and Safety 500</p> <p>20.3 Identification of Fungi 505</p> <p>20.4 Identification of Foodborne Molds Using MALDI- TOF MS 506</p> <p>20.4.1 Sample Preparation 506</p> <p>20.4.2 Database Building and Performance of MALDI- TOF for Identification of Foodborne Molds 507</p> <p>20.4.2.1 Database Building 507</p> <p>20.4.2.2 Performance of Foodborne Mold Database 508</p> <p>References 509</p> <p>Index 515</p>
<p><b>Haroun N. Shah</b> led the establishment of unique laboratory capabilities, transforming Public Health Laboratory Services’ identification of new and emerging threats through mass spectrometry combined with molecular technologies between 1999-2015. After his retirement, he continued to provide expert advice and training to industry and academia to advance innovations and embed new applications of proteomics across biosciences. <p><b>Saheer E. Gharbia</b> is the Deputy Director of Gastrointestinal Infection and Food Safety for the UK Health Security Agency and has led the COVID-19 Genomics Programme to support the response to the COVID-19 pandemic. She continues to develop tools for the analysis and interpretation of complex biological and pathogenic traits and works across the One Health Scientific Community to embed common surveillance mechanisms to detect and track emerging threats. <p><b>Ajit J. Shah</b> is a Professor in Bioanalytical Science in the Department of Natural Science, Middlesex University, UK. <p><b>Erika Y. Tranfield</b> is Scientific Affairs Manager Microbiology at Bruker. <p><b>K. Clive Thompson </b>is Chief Scientist at ALS, Life Sciences, UK, an analytical testing organisation in the UK and Ireland.
<p><b>Detailed resource presenting the capabilities of MALDI mass spectrometry (MS) to industrially and environmentally significant areas in the biosciences</b> <p><i>Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry </i>fulfills a need to bring the key analytical technique of MALDI mass spectrometric analysis into routine practice by specialists and non-specialists, and technicians. It informs and educates established researchers on the development of techniques as applied to industrially significant areas within the biosciences. Throughout the text, the reader is presented with recognized and emerging techniques of this powerful and continually advancing field of analytical science to key areas of importance. <p>While many scientific papers are reporting new applications of MS-based analysis in specific foci, this book is unique in that it draws together an incredibly diverse range of applications that are pushing the boundaries of MS across the broad field of biosciences. <p>Contributed to by recognized experts in the field of MALDI MS who have been key players in promoting the advancement and dissemination of authoritative information in this field, <i>Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry </i>covers sample topics such as: <ul><li> Oil microbiology, marine and freshwater ecosystems, agricultural and food microbiology, and industrial waste microbiology</li> <li> Bioremediation and landfill sites microbiology, microbiology of inhospitable sites (e.g. Arctic and Antarctic, and alkaline and acidic sites, and hot temperatures)</li> <li> Veterinary, poultry and animals, viral applications of MS, and antibiotic resistance using tandem MS methods</li> <li> Recent developments which are set to transform the use of MS from its success in clinical microbiology to a wide range of commercial and environmental uses</li></ul> <p>Bridging the gap between measurement and key applications, this text is an ideal resource for industrial and environmental analytical scientists, including technologists in the food industry, pharmaceuticals, and agriculture, as well as biomedical scientists, researchers, clinicians and academics and scientists in bio-resource centers.

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