product iamge

Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry: Industrial and Environmental Applications

This document was uploaded by one of our users. The uploader already confirmed that they had the permission to publish it. If you are author/publisher or own the copyright of this documents, please report to us by using this DMCA report form.

Download
Search on Amazon

Simply click on the Download Book button.

Yes, Book downloads on Ebookily are 100% Free.

Sometimes the book is free on Amazon As well, so go ahead and hit "Search on Amazon"

Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry

Detailed resource presenting the capabilities of MALDI mass spectrometry (MS) to industrially and environmentally significant areas in the biosciences

Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry 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.

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.

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, Microbiological Identification using MALDI-TOF and Tandem Mass Spectrometry covers sample topics such as:

  • Oil microbiology, marine and freshwater ecosystems, agricultural and food microbiology, and industrial waste microbiology
  • Bioremediation and landfill sites microbiology, microbiology of inhospitable sites (e.g. Arctic and Antarctic, and alkaline and acidic sites, and hot temperatures)
  • Veterinary, poultry and animals, viral applications of MS, and antibiotic resistance using tandem MS methods
  • 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

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.

Author(s): Saheer E. Gharbia, Ajit J. Shah, Haroun N. Shah, Erika Y. Tranfield, K. Clive Thompson
Publisher: Wiley
Year: 2023

Language: English
Pages: 558
City: Hoboken

Cover
Title Page
Copyright Page
Contents
List of Contributors
Preface
Chapter 1 Progress in the Microbiological Applications of Mass Spectrometry: from Electron Impact to Soft Ionization Techniques, MALDI-TOF MS and Beyond
1.1 Introduction
1.1.1 Algorithms Based upon Traditional Carbohydrate Fermentation Tests
1.1.2 Dynamic Changes in the Chemotaxonomic Era (c. 1970–1985) through the Lens of the Genus Bacteroides
1.1.3 Microbial Lipids as Diagnostic Biomarkers; Resurgence of Interest in MALDI-TOF MS with Advances in Lipidomics
1.2 The Dawn of MALDI-TOF MS: Establishing Proof of Concept for Diagnostic Microbiology
1.2.1 Development of a MALDI-TOF MS Database for Human Infectious Diseases
1.2.2 The Dilemma with Clostridium difficile: from Intact Cells to Intracellular Proteins, MALDI-TOF MS Enters a New Phase
1.3 Linear/Reflectron MALDI-TOF MS to Tandem Mass Spectrometry
1.3.1 Tandem MALDI-TOF Mass Spectrometry
1.3.2 Electrospray-based Mass Analysers
1.3.3 Tandem Mass Spectrometry
1.3.4 Mass Spectrometry-based Proteomics
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
1.3.6 Discovery Proteomics
1.3.7 Targeted Proteomics
1.3.8 Top-down Proteomics
1.3.9 Targeted Protein Quantitation
1.4 The Application of MALDI-MS Profiling and Imaging in Microbial Forensics: Perspectives
1.4.1 MALDI-MSP of Microorganisms and their Products
1.5 Hydrogen/Deuterium Exchange Mass Spectrometry in Microbiology
1.6 The Omnitrap, a Novel MS Instrument that Combines Many Applications of Mass Spectrometry
References
Chapter 2 Machine Learning in Analysis of Complex FloraUsing Mass Spectrometry
2.1 Introduction
2.2 An Improved MALDI-TOF MS Data Analysis Pipeline for the Identification of Carbapenemase-producing Klebsiella pneumoniae
2.2.1 Motivation
2.2.2 Materials and Methods
2.2.3 Spectra Acquisition
2.2.4 Results
2.2.5 Discussion
2.3 Detection of Vancomycin-Resistant Enterococcus faecium
2.3.1 Motivation
2.3.2 Materials and Methods
2.3.3 Results and Discussion
2.4 Detection of Azole Resistance in Aspergillus fumigatus Complex Isolates
2.4.1 Introduction
2.4.2 Material and Methods
2.4.3 Results
2.4.4 Discussion
2.5 Peak Analysis for Discrimination of Cryptococcus neoformans Species Complex and their Interspecies Hybrids
2.5.1 Motivation
2.5.2 Material and Methods
2.5.3 Results and Discussion
2.6 Conclusions
References
Chapter 3 Top-down Identification of Shiga Toxin (and Other Virulence Factors and Biomarkers) from Pathogenic E. coli using MALDI-TOF/TOF Tandem Mass Spectrometry
3.1 Introduction
3.2 Decay of Metastable Peptide and Protein Ions by the Aspartic Acid Effect
3.3 Energy Deposition during Desorption/Ionization by MALDI
3.4 Protein Denaturation and Fragmentation Efficiency of PSD
3.5 Arginine and its Effect on Fragment Ion Detection and MS/MS Spectral Complexity
3.6 Inducing Gene Expression in Wild-type Bacteria for Identification by Top-Down Proteomic Analysis
3.7 Top-down Proteomic Identification of B-Subunit of Shiga Toxin from STEC Strains
3.8 Furin-digested Shiga Toxin and Middle-down Proteomics
3.9 Top-down Identification of an Immunity Cognate of a Bactericidal Protein Produced from a STEC Strain
3.10 LC-MALDI-TOF/TOF
3.11 Conclusions
References
Chapter 4 Liquid Atmospheric Pressure (LAP) – MALDI MS(/MS) Biomolecular Profiling for Large-scale Detection of Animal Disease and Food Adulteration and Bacterial Identification
4.1 Introduction
4.2 Background to LAP-MALDI MS
4.3 Bacterial Identification by LAP-MALDI MS
4.4 Food Adulteration and Milk Quality Analysis by LAP-MALDI MS
4.5 Animal Disease Detection by LAP-MALDI MS
4.6 Antibiotic Resistance Detection of Microbial Consortia by LAP-MALDI MS
4.7 Future Directions for LAP-MALDI MS Applications
References
Chapter 5 Development of a MALDI-TOF Mass Spectrometry Test for Viruses
5.1 Introduction
5.2 Understanding the Systems Biology of the Virus and Viral Infections
5.3 Understanding the Nature of Viral Proteins and Molecular Biology
5.4 Virion Protein Solubilization and Extraction
5.5 Sampling and Virion Enrichment
5.6 Peak Identification: Quantification and Bioinformatics
5.7 Promise and Pitfalls of Machine Learning Bioinformatics
5.8 Accelerating MALDI-TOF Assay Protocol Development Using Pseudotypes/pseudoviruses
5.9 Understanding the Operational Parameters of your MALDI-TOF MS
5.10 Understanding the Operational Requirements of the Clinical Testing Laboratory: Validation and International Accreditation
5.10.1 Limitation and Advantages of CLIA LDTs
5.11 MALDI-TOF MS Screening Test for SARS-CoV-2s
5.11.1 Prepare Positive Control
5.11.2 Prepare Gargle-saliva Samples
5.11.3 Viral Particle Enrichment
5.11.4 Dissolution of Virions and Solubilization of Viral Proteins
5.11.5 MALDI-TOF MS
5.12 CLIA LDT Validation of a MALDI-TOF MS Test for SARS-CoV-2
5.12.1 Limit of Detection
5.12.2 Interfering Substances and Specificity
5.12.3 Clinical Performance Evaluation
5.12.4 Reproducibility
5.12.5 Stability
5.12.6 Validation Disposition
References
Chapter 6 A MALDI-TOF MS Proteotyping Approach for Environmental, Agricultural and Food Microbiology
6.1 Introduction
6.2 Serotyping of Salmonella enterica Subspecies enterica
6.3 Discrimination of the Lineages of Listeria monocytogenes and Species of Listeria
6.4 Discrimination of the Bacillus cereus Group and Identification of Cereulide
6.5 Identification of Alkylphenol Polyethoxylate-degrading Bacteria in the Environment
6.6 Conclusions and Future Perspectives
References
Chapter 7 Diversity, Transmission and Selective Pressure on the Proteome of Pseudomonas aeruginosa
7.1 Introduction: Diversity
7.1.1 P. aeruginosa: from ‘Atypical’ to Diverse
7.1.2 Phenotypical Diversity in Isolates from Different Environments
7.1.3 The Relationship Between Phenotypical and Proteomic Diversity
7.1.4 Techniques and Practical Considerations for Studying Proteomic Diversity
7.1.5 Proteomic Diversity and MS Applications
7.2 Transmission
7.2.1 The History of P. aeruginosa Transmission
7.2.2 Proteomics and P. aeruginosa Transmission
7.2.3 The Impact of Proteomic Diversity on Transmission
7.3 Selective Pressures on the Proteome
7.3.1 Tandem MS Systems for Studying Selected Proteomes
7.3.2 Microenvironment Selection
7.3.3 Antimicrobial Selection
7.4 Conclusions on Studies of the Proteome
7.5 Genomic Studies on Pseudomonas aeruginosa Strains Revealing the Presence of Two Distinct Clades
7.5.1 Phylogenomic Analysis Reveals the Presence of Two Distinct Clades Within P. aeruginosa
7.5.2 Identification of Molecular Markers Distinguishing the Two P. aeruginosa Clades
7.6 Final Conclusions
References
Chapter 8 Characterization of Biodegradable Polymers by MALDI-TOF MS
8.1 Introduction
8.2 Structural Characterization of Poly(-caprolactone) Using MALDI-TOF MS
8.3 Biodegradation Profiles of a Terminal-modified PCL Observed by MALDI-TOF MS
8.4 Bacterial Biodegradation Mechanisms of Non-ionic Surfactants
8.5 Advanced Molecular Characterization by High-resolution MALDI-TOF MS Combined with KMD Analysis
8.6 Structural Characterization of High-molecular-weight Biocopolyesters by High-resolution MALDI-TOF MS Combined with KMD Analysis
References
Chapter 9 Phytoconstituents and Antimicrobiological Activity
9.1 Introduction to Phytochemicals
9.2 An Application to Bacteriology
9.2.1 Allicin Leads to a Breakdown of the Cell Wall of Staphylococcus aureus
9.3 Applications to Parasitology
9.3.1 Drug Discovery
9.3.2 Parasite Characterization
9.4 A Proteomic Approach: Leishmania Invasion of Macrophages
9.5 Intracellular Leishmania Amastigote Spreading between Macrophages
9.6 Potential Virus Applications
Acknowledgements
References
Chapter 10 Application of MALDI-TOF MS in Bioremediation and Environmental Research
10.1 Introduction
10.2 Microbial Identification: Molecular Methods and MALDI-TOF MS
10.2.1 PCR-based Methods
10.2.2 MALDI-TOF MS
10.3 Combination of MALDI-TOF MS with Other Methods for the Identification of Microorganisms
10.4 Application of MALDI-TOF MS in Environmental and Bioremediation Studies
10.4.1 The Atmospheric Environment
10.4.2 The Aquatic Environment
10.4.3 The Terrestrial Environment
10.4.4 Bioremediation Research Applications
10.5 Microbial Products and Metabolite Activity
10.6 Challenges of Environmental Applications
10.7 Opportunities and Future Outlook
10.8 Conclusions
References
Chapter 11 From Genomics to MALDI-TOF MS: Diagnostic Identification and Typing of Bacteria in Veterinary Clinical Laboratories
11.1 Introduction
11.2 Genomics
11.3 Defining Bacterial Species Through Genomics
11.4 MALDI-TOF MS
11.5 Combining Genomics with MALDI-TOF MS to Classify Bacteria at the Subspecies Level
11.6 Data Exploration with MALDI-TOF MS
11.7 Validation of Typing Strategies
11.8 Future Directions
References
Chapter 12 MALDI-TOF MS Analysis for Identification of Veterinary Pathogens from Companion Animals and Livestock Species
12.1 Veterinary Diagnostic Laboratories and the MALDI-TOF Clinical Microbiology Revolution
12.1.1 MALDI-TOF MS: Reshaping the Workflow in Clinical Microbiology
12.1.2 Identification of Bacterial Pathogens Directly from Clinical Specimens
12.1.3 Prediction of Antimicrobial Resistance
12.1.4 Impact in Veterinary Hospital Biosecurity and Epidemiological Surveillance
12.2 Identification of Campylobacter spp. and Salmonella spp. in Routine Clinical Microbiology Laboratories
12.2.1 General Aspects on the Importance of Species/Subspecies and Serovar Identification of Campylobacter spp. and Salmonella spp.
12.2.2 General Aspects on Influence of Media/Culture Environment on Bacterial Species Identification by MALDI-TOF MS
12.2.3 Possibilities and Limits of Identification of Campylobacter spp. by MALDI-TOF MS
12.2.4 Possibilities and Limits of Identification of Salmonella spp. by MALDI-TOF MS
12.3 Identification and Differentiation of Mycoplasmas Isolated from Animals
12.3.1 Animal Mycoplasmas at a Glance
12.3.2 Laboratory Diagnosis of Animal Mycoplasmas
12.3.3 MALDI-TOF MS for the Identification of Animal Mycoplasmas
References
Chapter 13 MALDI-TOF MS: from Microbiology to Drug Discovery
13.1 Introduction
13.2 Microbial Fingerprinting
13.2.1 Environmental
13.2.2 Terrestrial Microbiology
13.2.3 Food and Food Safety
13.3 Mammalian Cell Fingerprinting
13.3.1 Differentiation of Cell Lines and Response to Stimuli
13.3.2 Cancer Diagnostics
13.3.3 Biomarkers
13.4 Drug Discovery Using MALDI-TOF
13.4.1 Enzymatic Assays
13.4.2 Cellular-based Assays for Drug Discovery
13.4.3 Automation in Drug Discovery
13.4.4 Assay Multiplexing
13.4.5 MS Imaging in Drug Discovery
13.4.6 MALDI-2
13.5 Limitations/Challenges, Future Outlook, and Conclusions
13.5.1 Sample Preparation Limitations
13.5.2 Data Analysis and Application of Machine Learning
13.6 Future Outlook/Conclusions
References
Chapter 14 Rapid Pathogen Identification in a Routine Food Laboratory Using High-throughput MALDI-TOF Mass Spectrometry
14.1 Introduction
14.2 MALDI-TOF MS in Food Microbiology
14.3 Review of Existing Confirmation Techniques and Comparison to MALDI-TOF MS
14.4 Strain Typing Using MALDI-TOF MS
14.5 Verification Trial
14.6 Limitations of MALDI-TOF MS Strain Typing and Future Studies
14.7 Listeria Detection by MALDI-TOF MS
14.8 Trial Sample Preparation Procedure
14.9 Initial Trial
14.10 Limit of Detection Trial
14.11 Method Optimization, Further Prospects, and Conclusions
References
Chapter 15 Detection of Lipids in the MALDI Negative Ion Mode for Diagnostics, Food Quality Control, and Antimicrobial Resistance
15.1 Introduction
15.2 Applications of Lipids in Clinical Microbiology Diagnostics
15.2.1 Use of Cell Envelope Lipids for Bacterial Identification
15.2.2 Detection of Cell Envelope Lipids and their Modifications to Determine Bacterial Drug Susceptibility
15.2.3 Detection of Lipids in MALDI Negative Ion Mode for Fungal Identification
15.2.4 Detection of Lipids in MALDI Negative Ion Mode for Parasite Identification
15.2.5 Detection of Lipids in MALDI Negative Ion Mode for Virus Identification
15.3 Applications of the Detection of Lipids in Negative Ion Mode MALDI-MS in Cancer Studies
15.3.1 Lipids and MALDI Negative Ion Mode for Diagnosis of Lung Cancer
15.3.2 Lipids and MALDI Negative Ion Mode for the Diagnosis of Breast Cancer
15.3.3 Lipids and MALDI Negative Ion Mode for Diagnosis of Other Cancers
15.3.4 Lipids and MALDI Negative Ion Mode for Drug–Cell Interactions and Prognosis
15.4 Applications of the Detection of Lipids and MALDI-MS in Alzheimer’s Disease Studies
15.5 Applications of MALDI in Negative Ion Mode and the Detection of Lipids in Toxicology
15.6 Lipids and MALDI Negative Ion Mode for Food Fraud Detection
15.7 Conclusions and Future Development of Lipids and their Detection in MALDI in Negative Ion Mode
Acknowledgments
References
Chapter 16 Use of MALDI-TOF MS in Water Testing Laboratories
16.1 Introduction
16.2 Application in a Drinking Water Laboratory
16.2.1 Introduction
16.2.2 Method Validation
16.2.3 Application Within Drinking Water Laboratory
16.3 Application in Water Hygiene and Environmental Laboratory Testing
16.3.1 Introduction
16.3.2 Legionella Testing
16.3.3 Wastewater and Sewage Sludge Microbiology
16.3.4 Healthcare Water Testing
16.3.5 Investigative Analysis
16.3.6 Method Validation
16.3.7 Conclusion on Suitability for Use in an Environmental Testing Laboratory
16.4 Potential Application for Cryptosporidium Identification
References
Chapter 17 A New MALDI-TOF Database Based on MS Profiles of Isolates in Icelandic Seawaters for Rapid Identification of Marine Strains
17.1 Introduction
17.2 Selection and Cultivation of the Strains
17.3 Genotypic Identification
17.4 MALDI-TOF MS Data Acquisition and Database Creation
17.5 Verification of the Accuracy of the Home-made Database
17.6 Conclusions
Funding
References
Chapter 18 MALDI-TOF MS Implementation Strategy for a Pharma Company Based upon a Network Microbial Identification Perspective
18.1 Introduction
18.1.1 Microbial Identifications from a Pharmaceutical Industry Perspective
18.1.2 Historical Evolution
18.2 Regulatory Requirements/Guidance for Microbial Identification
18.3 Strategic Approaches to MALDI-TOF Implementation Within the Modern Microbial Methods Framework
18.3.1 Incorporation of MALDI-TOF into a Technical Evaluation Roadmap
18.3.2 Initial Implementation Planning Stage
18.3.3 Implementation Strategy – From Feasibility Studies to Global Deployment
18.4 Conclusions
18.A Appendix
References
Chapter 19 MALDI-TOF MS – Microbial Identification as Part of a Contamination Control Strategy for Regulated Industries
19.1 Industry Perspective
19.1.1 Introduction to Regulated Industries
19.1.2 Contamination Control Strategy
19.1.3 Tracking and Trending EM Data
19.1.4 Drivers for Microbial Identification
19.1.5 Level of Resolution of an Identification
19.1.6 Global Harmonization
19.1.7 Validation Requirements for Regulated Industries
19.1.8 Summary
19.2 Technical Perspective
19.2.1 Identification Technologies
19.2.2 Phenotypic Systems
19.2.3 Proteotypic Systems
19.2.4 Genotypic Systems
19.2.5 The Importance of the Reference Database
19.2.6 MALDI-TOF in Regulated Industries
19.2.7 Outsourcing
19.2.8 Summary
19.3 MALDI-TOF MS Microbial Identification Workflow at a High-throughput Laboratory
19.3.1 MALDI-TOF MS Principles for Microbial Identification
19.3.2 Organism Cultivation for Microbial Identification with MALDI-TOF MS
19.3.3 Sample Preparation for Microbial Identification with MALDI-TOF MS
19.3.4 Sample Processing Workflow for Microbial Identification
19.3.5 Data Interpretation
19.3.6 Importance of a Sequence-based Secondary (or Fall-through) Identification System
19.4 MALDI-TOF MS Library Development and Coverage
19.4.1 Importance of Library Development Under a Quality System
19.4.2 Targeted Library Development for Gram-positive Bacteria and Water Organisms
19.4.3 Supplemental and Custom MALDI-TOF MS Libraries
19.5 Comparison of MALDI-TOF MS with Other Microbial Identification Methods
19.6 Future Perspectives
References
Chapter 20 Identification of Mold Species and Species Complex from the Food Environment Using MALDI-TOF MS
20.1 Fungal Taxonomy
20.1.1 Defining What Is a Fungal Species
20.1.2 Fungal Speciation within a Food Context
20.1.3 Delimiting Species
20.1.4 Foodborne Fungi within the Fungal Tree of Life
20.2 Impact of Molds in Food
20.2.1 Filamentous Fungi in Fermented Foods
20.2.2 Filamentous Fungi with Undesirable Impacts on Food Quality and Safety
20.3 Identification of Fungi
20.4 Identification of Foodborne Molds Using MALDI-TOF MS
20.4.1 Sample Preparation
20.4.2 Database Building and Performance of MALDI-TOF for Identification of Foodborne Molds
References
Index
EULA