Applied Genomics Of Foodborne Pathogens (food Microbiology And Food Safety)

"This book provides a timely and thorough snapshot into the emerging and fast evolving area of applied genomics of foodborne pathogens. Driven by the drastic advance of whole genome shot gun sequencing (WGS) technologies, genomics applications are becoming increasingly valuable and even essential in studying, surveying and controlling foodborne microbial pathogens. The vast opportunities brought by this trend are often at odds with the lack of bioinformatics know-how among food safety and public health professionals, since such expertise is not part of a typical food microbiology curriculum and skill set. Further complicating the challenge is the large and ever evolving body of bioinformatics tools that can obfuscate newcomers to this area. Although reviews, tutorials and books are not in short supply in the fields of bioinformatics and genomics, until now there has not been a comprehensive and customized source of information designed for and accessible to microbiologists interested in applying cutting-edge genomics in food safety and public health research. This book fills this void with a well-selected collection of topics, case studies, and bioinformatics tools contributed by experts at the forefront of foodborne pathogen genomics research."--Publisher's website Preface 6 Contents 8 Contributors 10 Chapter 1: Role of Whole Genome Sequencing in the Public Health Surveillance of Foodborne Pathogens 13 Introduction 13 Current Workflows in the Public Health Laboratories 13 The Ideal Public Health Laboratory System 15 Whole Genome Sequencing in Public Health 15 Combining Reference Characterization and Subtyping in Whole Genome Sequencing Based System for Public Health 19 Conclusions 21 References 22 Chapter 2: Global Microbial Identifier 24 Introduction 24 Next Generation Sequencing and Whole Genome Sequencing: A New Potential for Integrated Surveillance of Infectious Diseases 25 The Global Microbial Identifier (GMI) Initiative 28 Landscaping the Global Microbial WGS Field 29 GMI the Network 30 GMI the Database 31 GMI the Software 32 Metadata and Depth of Analysis 33 Quality Assurance and Testing 37 Concluding Remarks 38 References 40 Chapter 3: The Use of Whole Genome Sequencing for Surveillance of Enteric Organisms by United States Public Health Laboratories 43 Introduction 43 Traditional Foodborne Disease Subtyping Methods 44 WGS as a Subtyping Method for Surveillance 45 Current Workflow for WGS-Based Surveillance in Wadsworth Center/NY State Dept. of Health 46 Three WGS Case Studies 49 Case Study 1, a Retrospective Study that Resolved a Cluster in an Endemic PFGE Type 49 Case Study 2 a Near Real-Time Study that Revealed Multiple PFGE Types in a Single Genomic Cluster 49 Case Study 3: a Real-Time Analysis of a Cluster Associated with Bean Sprouts 51 Current State of Whole Generation Sequencing at Public Health Laboratories 53 Challenges to US PulseNet Laboratories of Adopting WGS 53 Cost and Efficiency 53 Bioinformatic Analysis of Data 54 Prioritization of Additional Clusters 55 QA/QC 56 The Promise of Uniform Workflows and the Reality 57 References 58 Chapter 4: Bioinformatics Aspects of Foodborne Pathogen Research 61 Introduction 61 Sequencing Technologies 62 Bioinformatics Approaches 62 Read Mapping Based Approaches 62 De Novo Approaches 63 De Novo Assembly and the Basics of Comparative Genomics 63 Comparative Genomics 64 Phylogenetics 65 Homologous Recombination 66 Genomic Epidemiology of Foodborne Pathogens 66 Microbiome Research and Foodborne Pathogens 68 General Principles and Pipelines 68 Examples of Microbiome Approaches in Study of Foodborne Pathogens and Spoilage Organisms 69 References 70 Chapter 5: The CGE Tool Box 75 Introduction 75 Prokaryotic Taxonomy 78 SpeciesFinder 79 Reads2Type 80 TaxonomyFinder 81 KmerFinder 81 Performance of Methods for Species Identification 82 Subtyping 84 The MLST Web-Service 84 Serotype 87 Serotyping of E. coli 87 Serotyping of Salmonella 87 Plasmids 88 Phenotyping 88 ResFinder 89 MyDbFinder 90 How to Make a Database for MyDbFinder 91 VirulenceFinder 91 PathogenFinder 92 Phylogeny 93 SNPtree, CSIPhylogeny, and NDtree 93 Metagenomic Samples 95 Work in Progress 96 Conclusion 97 References 98 Chapter 6: Genomic Diversity in Salmonella enterica 101 Introduction 101 Genetic Variation Within Salmonella enterica 101 Host Adaptation and Host Restriction vs Identification and Typing 103 Salmonella enterica Subspecies Enterica Serotype Enteritidis, an Example of a Monophyletic Group of Strains 104 Salmonella enterica Subspecies Enterica Serotype Montevideo, an Example of a Polyphyletic Group of Strains 105 Salmonella enterica Subspecies Enterica Serotype Typhimurium, a “Challenging” Group of Strains 106 Salmonella enterica Subspecies Enterica Serotype Choleraesuis, an Example of a Polyphyletic Group of Strains with Different Host Adaptations 108 The Special Case of Salmonella that Cause Human Enteric Fever 109 Detecting the Variation in Salmonella 110 Future Directions for Salmonella Investigations 112 References 113 Chapter 7: Verocytotoxin-Producing Escherichia coli in the Genomic Era: From Virulotyping to Pathogenomics 118 Verocytotoxin Producing E. coli: From the Origin to the “Next” Era 118 VTEC Pathogenomics and the Problem of Its Classification 119 The Discovery of the Mosaic Nature of VTEC Chromosome and the Attempts to Define Pathogenic VTEC in the Pre-NGS Era 121 Identification of New and Emerging VTEC Through WGS 123 NGS: A Promising Subtyping Approach to the Real Time Surveillance and Monitoring of VTEC Infections 126 References 129 Chapter 8: Campylobacter 136 Introduction 136 Future Applications of Genomics 137 Applications of Genome Sequencing to Campylobacter to Date 138 Issues in and Approaches to Applying WGS to Campylobacter Epidemiology, Attribution, Outbreak Detection and Other Areas 139 Descriptive Epidemiology of Campylobacter 139 Source Attribution 140 Outbreak Detection and Investigation 143 Virulence, Antimicrobial Resistance and Other Specific Areas in the Genome Era 145 Conclusion 147 References 148 Chapter 9: Genomics and Foodborne Viral Infections 153 Background 153 Foodborne Viruses: What Is Known 156 Rotavirus 156 Norovirus 157 Hepatitis A Virus 158 Hepatitis E Virus 159 Enteric Adenovirus 159 Astrovirus 160 Enterovirus Including Poliovirus 160 Foodborne Viral Disease Surveillance: Recognition/Identification 161 Use of Genomics-Based Tools for Foodborne Viral Disease Outbreak Detection: Identification/Characterization 164 Viral Metagenomics and Control of Foodborne Viral Illness: Characterization/Containment 166 Concluding Remarks 167 References 168 Chapter 10: Transcriptomics and Proteomics of Foodborne Bacterial Pathogens 175 Introduction 175 Transcriptomics 175 RNA Sequencing 175 Methodology of RNA-Seq Technology 176 Sequencing Platforms 177 Applications of RNA-Seq 178 Limitations and Challenges 180 ChIP Sequencing 181 Methodology of ChIP-Seq Technology 182 Applications of ChIP-Seq 183 Limitations and Challenges 185 Conclusions and Future Perspectives 185 Proteomics 186 Mass Spectrometry 187 Methodology of Mass Spectrometry Technology 187 Ionization Methods 188 Mass Analyzers 188 MS-Based Proteomic Analysis Strategies 190 Applications of Mass Spectrometry 191 Identification of Bacterial Pathogens 191 Quantitation of Proteins of Interest 192 Shotgun Proteomics 193 Protein–Protein Interactions 194 Protein Modifications 194 Limitations and Challenges 195 Protein Microarray 195 Methodology of Protein Microarray Technology 196 Applications of Protein Microarray 196 Quantitative Proteomics 196 Functional Proteomics 198 Limitations and Challenges 199 Conclusions and Future Perspectives 199 References 200 Index 209 Front Matter....Pages i-xi Role of Whole Genome Sequencing in the Public Health Surveillance of Foodborne Pathogens....Pages 1-11 Global Microbial Identifier....Pages 13-31 The Use of Whole Genome Sequencing for Surveillance of Enteric Organisms by United States Public Health Laboratories....Pages 33-50 Bioinformatics Aspects of Foodborne Pathogen Research....Pages 51-64 The CGE Tool Box....Pages 65-90 Genomic Diversity in Salmonella enterica ....Pages 91-107 Verocytotoxin-Producing Escherichia coli in the Genomic Era: From Virulotyping to Pathogenomics....Pages 109-126 Campylobacter....Pages 127-143 Genomics and Foodborne Viral Infections....Pages 145-166 Transcriptomics and Proteomics of Foodborne Bacterial Pathogens....Pages 167-200 Back Matter....Pages 201-205