Applied genomics of foodborne pathogens / Xiangyu Deng, Henk C. den Bakker, Rene S. Hendriksen, editors.
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...
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Full Text (via Springer) |
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| Other Authors: | , , |
| Format: | eBook |
| Language: | English |
| Published: |
Cham, Switzerland :
Springer,
[2017]
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| Series: | Food microbiology and food safety series.
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| Subjects: |
Table of Contents:
- Preface; Contents; Contributors; Chapter 1: Role of Whole Genome Sequencing in the Public Health Surveillance of Foodborne Pathogens; Introduction; Current Workflows in the Public Health Laboratories; The Ideal Public Health Laboratory System; Whole Genome Sequencing in Public Health; Combining Reference Characterization and Subtyping in Whole Genome Sequencing Based System for Public Health; Conclusions; References; Chapter 2: Global Microbial Identifier; Introduction.
- Next Generation Sequencing and Whole Genome Sequencing: A New Potential for Integrated Surveillance of Infectious Diseases The Global Microbial Identifier (GMI) Initiative; Landscaping the Global Microbial WGS Field; GMI the Network; GMI the Database; GMI the Software; Metadata and Depth of Analysis; Quality Assurance and Testing; Concluding Remarks; References; Chapter 3: The Use of Whole Genome Sequencing for Surveillance of Enteric Organisms by United States Public Health Laboratories; Introduction; Traditional Foodborne Disease Subtyping Methods.
- WGS as a Subtyping Method for Surveillance Current Workflow for WGS-Based Surveillance in Wadsworth Center/NY State Dept. of Health; Three WGS Case Studies; Case Study 1, a Retrospective Study that Resolved a Cluster in an Endemic PFGE Type; Case Study 2 a Near Real-Time Study that Revealed Multiple PFGE Types in a Single Genomic Cluster; Case Study 3: a Real-Time Analysis of a Cluster Associated with Bean Sprouts; Current State of Whole Generation Sequencing at Public Health Laboratories; Challenges to US PulseNet Laboratories of Adopting WGS; Cost and Efficiency.
- Bioinformatic Analysis of Data Prioritization of Additional Clusters; QA/QC; The Promise of Uniform Workflows and the Reality; References; Chapter 4: Bioinformatics Aspects of Foodborne Pathogen Research; Introduction; Sequencing Technologies; Bioinformatics Approaches; Read Mapping Based Approaches; De Novo Approaches; De Novo Assembly and the Basics of Comparative Genomics; Comparative Genomics; Phylogenetics; Homologous Recombination; Genomic Epidemiology of Foodborne Pathogens; Microbiome Research and Foodborne Pathogens; General Principles and Pipelines.
- Examples of Microbiome Approaches in Study of Foodborne Pathogens and Spoilage OrganismsReferences; Chapter 5: The CGE Tool Box; Introduction; Prokaryotic Taxonomy; SpeciesFinder; Reads2Type; TaxonomyFinder; KmerFinder; Performance of Methods for Species Identification; Subtyping; The MLST Web-Service; Serotype; Serotyping of E. coli; Serotyping of Salmonella; Plasmids; Phenotyping; ResFinder; MyDbFinder; How to Make a Database for MyDbFinder; VirulenceFinder; PathogenFinder; Phylogeny; SNPtree, CSIPhylogeny, and NDtree; Metagenomic Samples; Work in Progress.