Applied genomics of foodborne pathogens. ([2017])

• Record Type: Book
• Further Information: Note: Xiangyu Deng, Henk C. den Bakker, Rene S. Hendriksen, editors.
• Editors: Deng, Xiangyu; Bakker, Henk C. den; Henksen, Rene S
• 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.
• Publisher Details: Cham, Switzerland : Springer
• Publication Date: 2017
• Extent: 1 online resource
• Subjects: 664.001/579; Life sciences; Food -- Microbiology; Food Microbiology; TECHNOLOGY & ENGINEERING -- Food Science; Food -- Microbiology; Life Sciences; Food Microbiology; Food Science; Bioinformatics; Microbial Genetics and Genomics; Applied Microbiology; Science -- Life Sciences -- Anatomy & Physiology; Science -- Life Sciences -- Biology -- Microbiology; Science -- Biotechnology; Food & beverage technology; Molecular biology; Microbiology (non-medical); Food science; Bioinformatics; Microbial genetics; Microbial genomics; Microbiology; Electronic books
• Languages: English
• ISBNs: 9783319437514; 3319437518; 3319437496; 9783319437491
• Related ISBNs: 9783319437491
• Notes: Note: Includes bibliographical references and index.; Note: Online resource; title from PDF title page (SpringerLink, viewed February 3, 2017).
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