Role of Whole Genome Sequencing in the Public Health Surveillance of Foodborne Pathogens

Abstract

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. 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.