Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access

  title={Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access},
  author={Eduardo N. Taboada and Morag R. Graham and Jo{\~a}o Andr{\'e} Carriço and Gary Van Domselaar},
  journal={Frontiers in Microbiology},
Public health labs and food regulatory agencies globally are embracing whole genome sequencing (WGS) as a revolutionary new method that is positioned to replace numerous existing diagnostic and microbial typing technologies with a single new target: the microbial draft genome. The ability to cheaply generate large amounts of microbial genome sequence data, combined with emerging policies of food regulatory and public health institutions making their microbial sequences increasingly available… 

High Throughput Sequencing for Detection of Foodborne Pathogens

The published literature is reviewed, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts.

Complete Whole Genome Sequences of Escherichia coli Surrogate Strains and Comparison of Sequence Methods with Application to the Food Industry

As the food industry adopts WGS within its food safety programs, these data provide completed genomes for commonly used surrogate strains, with a direct comparison of sequence platforms and assembly strategies relevant to research/testing workflows applicable for both processors and regulators.

Investing in Food Safety for Developing Countries: Opportunities and Challenges in Applying Whole-Genome Sequencing for Food Safety Management

It was showed that some developed nations routinely use WGS in their food surveillance systems resulting in more precise understanding of the causes of outbreaks and key limiting factors for developing countries in adopting WGS for their food control systems were identified.

International Journal of Current Science and Multidisciplinary Research

The focus of this review is on the recent use and future potentialities of NGS in food microbiology application fields, with particular attention to food quality and safety areas and to current challenges.

Application of Whole Genome Sequencing (WGS) Approach Against Identification of Foodborne Bacteria

This chapter summarizes the information on the method developed and application of the whole-genome sequencing (WGS) in the past few years focusing on surveillance of AMR in foodborne pathogenic bacteria.

TORMES: an automated pipeline for whole bacterial genome analysis

MOTIVATION The progress of High Throughput Sequencing (HTS) technologies and the reduction in the sequencing costs are such that Whole Genome Sequencing (WGS) could replace many traditional

Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges

How WGS offers an opportunity to enhance the next-generation of foodborne AMR QMRA modeling is described, which allows for a more meaningful approach to explore genetic similarity among bacterial populations found at successive stages of the food chain, improving the estimation of the probability and magnitude of exposure to AMR hazards at point of consumption.

Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap

  • Celia Marietta Polle K. Agnettah M. June Melissa Ana Elm Carlos Lagrada Macaranas Olorosa Gayeta Masim Herr
  • Medicine, Biology
    BMJ Global Health
  • 2020
A roadmap for incorporating whole-genome sequencing into existing AMR surveillance frameworks, including WHO Global Antimicrobial Resistance Surveillance System is described, informed by ongoing, practical experiences developing WGS surveillance systems in national reference laboratories in Colombia, India, Nigeria and the Philippines.

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of foodborne microorganisms

WGS offers the highest level of bacterial strain discrimination for food-borne outbreak investigation and source attribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management.



Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response

Provided there is free-sharing of information by all clinical and public health laboratories, these genomic tools could spawn a global system of linked databases of pathogen genomes that would ensure more efficient detection, prevention, and control of infectious disease outbreaks worldwide.

Global Microbial Identifier

This overview describes the growing network of stakeholders behind GMI, the contours of the database, and the IT structures needed to serve the GMI user community.

Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing

SUMMARY The epidemiological investigation of a foodborne outbreak, including identification of related cases, source attribution, and development of intervention strategies, relies heavily on the

Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database

The FDA has created a United States-based open-source whole-genome sequencing network of state, federal, international, and commercial partners to provide an international rapid surveillance system for pathogen traceback, critical to support an effective public health response to bacterial outbreaks.

Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities

Findings from the survey recently conducted by Working Group 4 among GMI members are presented in order to ascertain NGS end-use requirements and attitudes towards NGS PT.

A Primer on Infectious Disease Bacterial Genomics

This work presents a comprehensive overview of a bacterial genomics projects from beginning to end, with a particular focus on the planning and computational requirements for HTS data, and provides a general understanding of the analytical concepts to develop a workflow that will meet the objectives and goals of HTS projects.

Toward a standards-compliant genomic and metagenomic publication record.

It is argued that an "eJournal," published under the Open Access paradigm by the Genomic Standards Consortium, could be an attractive publishing forum for a broader range of standardization initiatives within, and beyond, the GSC and thereby fill an unoccupied yet increasingly important niche within the current research landscape.

Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation.

  • B. JacksonC. Tarr P. Gerner-Smidt
  • Biology, Medicine
    Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
  • 2016
Whole-genome multilocus sequence typing and single nucleotide polymorphism analyses provided equivalent phylogenetic relationships relevant to investigations; results were most useful when interpreted in context of epidemiological data.

Evolving public health approaches to the global challenge of foodborne infections.

BIGSdb: Scalable analysis of bacterial genome variation at the population level

The Bacterial Isolate Genome Sequence Database (BIGSDB) represents a freely available resource that will assist the broader community in the elucidation of the structure and function of bacteria by means of a population genomics approach.