Abstract
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 and public, has served to open up the field to the general scientific community. This open data access policy shift has resulted in a proliferation of data being deposited into sequence repositories and of novel bioinformatics software designed to analyze these vast datasets. There also has been a more recent drive for improved data sharing to achieve more effective global surveillance, public health and food safety. Such developments have heightened the need for enhanced analytical systems in order to process and interpret this new type of data in a timely fashion. In this review we outline the emergence of genomics, bioinformatics and open data in the context of food safety. We also survey major efforts to translate genomics and bioinformatics technologies out of the research lab and into routine use in modern food safety labs. We conclude by discussing the challenges and opportunities that remain, including those expected to play a major role in the future of food safety science.
Highlights
The first complete sequence of a bacterial organism—Haemophilus influenzae—was generated in 1995, revealing for the first time the entire set of genetic information used to encode a free-living organism
The ability of Next-Generation Sequencing (NGS) technology to resolve the source of an outbreak was famously demonstrated during the 2010 Haiti cholera outbreak, the worst cholera epidemic in recent history killing at least 10,000 people and sickening well over 600,000 (Centers for Disease Control and Prevention [CDC], 2014)
Multi sector engagement and collaboration led to the creation of the Global Microbial Identifier (GMI) consortium (Wielinga et al, 2017), which envisions a global, interoperable analytical platform consisting of standardized pathogen genome databases, typing systems, and bioinformatics analysis tools for microbial and infectious disease identification, and diagnostics that will be made accessible to all nations with basic laboratory infrastructure (Global Microbial Identifier, 2017)
Summary
The first complete sequence of a bacterial organism—Haemophilus influenzae—was generated in 1995, revealing for the first time the entire set of genetic information used to encode a free-living organism. Two main NGS technologies emerged, primarily distinguished by the sequence fragment (“read”) length generated Short read technologies, such as those incorporated into the platform lines currently manufactured by Illumina and Life Technologies, generate read lengths from ∼100 to ∼600 bp with low per-base error rates (typically less than 1%) (Goodwin et al, 2016). These technologies are routinely used to assemble draft genome sequences containing multiple contiguous segments (contigs) with high accuracy and good coverage (>95% for an average bacterial genome). Early pioneering studies applying WGS to outbreak analysis demonstrated much promise for this new technology, widespread recognition of its power would first occur in 2011
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
