Whole-Genome Sequence Datasets: A Powerful Resource for the Food Microbiology Laboratory Toolbox

Whole-genome sequencing (WGS) technologies are rapidly being adopted for routine use in food microbiology laboratories worldwide. Examples of how WGS is used to support food safety testing include gene marker discovery (e.g., virulence and anti-microbial resistance gene determination) and high-resolution typing (e.g., cg/wgMLST analysis). This has led to the establishment of large WGS databases representing the genomes of thousands of different types of food pathogenic and commensal bacteria. This information constitutes an invaluable resource that can be leveraged to develop and validate routine test methods used to support regulatory and industry food safety objectives. For example, well-curated raw and assembled genomic datasets of the key food pathogens (Salmonella enterica, Listeria monocytogenes, and Shiga-toxigenic Escherichia coli) have been used in our laboratory in studies to validate bioinformatics pipelines, as well as new molecular methods as a prelude to the laboratory phase of the “wet lab” validation process. The application of genomic information to food microbiology method development will decrease the cost of test development and lead to the generation of more robust methodologies supporting risk assessment and risk management actions.

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

Clinical Microbiology Reviews ◽

10.1128/cmr.00056-16 ◽

2016 ◽

Vol 29 (4) ◽

pp. 837-857 ◽

Cited By ~ 75

Author(s):

J. Ronholm ◽

Neda Nasheri ◽

Nicholas Petronella ◽

Franco Pagotto

Keyword(s):

Food Safety ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Antibiotic Resistance Gene ◽

Virulence Gene ◽

Complete Information ◽

Gene Profiling ◽

Whole Genome Sequence ◽

Whole Genome ◽

Molecular Subtyping

SUMMARYThe epidemiological investigation of a foodborne outbreak, including identification of related cases, source attribution, and development of intervention strategies, relies heavily on the ability to subtype the etiological agent at a high enough resolution to differentiate related from nonrelated cases. Historically, several different molecular subtyping methods have been used for this purpose; however, emerging techniques, such as single nucleotide polymorphism (SNP)-based techniques, that use whole-genome sequencing (WGS) offer a resolution that was previously not possible. With WGS, unlike traditional subtyping methods that lack complete information, data can be used to elucidate phylogenetic relationships and disease-causing lineages can be tracked and monitored over time. The subtyping resolution and evolutionary context provided by WGS data allow investigators to connect related illnesses that would be missed by traditional techniques. The added advantage of data generated by WGS is that these data can also be used for secondary analyses, such as virulence gene detection, antibiotic resistance gene profiling, synteny comparisons, mobile genetic element identification, and geographic attribution. In addition, several software packages are now available to generatein silicoresults for traditional molecular subtyping methods from the whole-genome sequence, allowing for efficient comparison with historical databases. Metagenomic approaches using next-generation sequencing have also been successful in the detection of nonculturable foodborne pathogens. This review addresses state-of-the-art techniques in microbial WGS and analysis and then discusses how this technology can be used to help support food safety investigations. Retrospective outbreak investigations using WGS are presented to provide organism-specific examples of the benefits, and challenges, associated with WGS in comparison to traditional molecular subtyping techniques.

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GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians

BMC Genomics ◽

10.1186/s12864-021-07405-8 ◽

2021 ◽

Vol 22 (1) ◽

Cited By ~ 1

Author(s):

Jayanthi Gangiredla ◽

Hugh Rand ◽

Daniel Benisatto ◽

Justin Payne ◽

Charles Strittmatter ◽

...

Keyword(s):

Public Health ◽

Food Safety ◽

Data Storage ◽

Sequence Data ◽

Whole Genome Sequence ◽

Analysis Tool ◽

Whole Genome ◽

User Friendliness ◽

Computing Power ◽

Link Type

Abstract Background Processing and analyzing whole genome sequencing (WGS) is computationally intense: a single Illumina MiSeq WGS run produces ~ 1 million 250-base-pair reads for each of 24 samples. This poses significant obstacles for smaller laboratories, or laboratories not affiliated with larger projects, which may not have dedicated bioinformatics staff or computing power to effectively use genomic data to protect public health. Building on the success of the cloud-based Galaxy bioinformatics platform (http://galaxyproject.org), already known for its user-friendliness and powerful WGS analytical tools, the Center for Food Safety and Applied Nutrition (CFSAN) at the U.S. Food and Drug Administration (FDA) created a customized ‘instance’ of the Galaxy environment, called GalaxyTrakr (https://www.galaxytrakr.org), for use by laboratory scientists performing food-safety regulatory research. The goal was to enable laboratories outside of the FDA internal network to (1) perform quality assessments of sequence data, (2) identify links between clinical isolates and positive food/environmental samples, including those at the National Center for Biotechnology Information sequence read archive (https://www.ncbi.nlm.nih.gov/sra/), and (3) explore new methodologies such as metagenomics. GalaxyTrakr hosts a variety of free and adaptable tools and provides the data storage and computing power to run the tools. These tools support coordinated analytic methods and consistent interpretation of results across laboratories. Users can create and share tools for their specific needs and use sequence data generated locally and elsewhere. Results In its first full year (2018), GalaxyTrakr processed over 85,000 jobs and went from 25 to 250 users, representing 53 different public and state health laboratories, academic institutions, international health laboratories, and federal organizations. By mid-2020, it has grown to 600 registered users and processed over 450,000 analytical jobs. To illustrate how laboratories are making use of this resource, we describe how six institutions use GalaxyTrakr to quickly analyze and review their data. Instructions for participating in GalaxyTrakr are provided. Conclusions GalaxyTrakr advances food safety by providing reliable and harmonized WGS analyses for public health laboratories and promoting collaboration across laboratories with differing resources. Anticipated enhancements to this resource will include workflows for additional foodborne pathogens, viruses, and parasites, as well as new tools and services.

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The role of EML Consulting Services (QLD): a consulting food microbiology laboratory

Microbiology Australia ◽

10.1071/ma04341 ◽

2004 ◽

Vol 25 (3) ◽

pp. 41

Keyword(s):

Food Safety ◽

Turnaround Time ◽

Food Microbiology ◽

Microbiology Laboratory ◽

Safety Testing ◽

Consulting Services ◽

Food Quality And Safety ◽

Group A ◽

The Relationship

The relationship between the consulting microbiology laboratory and the food industry remains one of the most critical linkages within the framework of food quality and safety in the commercial setting. EML Consulting Services has cultivated such linkages for over 30 years. EML Consulting Services QLD is the Brisbane Laboratory of the Australian owned EML Group, a network of consulting microbiologists, chemists and allergenists incorporating five laboratories in three States. EML offers high quality food safety testing with minimal turnaround time, and expert consultancy which can evaluate facility and production processes for areas contributing to food safety and quality issues.

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30-OR: Whole Genome Sequence Analysis of Type 2 Diabetes Risk in 44,713 Humans of Diverse Ancestry in the TOPMed Study

Diabetes ◽

10.2337/db19-30-or ◽

2019 ◽

Vol 68 (Supplement 1) ◽

pp. 30-OR

Author(s):

HEATHER M. HIGHLAND ◽

JENNIFER WESSEL ◽

ALISA MANNING ◽

Keyword(s):

Type 2 Diabetes ◽

Sequence Analysis ◽

Genome Sequence ◽

Diabetes Risk ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Analysis

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Whole genome sequence comparison of endemic multi-resistant Escherichia coli clones

10.26226/morressier.56d5ba26d462b80296c94b2c ◽

2016 ◽

Author(s):

Tove Havnhøj Frandsen

Keyword(s):

Escherichia Coli ◽

Genome Sequence ◽

Sequence Comparison ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Comparison

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The Green Revolution and the Gene Revolution in Pakistan: Policy Implications (The Quaid-i-Azam Memorial Lecture)

The Pakistan Development Review ◽

10.30541/v44i4ipp.359-386 ◽

2005 ◽

Vol 44 (4I) ◽

pp. 359-386 ◽

Cited By ~ 5

Author(s):

Robert E. Evenson

Keyword(s):

Food Safety ◽

Green Revolution ◽

Policy Implications ◽

Gm Crops ◽

Regulatory Environment ◽

Memorial Lecture ◽

Regulatory Systems ◽

Cost Reductions ◽

The Cost ◽

Export Crops

Pakistan achieved high levels of Green Revolution Modern Variety (GRMV) adoption in the Green Revolution. Pakistan out-performed India and Bangladesh in the Green Revolution. Only China, among major countries, out-performed Pakistan in the Green Revolution. Pakistan does not have the food safety and environmental risk studies in place to support a regulatory environment for biotechnology. In effect, Pakistan is following the “precautionary principle” and applying it to science policy. This paper argues that this is a mistake. Pakistan is paying a “double penalty” for its inability to develop the regulatory systems required to take advantage of genetically modified (GM) crops. Not only does it lose the cost reductions enabled by GM crops, but because other countries have adopted GM crops, world prices are lower as a result and affect Pakistan’s export crops.

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