[3] Another consideration is the fact that other subtyping tools (e.g., ribotyping) provide insights (e.g., clustering) that may not be compatible with WGS. The level of WGS integration varied between companies, ranging from “not yet used” to “used routinely with in-house resources.” For those companies that have not yet used WGS, the advice would be to have a plan of action on how WGS could be accessed in case an urgent need arises. Genome sequencing is the most unbiased method to sequence the genome as it does not include a capture of specific targeted regions to prepare the library for sequencing (Fig. •    With the fast-evolving sequencing techniques, sequencers can quickly become obsolete. WGS is mostly applied when alternative subtyping methods are insufficient to differentiate isolates to a level that will allow companies to define the appropriate action for that particular case. This individualized avenue of health care is often referred to as “personalized medicine.”. A number of members representing the food industry have joined this working group; however, companies that provide sequencing technology or bioinformatics software, and could also provide valuable input in establishing this ISO standard, are currently missing. Method standardization through the International Organization for Standardization (ISO) is imperative for accreditation, alignment of methodology, and ensuring results will be internationally recognized.

The Human Genome Project is an attempt to: a.... All are true about the Human Genome Project and... What 'EXPERIMENT' did Craig Venter & Francis... What is RNA sequencing and how it is done?
To further exchange information among food industries, a network will be established.

Understanding the terminology, methodology, and critical points will allow companies to have a discussion on WGS, not only with authorities but also with other food companies and raw material suppliers. However, thinking through the issues surrounding personal genomics now, rather than later, may help to avoid potential pitfalls and ensure that the good outweighs the bad.

For the food industry to assess the competency of a third-party laboratory in genomics, a specific checklist covering the points that are critical for WGS analysis would be beneficial. 5. The relative high cost of the analysis that provides a retrospective result can be difficult to justify. Another extremely important benefit of the Human Genome Project is the development of new technology. There are many benefits of sequencing the genome of an organism. This included the absence of a legal framework, potential regulatory obligations and/or pressure to share WGS data, and lack of clarity on data ownership (Figure 1). Models of Implementation

“Genomics of Foodborne Pathogens for Microbial Food Safety.” Curr Opin Biotechnol 49:224–229. It was recognized that the proactive sequencing of all pathogen isolates could bring additional insights. However, it should be noted that more companies were invited to participate in the survey/workshop but declined to do so. Even if WGS analysis is outsourced, internal expertise for all three parts is still needed to correctly interpret the results and relate these to the manufacturing setting. Moreover, for these organisms, there are highly specific and sensitive methods that can provide more reliable insights. The application of these genomics tools is much broader compared with WGS, as illustrated in Figure 2, which includes the responses of all companies (n = 17 for this question), including those not yet using these tools. The subtyping tools that were mentioned include serotyping, ribotyping, pulsed-field gel electrophoresis, or matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. By Adrianne Klijn, Deann Akins-Lewenthal, Bala Jagadeesan, Leen Baert, Anett Winkler, Caroline Barretto, and Alejandro Amézquita. However, in terms of practicalities, there are barriers like those for WGS.

Even though the approaches are interesting and can give multiple answers from a single analysis, in some situations, it can be a convoluted approach, whereas a simple phenotypic analysis can provide a quicker answer. Such a scheme should cover the entire process, including the laboratory and bioinformatics parts. The point of view from authorities and academia is well-documented, but a broad perspective on its use by the food industry has been missing so far. 2019.

Where do we draw the line? Furthermore, WGS does not give a simple yes/no answer, but it instead provides functions of relatedness of isolates (genetic similarity), which still need appropriate interpretation. Click here to read about how one father’s blog played a pivotal role in connecting families whose children turned out to have the same rare (and at the time, undiagnosed) medical condition. 29.2 C). •    Capital expenditure investment needed to build in-house capability. Deann Akins-Lewenthal is the senior director of Food Safety and Enterprise Laboratory Services for Conagra Brands in Omaha, NE. It was highlighted that regulators could share examples of cases where companies have been exonerated using WGS, which could help promote the use of and increase confidence in WGS. The bioinformatics part is outsourced less.

Further complexities are linked to the methodology and relevant quality parameters for both the laboratory part (DNA extraction, library preparation, and sequencing), bioinformatics analysis, and, in particular, setting relevant single nucleotide polymorphism/allelic thresholds.

Another barrier is the time-to-results, which is usually more than 1 week. The Human Genome Project is a very ambitious undertaking and it required a lot of new technological developments in order to make it possible. In addition, all pathogen isolates that are collected through the agency’s current surveillance and inspection programs are being sequenced. “Interpreting Whole-Genome Sequence Analyses of Foodborne Bacteria for Regulatory Applications and Outbreak Investigations.” Front Microbiol 9:1482. As described in the literature, WGS data can be used for more than just pathogen source tracking. The possibility of benefits also comes with potential for harm, unintended consequences, and the altering of how we think about a number of cultural, personal, and biological issues. Learn more. Three applications of this genome sequencing include... Our experts can answer your tough homework and study questions. In 2014, a new work item proposal was submitted to the general committee for microbiology methods (TC 34/SC 9) and, after acceptance, the working group Whole-Genome Sequencing for Typing and Genomic Characterization was formed to develop a standard for WGS, ISO 23418. WGS and Its Use by the Food Industry The laboratory part (DNA extraction, library preparation, and sequencing) is frequently outsourced. Therefore, it is important to match the tool with the question that needs to be answered. Who bears the most risk? Other Applications of WGS There are also concerns about misinterpretation of data generated during internal investigations. Of these nine companies, five are using meta-barcoding, two are using metagenomics, and two companies are using a combination. Essentially this process determines the exact sequence of nucleotide bases that form DNA. Building a consortium with several interested food companies could be a more cost-effective approach. Whole-Genome Sequencing | June/July 2020 The Benefits and Barriers of Whole-Genome Sequencing for Pathogen Source Tracking: A Food Industry Perspective.

Even more so considering the fact that there are already established systems in place to eliminate pathogens from the value chain and production environment.

The survey and discussions provided unique insights into how, when, and for what purposes WGS is used by these companies. The lack of method standardization was also highlighted as a barrier. Prior to the workshop, a survey was sent out to collect information. 4. apps.who.int/iris/handle/10665/272430. Approximately how many nucleotide bases are in the... Why are chromosomes cut into fragments for... How is DNA Organized into Chromosomes? Although the level of WGS integration varies between companies, there was clear alignment that WGS has the highest discriminatory power of all subtyping tools and is sometimes the only tool that can give a conclusive answer, laboratory cross-contamination being a case in point. This cross-contamination can originate from proficiency testing scheme (PTS) strains or laboratory control strains or other wild-type isolates being tested in the same facility. There is a need to have an independent PTS that will be open to all laboratories, including the food industry and third-party laboratories. In addition to medical benefits, some believe that the advent of widespread sequencing could foster new connections among different people or groups.
It can also be used to predict potential virulence of strains as well as shelf life and spoilage potential of products. Nadon, C, et al.