Using WGS requires ‘paradigm change’ in data processing

By Joseph James Whitworth contact

- Last updated on GMT

WGS: Challenges and opportunities
WGS: Challenges and opportunities

Related tags: Food safety, European union

Using whole genome sequencing (WGS) for food safety and public health requires a ‘paradigm change’, according to a report.

It details findings from a European Food Safety Authority (EFSA) event which gathered scientists, representatives of international and European organisations and national food safety authorities.

The 20th​ meeting in the EFSA Scientific Colloquium Series​ was held in June 2014 and concluded that a paradigm change is required in data processing.

It recommended WGS be initiated as soon as possible to exploits its potential.

The US Centers for Disease Control and Prevention (CDC) and the Food and Drug Administration (FDA) have a more wide-spread application of WGS but in the European Union (EU) there is limited experience in its use.

Data quality concerns

Definition of standards for data quality and analysis and interpretation are needed as without these, comparison between multiple laboratories and analysis will be very complex, error-prone and unreliable.

The biggest threat to successful implementation and use of WGS in public health is no longer technical but related to the sharing of data, said Peter Gerner-Smidt from the CDC.

“If the political, legal and psychological obstacles to free data sharing are not removed, genomics cannot possibly reach its potential for food safety but will be reduced to that of any other typing method.”

Legal obstacles are expected and a balance must be struck between desirable complete openness from a food safety point of view and privacy and related concerns as part of confidentiality.

The participants warned ignoring these issues is likely to considerably delay the successful large-scale implementation of WGS for public health at international level.

Sample preparation metrics are also needed since they can be used to exclude a sample from being sent to a sequencer, or for validating posterior analysis.

Adoption of appropriate quality assurance/quality control (QA/QC) measures; development and harmonisation of SOPs; the establishment of database infrastructure and generation and dissemination of appropriate sets of genomic data are needed to make WGS a routine application.

EU recommendations​ 

EFSA has strengthened collaboration with the European Centre for Disease Prevention and

Control (ECDC) and the European Union Reference Laboratories (EURLs) leading to the development of systems for molecular typing of foodborne pathogens.

A number of recommendations were made including EFSA encouraging scientific research on WGS and implementing results to benefit food safety, starting a communication strategy on the topic with the ECDC and stressing the urgency of using WGS for food safety in the EU.

Currently only a few organizations are investing in WGS approaches for real-time analysis of foodborne pathogens but many institutes are exploring the approaches through research collaborations or ‘in house’ using bench-top machines.

A major difference between WGS and the classical typing methods is it allows all genes to be included in the analysis, instead of a well-defined subset or variable intergenic regions so it will yield new insight.

The report said it is not clear whether new legislation is required for optimal utilization of WGS, or if the existing legal framework is sufficient.

Related topics: Food Safety & Quality

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