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Sequencing alone ‘not enough’ to ensure food safety management

By Joe Whitworth+

06-Jan-2017
Last updated on 06-Jan-2017 at 13:30 GMT2017-01-06T13:30:47Z

©iStock/royaltystockphoto
©iStock/royaltystockphoto

Whole Genome Sequencing (WGS) is advantageous but does not replace the need for basic epidemiology, according to experts.

While the technology has advantages over the multiple traditional culture-based methodologies in food bacteriology it does not replace epidemiology, health surveillance and food monitoring, they said.

Comments were made at the ninth Global Microbial Identifier (GMI) meeting at the Food and Agriculture Organization of the United Nations (FAO) in Rome.

It was attended by 175 participants from 50 countries including 26 developing nations.

Foundation needed

Sequencing alone, described as the ‘simplest part of the process’, was not enough, said participants.

The importance of collaboration among clinicians, laboratory experts, epidemiologists, food/environment inspectors was needed to benefit from the technology and achieve the goals of food safety management, which are to save lives and reduce economic losses.

Many developing countries are still creating basic functional surveillance and monitoring systems.

If there is no isolate to analyze the implementation of WGS has no usefulness, said participants.

Equally important is functional authorities/agencies to act on data produced through WGS, they added.

In countries where there is no such infrastructure, establishing systems that include routine collection and analysis of food and environmental samples is a key pre-requisite to doing WGS.

Where there is no facility or equipment for WGS, and/or no sufficient capacities in use/interpretation, implementing it requires a high cost of initial investment in setting up and maintaining the working environment for routine use.

“If a given country already has an effective food control system, WGS will likely reduce the cost of food safety management, and if the country still needs to strengthen the basic food control system, it can be expensive.”

Participants from developing countries also expressed the need to discuss capacity, regulatory and resource implications prior to considering the new technology.

If some countries use WGS for food safety management, they are likely to apply the same system for imported food.

However, many developing countries with limited capacity and resources may not be able to provide the same level of WGS-based data on food products they export.

Multi-use WGS

Participants recognized benefits of using WGS not only as a regulatory tool but applications including supply chain management, quality assurance and process evaluation.

Use is likely to help competent authorities ensure they are in compliance with relevant international trade agreements and practices and results in trade partners having increased confidence in a nation’s food control system.

WGS provides a basic common language suitable for electronic exchange globally. This is an added value over current methods of data sharing, because it provides context for local investigations, using globally available data, said participants.

It is cost effective, because routine use will eventually replace multiple traditional subtyping methods necessary to characterize pathogens, which vary according to the target of interest.

The cost of sequencing and analysis is declining over time, even though the cost of reagents and initial investment are still too expensive for many countries.

Interpretation of WGS data (bioinformatics)

Relying solely on WGS data to make food safety management decisions is not yet recommended as sequencing results can contain errors, including sequence-specific ones.

Also errors during the interpretation process, including human ones should be considered. False negative results due to poor analysis could lead to bad decisions which could damage the credibility of a country’s food control system.

The sensitivity can lead to detecting trace level of microorganisms, in every environment, and possibility to share such results in a public domain can make some hesitant to use WGS and openly share relevant data.

The WGS data, generally stored in the FASTQ format in the data repositories, are very big with accumulated file size in the range of tera- and peta-bytes.

Challenges will also emerge around the trust of data producers, generators and collectors regarding the use of their data.

GMI 10, organized by Technology and Food Safety Services (TECSIA) and the GMI Steering Committee, will be at the Sheraton Hotel, Cabo San Lucas, Mexico, 15-17 May 2017.

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