The World Health Organization is encouraging all countries to look at how whole genome sequencing  can be used to improve their foodborne disease surveillance and response system.

Used as part of such a system, whole genome sequencing (WGS) can increase the speed with which illnesses and food contamination are detected and the detail in which they are understood. That information leads to quicker and more targeted interventions, according to the international agency.

Data from the European Food Safety Authority shows that by the end of 2016, WGS was being used in labs in 17 out of 30 countries.

A landscape paper prepared by technical experts from laboratories and public health authorities summarizes the benefits and challenges in implementation of WGS and describes issues developing countries may face. WGS-based prospective surveillance places greater responsibility on public health labs and requires collaboration between the lab and public health units, including real-time data sharing.

The U.S. Food and Drug Administration has been using WGS since 2008. Consequently, the FDA and U.S. Centers for Disease Control and Prevention, as well as state laboratories, have access to an ever-increasing data base of specific serotypes of pathogens.

Previous standard typing methods for many foodborne bacterial pathogens were antigen testing, pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem-repeat analysis (MLVA). However, these methods have a lower level of strain discrimination than WGS.

The WHO report said isolation of foodborne pathogens by culture remains a critical step with the introduction of culture-independent diagnostic (CID) testing or molecular tools. Health care providers who use CID testing frequently do not take steps to make sure a portion of patient samples are retained for more specific analysis.

“While molecular diagnostics may improve sensitivity and specificity, increasing reliance on these methods may result in a loss of critical information, as pathogens are less often recovered by culture and submitted for analysis, thus hampering surveillance efforts,” according to the WHO.

Using WGS can exclude outbreak relations. For example, when a parallel increase in Salmonella Newport infections were reported in The Netherlands and Ireland, WGS revealed they were not related and there was no cross-border outbreak.

Whole genome sequencing has increased the ability to distinguish between outbreak-related and sporadic cases, to link sporadic cases to food and animal sources, and to identify points of contamination and areas requiring intervention during product trace-back and recalls.

It can be used to exclude wrongly suspected sources of infection such as a specific food, which helps prevent economic damage to industry.

“This greater sensitivity will allow limited resources to be better focused on outbreaks that are more likely to be solved, which could lead to faster resolution of outbreak investigations; however, it is important to note that WGS will identify more links and clusters than are able to be acted upon,” according to the report.

“While rapid availability of outbreak data can reduce the economic loss to some extent, this creates a predicament for the food provider in rapidly releasing information that will benefit health, but that may be harmful to their industry.”

Implementation of WGS will require extra resources and technical training and it is important that historical information is not lost. In low resource settings, data storage and transfer could pose a challenge due to infrastructure and technical requirements.

To implement WGS there needs to be a basic epidemiology, surveillance and food monitoring and testing infrastructure already in place which many low-income countries are still developing. Sufficient lab capacity, shipping requirements for reagents with limited shelf life, and functional agencies that can act on the data produced through WGS are other challenges.

A key component of the transition to WGS in low-income countries will be training.

Cost estimates for establishing sequencing capabilities for public health labs transitioning from PFGE to WGS vary between US$100,000 and US$700,000, depending on throughput of isolates and the need for draft or complete genomes.

“While the cost of sequencing has declined over time with the development of less expensive technology and platforms, the equipment and reagents are still expensive for many countries, and may be a barrier to implementation for low-income countries,” according to the report.

For data sharing, there are technical challenges as well as legal and ethical hurdles.

“The legal ownership of WGS data produced from isolates collected by different institutes and from different sources is an issue. This may be a particular concern for data on isolates from commercial parties, collected for example by food safety authorities),” according to the WHO report.

“Some scientists may choose to hold onto their data for fear that others may use them unethically. A functioning and effective global WGS data-sharing mechanism will only be possible if all users can be sure that sharing their data will not work against them.”

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