Whole genome sequencing (WGS) provides a level of additional information that more than balances out the additional costs if used effectively, according to a recent study.

Researchers evaluated costs and benefits of routine WGS through case studies at eight laboratories in Europe and the Americas, including five which work with foodborne pathogens. All labs reported benefits from using WGS for pathogen identification and surveillance.

Work focused on the investment case for implementing WGS compared with conventional methods, based on costs and benefits in different periods between April 2016 and April 2019. For the five labs that do surveillance of foodborne pathogens, the reference period was typically a year.

These institutions — Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna (IZSLER, Italy), Administración Nacional de Laboratorios e Institutos de Salud (INEI-ANLIS, Argentina), Maryland Department of Health (MDH), Public Health Agency of Canada (PHAC), and Public Health England (PHE) — use WGS for characterization of bacterial isolates in pathogen surveillance, mostly Salmonella, Listeria, E. coli and Shigella.

In the 12-month period, IZSLER did 175 routine surveillance samples, INEI-ANLIS did 320, MDH did 1,767, PHAC did 8,630 and PHE did 15,791, according to the study published in the journal Eurosurveillance.

Higher costs vs. more info
Costs considered included equipment, consumables, staff and other expenses directly accrued by the institutions. Cost of equipment for the WGS workflow in the year of purchase ranged from €75,000 ($91,400) to €3.2 million ($3.9 million) for several sequencers and custom bioinformatics infrastructure.

The economic evaluation compared costs of using WGS to processing the same number of samples with the next-best conventional methods for pathogen identification and characterization.

Overall per-sample costs of WGS exceeded the price of conventional methods in all labs analyzed. Use of WGS was between 1.2 and 4.3 times more expensive. The average cost for the five reference labs that used WGS for routine surveillance of foodborne pathogens was €209 ($255) per sample.

Foodborne labs often relied on less costly equipment for conventional methods than the other sites and had a greater difference between the equipment costs for WGS and for conventional methods.

IZLER reported that the introduction of WGS had changed how food safety officials conduct sampling, by moving from looking at products to environmental sampling.

For foodborne pathogens, WGS analysis provided insights into how bacterial strains diversify over time, allowing strains to be identified as linked when they would have been considered unrelated under previous methods, according to PHE.

Outbreak detection impact
Labs that used WGS in routine surveillance of foodborne pathogens said there was a simplification of workflows and a reduced number of hands-on steps for analysis. The usual turnaround time was 5 to 10 days for WGS analysis. The time for full analysis of a foodborne pathogen using conventional methods was typically 4 to 15 days, depending on the pathogen and analysis required.

WGS affected the number and size of clusters detected and can reduce cases of illness, if public health systems are equipped and adequately funded to take effective measures. Clusters identified with conventional methods were confirmed or split with the help of sequence data, and a larger number of smaller outbreaks was found.

PHAC reported the number of Listeria outbreaks detected had decreased in the first year of WGS implementation, as PFGE had been detecting ones that did not exist and had led to an inefficient use of resources investigating non-existent outbreaks.

WGS allowed PHAC to identify 17 separate outbreaks of Salmonella Enteritidis infections associated with raw frozen breaded chicken products, which had not been picked up with conventional methods.

For the five labs that conduct Salmonella surveillance, researchers calculated the number and proportion of reported cases of salmonellosis that would need to be avoided to make use of WGS cost-neutral. The annual number to break even on costs ranged from one within INEI-ANLIS’ area of jurisdiction in Argentina to 82 within PHAC’s area of Canada.

The break-even analysis indicates that for Salmonella surveillance, only a modest percentage of reported salmonellosis cases would need to be avoided each year through the use of WGS to make adoption of the technology cost-neutral from a public health perspective, according to researchers.

The research took place through the COMPARE EU project funded by Horizon2020 that began in 2014 and ended in 2019.