A new study has demonstrated that the use of whole genome sequencing (WGS) has greatly reduced the burden of non-typhoidal Salmonella infections in Australia. Researchers estimate that the use of WGS in routine pathogen surveillance prevents thousands of foodborne salmonellosis cases and delivers millions in cost savings annually.

Published in The Lancet Regional Health—Western Pacific, the study is part of the Australian Pathogen Genomics Program (AusPathoGen), a comprehensive national program investigating pathogen genomics for public health in Australia. The research was led by researchers at Australian National University, in collaboration with the University of Melbourne, the University of Sydney, and public health and epidemiology departments in Victoria and Queensland.

The Burden of Foodborne Salmonellosis in Australia

According to figures from 2019, in Australia alone, foodborne pathogens account for 4.7 million illnesses annually, costing an estimated $1.7 billion USD (adjusted for inflation). Non-typhoidal Salmonella is one of the foodborne pathogens with the greatest public health and economic burden, accounting for 62,000 cases per year and costing $97 million.

The Need to Provide Evidence of WGS’ Success

WGS is recognized for enabling faster, more precise foodborne illness outbreak detection compared to traditional typing methods. However, its higher cost has raised questions about whether the benefits justify the investment. Despite its widespread application, empirical evidence about its success is scarce, with most data coming from small-scale studies or simulations, leaving a gap in large-scale, real-world data.

Adoption of WGS Across Australia

The research team assessed the impact of WGS by analyzing 15 years of national surveillance data from the National Notifiable Diseases Surveillance System (NNDSS), covering non-typhoidal Salmonella cases reported between 2009 and 2024. Using advanced statistical models, the study controlled for factors such as state-level differences, seasonal trends, and concurrent public health interventions.

Salmonella cases before and after WGS adoption were compared. Victoria was the first state to integrate the technology in 2016, shortly followed by New South Wales and Queensland. Tasmania and the Northern Territory implemented WGS most recently. At the time of the study, the Australian Capital Territory was the only jurisdiction that had not yet fully adopted WGS (and was therefore excluded from data analysis in the study), but the state benefits from WGS indirectly through sample sharing.

WGS Implementation Associated with Notable Reductions in Salmonellosis Cases

Analysis of the data showed an average 11.6–17.5 percent decrease in non-typhoidal Salmonella infections potentially attributable to WGS implementation. This reduction was most significant among the top 20 Salmonella serovars, which account for 72 percent of cases, with an average effect of 26.7 percent.

Based on these reductions, the researchers estimated that WGS likely prevents 7,200–10,900 cases annually, translating to $11.3–$17 million in savings. These cost savings surpass the break-even point calculated by the researchers, the net benefit of WGS is an estimated $4.2 million.

Findings are Consistent with International Studies

To the researchers’ knowledge, the present study is the first to use national-scale, longitudinal data to quantify WGS’ impact on foodborne disease surveillance in Australia.

The findings align with international research suggesting the benefits of WGS for foodborne pathogen surveillance, but show a stronger effect than recent U.S. estimates (1.5 percent reduction in salmonellosis burden) and more modest than Canadian simulations (50–70 percent reduction in salmonellosis burden). Additionally, a 2024 Canadian study analyzing the impact of WGS adoption on foodborne illness detection and response for four major pathogens found improvements in the number of outbreaks identified.

The findings are also consistent with a case study in Europe and America which found that, although WGS costs 2–4 times more than conventional methods, the percentage of non-typhoidal Salmonella cases needed to be avoided to break even is minimal.

Overall, the results confirm that WGS is not only valuable for food safety and public health but also economically viable.