Study: Listeria Surveillance in Australia Benefited from Decentralized Genome Sequencing
A study by researchers at the University of Melbourne and other Australian institutions revealed a drop in turnaround times in the national Listeria monocytogenes genomic surveillance system after decentralized sequencing was adopted.
The study was published in Emerging Infectious Diseases, a publication of the U.S. Centers for Disease Control and Prevention (CDC).
In Australia, invasive listeriosis has been a notifiable disease since 1991 and is recorded in the National Notifiable Diseases Surveillance System (NNDSS). Public health monitoring and action is managed by OzFoodNet, the national foodborne disease surveillance network. In 2010, the National Enhanced Listeriosis Surveillance System (NELSS) was established to collate both enhanced epidemiologic data from cases and molecular laboratory data from isolates.
Once NELSS was established, the National Listeria Reference Laboratory (NLRL), based at the Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL) in the state of Victoria, was tasked with providing national molecular characterization of all referred L. monocytogenes samples.
As a federation, Australia’s eight jurisdictions are independently responsible for their public health activities, including pathogen genomics. Since 2016, genomic sequencing capacity has expanded in Australia; MDU PHL continued WGS for Victoria, and four additional jurisdictions successively became responsible for their own L. monocytogenes whole-genome sequencing (WGS) during 2018–2023. The other three jurisdictions still refer samples to the NLRL for WGS.
“We investigated the timeliness and continued evolution of national L. monocytogenes surveillance from the perspective of the transition to a decentralized sequencing model,” the researchers report.
Using 1,204 samples collected during 2016–2023, the researchers observed statistically significant reductions in the median time from sample collection to the issuance of a national genomic surveillance report to 26 days, despite sample numbers doubling in 2022 and 2023.
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During 2016–2018, all jurisdictions referred samples to the National Listeria Reference Laboratory for sequencing and analysis, but as jurisdictional sequencing capacity increased, four jurisdictions transitioned to sequencing their own samples and referring sequence data to the national laboratory. One jurisdiction had well-established genomics capacity, transitioned without noticeable disruption, and continued to improve.
Another three jurisdictions initially had increased turnaround times, highlighting the need for defined sequence referral mechanisms. “Overall, timeliness and throughput improved, and sequencing decentralization strengthened Australia’s genomic surveillance system while maintaining timeliness. The practices described could be beneficial and achievable in other countries,” the researchers report.
The entire study—“Effects of Decentralized Sequencing on National Listeria monocytogenes Genomic Surveillance, Australia, 2016–2023”—can be found here.
