Effects of Decentralized Sequencing on National Listeria monocytogenes Genomic Surveillance, Australia, 2016–2023

Abstract

We assessed turnaround times in the national Listeria monocytogenes genomic surveillance system in Australia before and after decentralized sequencing. Using 1,204 samples collected during 2016–2023, we observed statistically significant reductions in median time from sample collection to issuance of national genomic surveillance report to 26 days, despite sample numbers doubling in 2022 and 2023. During 2016–2018, all jurisdictions referred samples to the National Listeria Reference Laboratory for sequencing and analysis, but as jurisdictional sequencing capacity increased, 4 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 3 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.