V.MFS.0460 - Molecular risk assessment of Salmonella in red meat
| Project start date: | 30 November 2021 |
| Project end date: | 28 November 2023 |
| Publication date: | 17 October 2023 |
| Project status: | In progress |
| Livestock species: | Grain-fed Cattle, Grass-fed Cattle, Sheep, Goat, Lamb |
| Relevant regions: | National |
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Summary
Salmonellosis remains a significant public health issue, and foods of animal origin are most frequently considered to be the vehicle through which humans are infected. Regulatory authorities in the US are considering changes to their position on Salmonella which may require a response from Australian exporters. This work will characterise the genes in Salmonella isolated from red meat sources using approaches emerging from the US regulator that will help to classify the Salmonella as being a high or a low risk to human health. The data collected will help to prepare industry and government to respond to expected regulatory changes in the US.
Objectives
The project was designed to provide initial genomics insights into Australian red meat and human derived Salmonella. The objectives of the project were (i) to determine if Australian isolates align with the major disease-causing serovars identified in US human cases which are referred to as highly pathogenic Salmonella (HPS) or DENT (i.e. Enteritidis, Typhimurium, 1,4,[5],12: i:-, Newport, and the invasive serotype Dublin) and (ii) conduct genomic analyses, including comparisons with publicly available Salmonella sequences to determine if Salmonella from Australian red meat supply chains align with Salmonella Australian human clinical cases of salmonellosis.
Key findings
Except for S. Typhimurium, few Salmonella from Australian red meat sources belonged to the major HPS serovars. Phylogenetic trees showed that some serovars of Australian Salmonella isolates clustered mostly by host (animal or human for S. Typhimurium and S. Infantis), while other serovars did not cluster by host (S. Saintpaul and S. Bovismorbificans). Several virulence genes were shown to be highly associated with some serovars but not others. Isolates from the same serovar mostly had similar virulence gene profiles, regardless of source (animal vs human), however, a small number of genes were shown to be more prevalent in humans, while others were more prevalent in animals. AMR genes were detected in very low percentages of the Salmonella isolates, with most AMR genes absent from most animal derived strains.
Benefits to industry
The database of Salmonella sequences, genomics capability and workflows developed in this project will serve as a valuable resource for industry to better understand and manage risks associated with Salmonella. In addition, data can be used to inform risk management practices that in turn minimise the reputational, trade and public health risks associated with contaminated beef entering domestic and export markets.
Future research
In the absence of international standards, we recommend assessing the performance of bioinformatics-based typing methods against traditional ‘gold standard’ characterisation tools or commercial test methods for identifying HPS (when/if they become available). Additional surveys of Salmonella could be undertaken on animals across a broader range of different sample sites (e.g., hides and lymph nodes) to identify potential carcase contamination pathways for HPS. Further attempts should be made to establish collaborations with US-based researchers to access propriety information for deeper assessment of HPS and DENT serovars. Comparison of Australian HPS with international HPS should be conducted. Collaborations should be pursued with local public health labs to gain access to richer metadata sets for improved risk characterisation. When/if available, rapid systems should be trialled for the semiquantitative or quantitative detection of high-risk Salmonella.
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For more information Contact Project Manager: John Marten |
