Abstract
The purpose of the study was to apply a Bayesian source attribution model to England and Wales based data on Salmonella Typhimurium (ST) and monophasic variants (MST), using different subtyping approaches based on sequence data. The data consisted of laboratory confirmed human cases and mainly livestock samples collected from surveillance or monitoring schemes. Three different subtyping methods were used, 7-loci Multi-Locus Sequence Typing (MLST), Core-genome MLST, and Single Nucleotide Polymorphism distance, with the impact of varying the genetic distance over which isolates would be grouped together being varied for the latter two approaches. A Bayesian frequency matching method, known as the modified Hald method, was applied to the data from each of the subtyping approaches. Pigs were found to be the main contributor to human infection for ST/MST, with approximately 60% of human cases attributed to them, followed by other mammals (mostly horses) and cattle. It was found that the use of different clustering methods based on sequence data had minimal impact on the estimates of source attribution. However, there was an impact of genetic distance over which isolates were grouped: grouping isolates which were relatively closely related increased uncertainty but tended to have a better model fit.
Highlights
Salmonella is a common cause of foodborne illness in people, with over 90,000 cases reported in Europe annually (ECDC, 2016)
While there were no major differences between source attribution estimates for the different clustering methods/distances, there were some differences in the findings
The source attribution estimate for game birds varied from 2.3% (SNP distance of 10 to group isolates) to 6.0% (SNP, HCC distance of 100 to group isolates) (Table 4)
Summary
Salmonella is a common cause of foodborne illness in people, with over 90,000 cases reported in Europe annually (ECDC, 2016). Salmonella is the second most common cause of gastrointestinal illness in the United Kingdom (UK), after Campylobacter. The number of United Kingdom laboratory reports of Salmonella in people in 2016 was 8,630 (PHE, 2018). A prospective community study determined that the true level of Salmonella infection in the United Kingdom could be five times greater in the community (Tam et al, 2012b). SE cases are largely linked to contact or consumption of poultry or eggs, ST Source Attribution Using Sequence Data whereas ST is present in a wide range of animal species and so it is more difficult to determine the source of ST cases
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