Bayesian Source Attribution of Salmonella Typhimurium Isolates From Human Patients and Farm Animals in England and Wales

被引:11
|
作者
Arnold, Mark [1 ]
Smith, Richard Piers [1 ]
Tang, Yue [2 ]
Guzinski, Jaromir [2 ]
Petrovska, Liljana [2 ]
机构
[1] Anim & Plant Hlth Agcy APHA, Dept Epidemiol Sci, Addlestone, Surrey, England
[2] Anim & Plant Hlth Agcy APHA, Dept Bacteriol, Addlestone, Surrey, England
来源
FRONTIERS IN MICROBIOLOGY | 2021年 / 12卷
关键词
source attribution; Salmonella Typhimurium; Bayesian modelling; SNP distance; multi locus sequence typing; core-genome multi locus sequence typing;
D O I
10.3389/fmicb.2021.579888
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
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.
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页数:11
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