Abstract
Salmonella enterica is a common cause of minor and large food borne outbreaks. To achieve successful and nearly ‘real-time’ monitoring and identification of outbreaks, reliable sub-typing is essential. Whole genome sequencing (WGS) shows great promises for using as a routine epidemiological typing tool. Here we evaluate WGS for typing of S. Typhimurium including different approaches for analyzing and comparing the data. A collection of 34 S. Typhimurium isolates was sequenced. This consisted of 18 isolates from six outbreaks and 16 epidemiologically unrelated background strains. In addition, 8 S. Enteritidis and 5 S. Derby were also sequenced and used for comparison. A number of different bioinformatics approaches were applied on the data; including pan-genome tree, k-mer tree, nucleotide difference tree and SNP tree. The outcome of each approach was evaluated in relation to the association of the isolates to specific outbreaks. The pan-genome tree clustered 65% of the S. Typhimurium isolates according to the pre-defined epidemiology, the k-mer tree 88%, the nucleotide difference tree 100% and the SNP tree 100% of the strains within S. Typhimurium. The resulting outcome of the four phylogenetic analyses were also compared to PFGE reveling that WGS typing achieved the greater performance than the traditional method. In conclusion, for S. Typhimurium, SNP analysis and nucleotide difference approach of WGS data seem to be the superior methods for epidemiological typing compared to other phylogenetic analytic approaches that may be used on WGS. These approaches were also superior to the more classical typing method, PFGE. Our study also indicates that WGS alone is insufficient to determine whether strains are related or un-related to outbreaks. This still requires the combination of epidemiological data and whole genome sequencing results.
Highlights
Salmonella is a common cause of infectious disease in human and animals
Only a limited number of serovars that are responsible for most infections and in Europe, the most prevalent S.enterica serovars isolated from humans are Enteritidis and Typhimurium, responsible for over 75% of the human cases of salmonellosis [3]
Different typing methods are commonly used as a central part of the detection and investigation of Salmonella outbreaks, for instance, serotyping, phage typing, pulse-field gel electrophoresis (PFGE) and multilocus variable number of tandem repeat analysis (MLVA) [6,7,8]
Summary
Salmonella is classically divided into species S.bongori and S.enterica; the latter further divided into more than 2,500 different serotypes [1,2]. It is, only a limited number of serovars that are responsible for most infections and in Europe, the most prevalent S.enterica serovars isolated from humans are Enteritidis and Typhimurium, responsible for over 75% of the human cases of salmonellosis [3]. PFGE has been the gold standard for epidemiological investigations of foodborne bacterial pathogens including Salmonella [9]. MLVA has major benefits in epidemiological surveillance of some Salmonella [10], but serotype specific protocols are needed for high discrimination
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