Rapid detection and serovar identification of common Salmonella enterica serovars in Canada using a new pyrosequencing assay

Serotyping of Salmonella enterica subspecies enterica is a critical step for foodborne salmonellosis investigation. We have developed a new assay to identify Salmonella enterica subsp. enterica (S. enterica) serovars based on a triplex polymerase chain reaction (PCR) with pyrosequencing for amplicon confirmation and phylogenetic discrimination of strain. The top 54 most prevalent serovars of S. enterica in Canada were examined with a total of 23 single nucleotide polymorphisms (SNPs) and/or variations (SNVs) located on three genes (fliD, sopE2, and spaO). Seven of the most common serovars, including Newport, Typhi, Javiana, Infantis, Thompson, Heidelberg and Enteritidis are successfully distinguished from the other serovars based on their unique SNP/SNV combinations. The remaining serovars, including Typhimurium, ssp I 4,[5],12:i:-, and Saintpaul are further divided into 47 subgroups that demonstrate the relatedness to phylogenetic classifications of each serovar. This pyrosequencing assay is not only cost-effective, rapid, and user-friendly, but also provides phylogenetic information by analysing 23 selected SNPs. With the additional layer of confidence to the PCR results and the accuracy and speed of pyrosequencing, this novel method would benefit the food industry and provides a tool for rapid outbreak investigation through quick detection and identification of common S. enterica serovars in Canada.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author