Abstract
Salmonella serotyping remains the gold-standard tool for the classification of Salmonella isolates and forms the basis of Canada’s national surveillance program for this priority foodborne pathogen. Public health officials have been increasingly looking toward whole genome sequencing (WGS) to provide a large set of data from which all the relevant information about an isolate can be mined. However, rigorous validation and careful consideration of potential implications in the replacement of traditional surveillance methodologies with WGS data analysis tools is needed. Two in silico tools for Salmonella serotyping have been developed, the Salmonella in silico Typing Resource (SISTR) and SeqSero, while seven gene MLST for serovar prediction can be adapted for in silico analysis. All three analysis methods were assessed and compared to traditional serotyping techniques using a set of 813 verified clinical and laboratory isolates, including 492 Canadian clinical isolates and 321 isolates of human and non-human sources. Successful results were obtained for 94.8, 88.2, and 88.3% of the isolates tested using SISTR, SeqSero, and MLST, respectively, indicating all would be suitable for maintaining historical records, surveillance systems, and communication structures currently in place and the choice of the platform used will ultimately depend on the users need. Results also pointed to the need to reframe serotyping in the genomic era as a test to understand the genes that are carried by an isolate, one which is not necessarily congruent with what is antigenically expressed. The adoption of WGS for serotyping will provide the simultaneous collection of information that can be used by multiple programs within the current surveillance paradigm; however, this does not negate the importance of the various programs or the role of serotyping going forward.
Highlights
IntroductionSalmonella enterica is one of the most prevalent foodborne pathogens world-wide and a major causative agent of gastroenteritis in North America (Kim et al, 2006; Hendriksen et al, 2011; Parmley et al, 2013; Thomas et al, 2013; World Health Organization, 2015)
There is some evidence that certain minor antigenic factors such as O:6 are variably expressed, which would mean that serovars such as Hadar (6,8:z10:e,n,x) and Istanbul (8:z10:e,n,x) are one and the same (Mikoleit et al, 2012)
An updated White-Kauffmann-Le Minor (WKL) scheme could potentially resolve these issues thereby reducing the number of inconclusive matches recorded by SeqSero; as serovars with these antigenic formulas were reported as both possible options
Summary
Salmonella enterica is one of the most prevalent foodborne pathogens world-wide and a major causative agent of gastroenteritis in North America (Kim et al, 2006; Hendriksen et al, 2011; Parmley et al, 2013; Thomas et al, 2013; World Health Organization, 2015). Serotyping is performed through the phenotypic characterization of the O and H antigens via the slide agglutination test, in which the clumping of cells is observed in response to specific antisera This technique is widely used (Wattiau et al, 2011), it can be time consuming and laborious (Kim et al, 2006; Wattiau et al, 2011; Zhang et al, 2015), and still leave five to eight percent of all Salmonella isolates untypeable (Kim et al, 2006)
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