Salmonella serotyping using a targeted genome sequencing approach

Salmonella is a common bacteria found in the intestinal tracts of warm-blooded animals, and is a leading cause of human foodborne illness. In order to identify Salmonella outbreaks and perform source tracking, public health laboratories have employed serotyping as a preferred approach. Traditional serotyping evaluates two structural antigens: the membrane bound O antigen and the flagellar H antigen. Adding complexity to the ability to source track is the vast antigenic diversity displayed by Salmonella species. There are over 2,500 known serotypes of Salmonella, though less than 100 serotypes account for most human infections. The current serotyping method requires expression of the target antigen, are subject to antisera lot inconsistencies and shelf life, and require scientific expertise in interpreting agglutination reactions.

The advent of molecular sequencing has greatly accelerated the pathogen detection and characterization processes. Whole genome sequencing (WGS) has allowed for rapid, accurate and detailed analysis of virulence genes and is gaining acceptance as a tool for outbreak investigation and isolate identification. The goal of this talk is to introduce targeted amplicon sequencing as a tool for Salmonella serotyping. Targeted amplicon sequencing evaluates specific regions within the pathogen genome, rather than sequencing the entire genome as with WGS. In this talk, the following will be accomplished: presentation of sequencing evolution through WGS; targeted amplicon sequencing will be explained; a comparative assessment of targeted amplicon sequencing to traditional serotyping will be discussed (including assay accuracy, serotype coverage, sample analysis cost and turn around time, as well as other benefits).