Science: Salmonella serotyping using next-generation sequencing

Recently, there has been a lot of attention around next-generation sequencing—whole genome sequencing (WGS) in particular—for outbreak investigations. Neogen has posted a few articles on our blog and foodsafetytech.com to help articulate the applications of whole genome sequencing.

While whole genome sequencing is being used as a replacement for pulsed-field gel electrophoresis (PFGE), some companies and industries still rely on lower resolution techniques to simply subtype organisms as an initial piece of information on source tracking. For example, if Salmonella is a recurring issue within a production environment, serotyping can be used to eliminate a point source between different serotypes. However if the serotypes match, it cannot be inferred that the serotypes are the exact same organism, and WGS would provide additional resolution.

A unique application of next-generation sequencing is targeted amplicon sequencing. Instead of sequencing genetic information that does not provide usable genetic data, a targeted amplicon approach allows for only specific genes of interest to be amplified, identified and then aggregated to help serotype a Salmonella isolate. One example of this approach is NeoSeek Salmonella serotyping, which uses specific regions of the Salmonella DNA that can be mapped or bar coded for a serotype ID. NeoSeek leverages a few key genetic regions of the Salmonella genome. These genes code for the O-antigen, H-antigen and an additional area called the ISR region. The combination of these genes, when identified, coordinates with a traditional Kauffmann-White scheme used in traditional microbiology. However, because NeoSeek is a molecular serotyping method, antigens that may not be expressed can still be identified and used in correctly identifying the isolate.

Since targeted amplicon sequencing allows for the identification of key genes needed to make a determination of a sample, this approach is useful for serotyping and in a targeted metagenomics approach, such as 16S metagenomics. NeoSeek Salmonella serotyping is precise because it uses a combination of genes that comprises approximately 4,500 base pairs. For comparison, a DNA probe or Isothermal marker used in Salmonella species assays are approximately 100 base pairs.

NeoSeek Salmonella serotyping is an example of next-generation sequencing beyond WGS. The service allows companies to obtain serotypes without the limitations of extensive antigen libraries and a seasoned microbiologist for interpretation.