Salmonella Identification Techniques
Pathogen strain typing may be useful to help identify the source of contamination or to assess outbreak association risk; however, it may not be necessary depending on whether affected product has been released to commerce. If product has been released into commerce resulting in a recall, there may be regulatory pressure to determine strain type to see if it matches strains that have been involved in past or current outbreaks. Strain typing is also valuable in tracking the source of the strain, such as contaminated ingredients or processing environment locations.
What is serology testing?
The process of identifying certain bacteria by the reactions that take place between specific antibodies (antisera) and specific bacteria cell-surface antigens is the science of serology. By documenting which antibodies are reactive (through observation of agglutination reactions) and which are not reactive, bacteria can be classified into those groups that share similar reaction profiles. Eventually through a process of iterative elimination testing, various antisera against both O (outer surface) and H (flagellar) antigens allow for more specific (smaller and smaller) groupings until the final group consists of only one serotype.
In food microbiology, Salmonella, Listeria monocytogenes, and E. coli are the most common bacteria for which serotyping is used for strain differentiation. Additional technology options are available for identifying/classifying pathogens such as traditional biochemical profiling and whole genome sequencing (WGS) using next generation sequencing (NGS).
Whole genome sequencing vs serotyping
When a microbial genus or species is identified, sometimes it is useful to know if one isolate is related to another. As described in the last segment, serology is useful in food microbiology for the identification of a small subset of organisms. In theory, any living organism can be identified through whole genome sequencing. Both technologies rely on databases of information that function as the reference against which unknowns are compared.
For serotyping, these databases have long since been complete. However, for Whole Genome Sequencing (WGS), there are many large gaps as the vast majority of microorganisms have not been sequenced completely. For example, in food microbiology, not all Salmonella serotypes have been subjected to WGS though that gap is closing very fast. Because of this gap, attaching a serotype to a sequence is not always possible. Whole Genome Sequencing has what we call greater “resolution”. Think of it like a zoom lens on a camera or microscope. Serotyping might be at 1000X, but to know “everything” about an identification of an organism, you need the genotype (the WGS) and this may require a 5000X or even 10000X zoom lens to see. Only WGS can resolve that deeply. In practice however, that great a resolution is usually not needed, and as you might imagine a ton of data is generated in the process of obtaining a WGS.
Dealing with that data (the field of bioinformatics) is still a difficult and slow process. The main draw to serotyping is that it has been around a long time and many companies have existing databases of information describing the serotypes they have encountered before. They just need the serotype so they can know if it one they have seen in the past, and classical Kaufmann-White Salmonella serotyping is a reliable, affordable way to get it.
So which is best to use? Well it really depends on what you need so everyone's solution is different.
But why would you further identify or characterize Salmonella isolates?
The most common reason would be for source tracking of potential routes of contamination in a production environment. Basically answering the question, has this particular strain been isolated before in ingredients, products, or in the environment? Further, it may be possible to track the isolate through the production process and determine how it might have become out of control. Source tracking becomes essential in outbreak and/or product recall investigations.
Depending on regulatory expectations there may be industry-specific requirements in poultry or meat processing that are specific for Salmonella Enteritidis, Salmonella Typhimurium, or other serotypes so those isolates must be identified. Another example includes large poultry companies that vaccinate their flocks and desire to assess efficacy against strains that are circulating in their production facilities in order to prepare appropriate vaccines for the following year.
Salmonella Identification with Eurofins
Eurofins has a scientific team dedicated to performing these techniques. Our team currently has a list of the top 26 Salmonella strains we frequently encounter and have appropriate antisera on hand to identify hundreds of additional strains. Our serotype identification success rate is greater than 90%.
With so many Salmonella strains found in nature, there are unique situations where we come across a strain not covered by our current antisera menu. In these instances, we can procure additional antisera but these less-common antisera occasionally are difficult to obtain from providers. In addition, these less-common antisera are very costly (~$600/vial from suppliers), which is why we do not keep them all on hand due to infrequent use and limited storage shelf life. Should more routine use be desired by a customer, we are happy to entertain stockage of such antisera in our inventory. That said, most customers get enough information from O type and factor 1 antisera.
For further questions related to Salmonella identification for a particular product or matrix...
