Description

Serotype

Microorganisms of a given serotype are classified together based on "cell surface" antigens, allowing the epidemiological classification of organisms that is more specific than the species level.  Antigens are suface proteins, antigen types (O, H, K, A) are based on the location of the antigen on the organism (oldest reference on this subject so far):  Kauffman F.  The serology of the coli group. J Immunol. 1947 Sep;57(1):71-100    http://www.jimmunol.org/content/57/1/71.abstract

Taxonomically and in the SNOMED CT Organism hierarchy, serotypes are subtypes of formal Linnaean classes.  Most are subtypes of either species or subspecies.  A few are subtypes of more general classes. 

Biotype

Microorganisms of a given biotype are classified together based on specific variation in biologic behavior (e.g. toxin producing).

Taxonomically and in the SNOMED CT Organism hierarchy, biotypes are usually subtypes of formal Linnaean classes.  Some are classes created at the genus level for grouping of species subtypes.

Issues:

1. Serotype methodology and the basic relationship between laboratory test results and organism names is relatively consistent.

2. Serotype biology varies with organism category.  This includes location of the antigens on the bacteria as well as the complexity and number of serotypes. Serotype terminology for some bacteria classes is formalized, governance exists, lists are published but this is not always the case.  Classes with significant serotype content:

   1. Enterobacteraciae

      1. Salmonella

         1. Serotype terminology maintained by WHO (WHO-CC) and CDC. 

         2. Specific serotype names (terms, descriptions) generated by laboratories are not identical to the some portion of existing "recognized names" that are created by WHO-CC.

            1. Some antigens are optional
         3. Laboratory reports and epidemiology networks generate unpublished serotypes.
            1. lag time from lab report and inclusion in SNOMED CT.
         4. PhD thesis on automating serotype naming (link)

      2. E. coli

         1. Very similar to Salmonella
         2. Less formal

      3. Shigella

         1. Very similar to Salmonella
         2. Less formal

   2. Vibrio

   3. Listeria

   4. Streptococci

   5. Aspergillus

   6. Chlamydia

   7. Viruses

3. Several different features of bacteria may produce a biotype.  There are also context dependent classifications.  Most frequently:

   1. Laboratory context
      1. Production of toxin (enterotoxigenic)
      2. Red cell hemolysis on blood agar
   2. Clinical context
      1. Pathologic behavior (enteropathogenic)

Objectives:

1. Create general terming rules for serotype content.
2. Create a general logical model for serotype content.
   1. Determine nature and placement of antigen (value) content in SNOMED CT
   2. Determine attributes
3. Initiate one or more SNOMED CT content projects to address inconsistencies and deficiencies.

Team

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