Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Comment: Published by Scroll Versions from space SCTC and version 1.7

Microbiology Editorial Guidelines 

The current page will no longer provide the SNOMED CT Content Development Canadian Editorial Guidelines for Microbiology.

All implementers are requested to align to

access the latest Microbiology Editorial Guidelines now available in the current release of the . Microbiology specific guidelines are listed in the following section of the SNOMED CT Editorial Guide:

and follow the guidelines listed in the Observable Entity and Microbiology Test Results

. These pages describe Infoway’s approach to applying the Editorial Guidelines from SNOMED International to create SNOMED CT concepts for Microbiology. This includes:

 Generic Canadian Editorial

 

English Generic Editorial

Guidelines

Canada Health Infoway (Infoway) publishes

English

GenericCanadian Editorial Guidelines. These guidelines should also be consulted, along with the SNOMED International Guidelines prior to creating and submitting any new content for submission to Infoway.

Microbiology References

References are required when submitting requests for new concepts.

Here

 

SNOMED International

For content that meet the International inclusion criteria, here is the list of a few resources that SNOMED International considers when reviewing the changes applicable to the Organism hierarchy:

Bacteria:

Fungus:

Viruses:

Parasites:

General

Organism Naming Conventions

 

  • The SNOMED Editorial Guide includes naming conventions that apply to all SNOMED CT concepts. However, additional principles apply to the naming of concepts in the Organism hierarchy, and these differ from the general naming conventions, so it’s important to familiarize themselves with the detailed rules found in the Organism Naming Conventions in section of the Editorial Guide. (https://confluence.ihtsdotools.org/display/DOCEG/Organism+Naming+Conventions)
  • When considering a name, the first task is to consider if the  whether the concept represents an organism or taxonomic group of organisms that has a scientific name in the Linnaean taxonomy e.g. Escherichia coli (organism) or Genus Escherichia coli (organism) or Family Enterbacteriaceae (organism) . 
  • The non-Linnaean categories of organisms are reflected in SNOMED CT concepts which identifies a staining property, a physiological characteristic (that the organism requires oxygen) and a description of the organism’s morphology (that it is rod-shaped). These are among the properties used in a laboratory to determine the identity of a bacterial organism in a specimen, culture, or isolate. e.g Gram-negative aerobic rod (organism) or Deoxyribonucleic acid virus (organism) 

  • The Editorial guide specifies the source listed above to be considered when determining an organisms current name.

Serotypes and Serogroup in Microbiology

A serotype or serovar is a distinct variation within a species of bacteria or virus or among the immune cells of different individuals. Microorganisms, viruses, or cells are classified together based on their cell surface antigens, allowing the epidemiologic classification of organisms to the subspecies level. 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 surface proteins that based on its location on the organism are classified as types O, H and K. Serotype biology does vary with the organism category and includes the location of the antigens on the bacteria as well as the complexity and number of serotypes.

A group of serotypes with common antigens is called a serogroup or sometimes serocomplex. An example of this is the Salmonella enterica subsp. arizonae (organism) (ConceptID 397502001) which infects the human gut and is responsible for various diarrheal infections across the globe.

Authoring E Coli Serogroup for H

Conventional Escherichia coli (E. coli) O:H serotyping by agglutination of somatic and flagellar antigens with the use of anti - E. Coli polyclonal antiserum is time-consuming, expensive, and available only in a small number of reference laboratories. When reporting the H antigen, it should be remembered that the O antigen is always present. In Canada, it is only a few that have reported it over the years untyped or untypable O antigens. For all organisms, the flagellar has to have the somatic.
For the Ecoli with H typed we have examples like Escherichia coli serotype O7: H18, where the parent is
458090002 |Escherichia coli serogroup O7 (organism)| Parent
458099001 |Escherichia coli serotype O7: H18 (organism)| Child

For E Coli where the O antigen is not typed or was unable to be typed, the guidance is to use E coli serogroup O undetermined: H
Escherichia coli serogroup O undetermined: H (organism), indicate that the O is textual as undetermined as it is not known
Escherichia coli serogroup O (organism)| Parent
• E coli serogroup O undetermined: H (Child)
o Escherichia coli serogroup O undetermined:H19 (organism) Child




SNOMED Canadian Edition

For content that meet the only National inclusion criteria, here is the list of a few resources that is suitable for SNOMED Canadian Edition considers when reviewing the changes applicable to the Organism hierarchy. These references are suitable when a request does not meet the inclusion criteria for submission for SNOMED International. 

General: