Semantics Examples

The examples presented here are primarily intended to illustrate the implementation of the rules established for ARS for handling semantics, i.e., the interaction of LOINC and SNOMED-CT as the two central terminologies for representing microbiological data.

The representation of sequential diagnostics with sequential transmission of results taking lifecycle management into account is not the goal of these examples. For this see the chapter Life-cycle-management. Arrows in these examples indicate which examination step, represented by an "observation," has been triggered by a previous examination. For example, a phenotypic susceptibility test is triggered by the detection and identification of a pathogen. In FHIR, this corresponds to the relationship between observations through "triggeredBy" (see also Laboratory Test (Observation)).

Each "Observation" also references the resource "Specimen." For reasons of clarity, this reference has only been shown for one "Observation" in the examples.

Methods that are not always routinely performed simultaneously as part of a diagnostic test series are sometimes represented within a single example in the following examples, e.g., MALDI-TOF and multiplex PCR in pathogen identification, or carbapenemase rapid testing and carbapenemase PCR for determining the carbapenemase group. The aim of these examples is to demonstrate the application and interplay of the terminologies and thus to represent codes that can be used repeatedly for different diagnostic steps in accordance with the formulated rules for handling the semantics.

Overview of Examples in this Chapter

Example 1 - Detection of Klebsiella pneumoniae in aerobic blood culture with non-susceptibility to carbapenems and detection of KPC-2 carbapenemase

Example 2 - Detection of Pseudomonas aeruginosa in an aerobic blood culture with non-susceptibility to penicillins, cephalosporins, and carbapenems

Example 3 - Invasive meningococcal disease with detection of Neisseria meningitidis, serogroup B, in blood culture and CSF

Example 4 - Direct and indirect detection of Clostridioides difficile

Example 5 - Screening for MRSA

Example 6 - Resistance Classifications - MRGN

Example 7 - Direct and indirect detection of measles virus

Example 8 - Detection of Candida auris

Example 9 - Detection of Aspergillus

Example 10 - Detection of Plasmodium ovale using a rapid test and microscopic detection in a thick droplet