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

The procedures depicted in this example are:

• Bacterial culture
• Microscopy
• Multiplex PCR
• Serotyping
• Ag detection by latex agglutination

This example shows that the representation of the same diagnostic steps for pathogen detection does not differ in the application of the codes in "Observation.code", "Observation.value" and "Observation.method" depending on the specimen examined. According to the established rules for handling semantics, the LOINC codes used in "Observation.code," in particular, should be non-specific for the specimen (axis "system"). Identical diagnostic steps are depicted in the same way with regard to the question in "Observation.code" and the method used in "Observation.method", regardless of the specimen. The specimen is described using the FHIR resource "Specimen."

• In this example, the starting specimen, blood culture and CSF sample, are mapped in the FHIR resource "Specimen" as "Specimen.type" and all "Observations" that depict the diagnostic steps and their results refer to the single FHIR resource "Specimen".

Diagnostics from Blood Culture

• The results of the anaerobic blood culture have been omitted in this example.
• Growth occurs in the aerobic blood culture. Gram-negative diplococci can be detected in microscopy performed after culture enrichment.
• Neisseria meningitidis can be detected in multiplex PCR performed directly from the aerobic blood culture bottle. For the sake of clarity, a larger selection of analytes from a multiplex PCR from blood cultures is not shown in this example. Only the "observation" with the detection of Neisseria meningitidis is shown.
• This example makes it clear that in addition to referencing each individual "observation" to the "specimen," it is also necessary to referencing each observation to the other.
  • The microscopy is performed after culture enrichment. The "Observation" with a description of the microscopy references the "Observation" describing the result of the culture enrichment via "triggeredBy".
  • The multiplex PCR is performed directly on the source material and references the "Specimen" alone.
  • Serotyping is only performed after the pathogen has been detected using multiplex PCR and accordingly also refers to the "observation" that describes the molecular diagnostics.
• In this example, serotyping is performed from blood culture material. A LOINC code is used for serotyping, which, depending on the test or test kit used, asks for the detected Neisseria meningitidis serotype. The LOINC code "70172-2 Neisseria meningitidis serogroup [Identifier] in Specimen" allows the answer that a Neisseria meningitidis serogroup was not detected or to describe which serogroup was detected. The answer can be represented using SNOMED codes, e.g., "103480009 Neisseria meningitidis serogroup B (organism)".

Diagnostics from CSF

• Microscopy, multiplex PCR, and antigen detection are performed on CSF. All three diagnostic steps refer solely to the specimen; there is no further interdependence between the observations.
• The "Observation" describing microscopy and multiplex PCR, two diagnostic steps that in this example are performed on both the blood culture and the CSF sample, have the same LOINC code "41852-5 Microorganism or agent identified in specimen" and "49671-1 Neisseria meningitidis DNA [Presence] in Specimen by NAA with probe detection" in "Observation.code" for the same question, and the same SNOMED codes "708061008 Gram stain technique (qualifier value)" and "1303998006 Multiplex polymerase chain reaction technique (qualifier value)" in "Observation.method". The only difference lies in the reference to the "Specimen" describing the different starting specimen. For the sake of clarity, this example also omits the depiction of additional analytes from a multiplex PCR from CSF, and only presents the "observation" with the detection of Neisseria meningitidis.
• In addition, although certainly not performed following a multiplex PCR in routine diagnostics, Neisseria meningitidis antigen detection using latex agglutination is described. This example demonstrates that, in accordance with the rules for handling semantics, a LOINC code specific to the analyte (the "component" axis) was selected based on the test question or test approach. Here, the question about the presence of Neisseria meningitidis Ag is posed with the LOINC code "31912-9 Neisseria meningitidis Ag [Presence] in Specimen". The answer can be "positive" or "negative". The corresponding SNOMED codes are used in this example.