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

The procedures illustrated in this example are:

• Bacterial culture
• Light microscopy after Gram staining
• MALDI-TOF
• Microdilution for phenotypic resistance testing (qualitative results)
• Rapid carbapenemase test
• Carbapenemase PCR
• Carbapenemase sequencing

In this example, only one LOINC code, "41852-5 Microorganism or agent identified in specimen", is used for all methodological steps for pathogen identification. This LOINC code reflects the requirement for non-specific pathogen detection and asks whether a pathogen was found in the submitted material, and if so, which one.

The received blood culture bottles are considered two different materials and are coded accordingly in the FHIR resource "Specimen" as aerobic and anaerobic blood culture bottles using SNOMED codes in "Specimen.type". This corresponds to the idea that the material received by the laboratory is coded under "Specimen.type".

• No growth occurs in the anaerobic blood culture bottle after incubation. This result is mapped to the FHIR resource "Observation." The method specified in "Observation.method" is culture with the SNOMED code "703725008 | Culture technique (qualifier value)". The result of the culture enrichment in the anaerobic blood culture bottle is negative; no growth occurs. The result is described as "Observation.valueCodeableConcept" with the SNOMED code "264868006 No growth (qualifier value)".
• Growth occurs in the aerobic blood culture bottle after incubation. This result can be represented analogously to the result of the incubation of the anaerobic blood culture bottle. In "Observation", the same SNOMED code "703725008 | Culture technique (qualifier value)" is specified as "Observation.method". The result of this diagnostic step is the detection of pathogen growth. The result is represented with the SNOMED code "410607006 | Organism (organism)".

The microscopy result within the scope of this bacteriological diagnosis is of secondary importance for ARS and does not need to be part of the transmission (see also the section "Content to be transmitted for ARS" in the "Semantics" chapter). Microscopy is depicted in this example to illustrate that the rules established for handling semantics in the interaction of LOINC and SNOMED-CT in the ARS profiles are also applicable to other use cases. For the microscopy, the staining procedure used is described as the method. The selection of the appropriate microscopic procedure, in this example, light microscopy, is assumed.

The method for pathogen identification in this example is MALDI-TOF. In accordance with the rules for handling semantics, the LOINC code "41852-5 Microorganism or agent identified in specimen" also reflects the question behind the procedure for this diagnostic step. The method is specified as "Observation.method" with the SNOMED code "83581000052107 Matrix assisted laser desorption ionization time of flight mass spectrometry technique (qualifier value)". The MALDI-TOF result is pathogen detection, which in this example is specified as "Observation.valueCodeableConcept" with the SNOMED code "56415008 Klebsiella pneumoniae (organism)".

In this example, phenotypic resistance testing is performed using microdilution. LOINC codes specific to the active ingredient are used (see also the section "FHIR Profiles and Application of Terminologies - Phenotypic Resistance Testing" in the "Semantics" chapter). A selection of active ingredients is shown here as an example. For phenotypic resistance testing, it is essential for ARS to display the results of all tested substances (see also the section "Content to be Transmitted for ARS" in the "Semantics" chapter). This example assumes that only the interpreted result, classified as "susceptible," "susceptible with increased exposure" or "intermediate," and "resistant" (SIR), is available in the laboratory information system. The corresponding SNOMED codes are specified in "Observation.valueCodeableConcept." An example considering qualitative results can be found in Example 2.

• The norm used to interpret the results of phenotypic resistance testing, e.g., EUCAST, should be specified in the extension "Observation.referenceRange.extension:norm".

In this example, a rapid carbapenemase test and a PCR are performed after phenotypic carbapenem non-susceptibility. Both methods can detect the presence of a carbapenemase belonging to a carbapenemase group. Subsequent sequencing can determine the carbapenemase. In accordance with the rules for dealing with semantics for molecular methods, the individual analytes of the rapid test, PCR, and sequencing are represented by single "observations." In this example, all methods for detecting carbapenemase groups and carbapenemases are presented for clarity.

As described in the section "Content to be Transmitted for ARS" in the "Semantics" chapter, it is not necessary to transmit all steps of microbiological diagnostics, in accordance with the objectives of ARS. In this example, it is important to transmit the diagnostic results from the anaerobic and aerobic blood culture bottles.

• For the anaerobic blood culture bottle, the negative result of the culture enrichment should be submitted as shown.
• For the aerobic blood culture bottle, the result of the MALDI-TOF test as well as the complete phenotypic and genotypic resistance testing must be submitted. The "observations" with the culture enrichment and microscopy results can be omitted.