Description of the information model for the KDS module Microbiology

The extension module Microbiology comprises the information for the detection and description of microorganisms such as bacteria, viruses and fungi. The information model describes the various microbial examinations (Observations) using different diagnostic methods such as:

• Culture and Microscopy
• Molecular diagnostics
• Serology / Immunology

Other properties of the microorganism which could possibly be determined or deduced using multiple methods have been grouped under the following category:

• Further properties of the organism

Culture and Microscopy

The profiles modelled under the two diagnostic methodologies microbiology culture and microscopy describe information related to the detection of the microorganism, to the colony count, to the antimicrobial susceptibility and to the microscopic description of the findings. The LOINC code for the detection of the microorganism is generic “Microorganism identified in Unspecified specimen by Culture” , the name of the specific microorganism detected or examined is defined in the component of the FHIR observation. The Colony count profile foresees both the possibility of a numerical as well as semiquantitative value. For the susceptibility tests an intensional value set including all LONC codes referring to antimicrobial phenotypic susceptibility was established. Results can be expressed both using the EUCAST system as well as CLSI. Microscopy information includes specific methodology used, morphology , Barlett and Nugent score.

Molecular diagnostics

Also in this case the name of the test is generic “Microorganism identified in Isolate or Specimen by Molecular genetics method” and the name of the microorganism is specified separately. Possible numerical results of the observation can be described as component elements, such as the PCR cycle threshold or the quantitative measurement of antibodies.

Serology and Immunology

The information included in this section describe both qualitative and quantitative results concerning antigen and antibody investigations as well as avidity.

Further properties of the organism

As genomic tests become increasingly more relevant in microbiology investigations, many properties of the microorganism such as mechanism of resistance, virulence factor and MDRO class can be determined using this technique. However, some of these properties can also be inferred by the results of tests that use phenotypical methods. Additionally, some molecular tests can predict resistance behaviours which can be observed only through phenotypical susceptibility testing. For this reason we have arranged the information concerning the properties of the microorganism in a separate group. Information about the MRGN classification according to the Robert Koch Institut is also specified.