MIMIC Implementation Guide - Local Development build (v1.3.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

Microbiology Background

Microbiology Subset

The microbiology data in MIMIC-IV-on-FHIR provides great real-world data for microbiology workflows. The microbiology data can be pulled out of MIMIC-IV-on-FHIR as a subset to test and explore in more lab focused applications.

Relevant profiles in Medication subset

• MimicEncounter
• MimicObservationMicroOrg
• MimicObservationMicroSusc
• MimicObservationMicroTest
• MimicPatient
• MimicSpecimen

Filter Microbiology data

To retrieve all microbiology resources, a search should be applied to MimicPatient. Searching for Patient resources returning all linked resources that have a profiles of MimicEncounter, MimicObservationMicroOrg, MimicObservationMicroSusc, MimicObservationMicroTest, MimicSpecimen.

Microbiology Workflow

The MIMIC data is mapped into three microbiology profiles in FHIR. The microbiology framework is:

• Test: The test being completed
• Organism: The organism the test is completed on
• Susceptibility:The organisms antibiotic susceptibility result

In FHIR the test->organism->susceptibility framework becomes ObservationMicroTest->ObservationMicroOrg->ObservationMicroSusc. Each of the profiles is based on the US Core ObservationLabs profile.

Example microbiology event

A typical microbiology event is a urine sample being tested for susceptability. The diagram below shows how this microbiology event would be represented in FHIR: