FHIR Microbiology

FHIR Microbiology

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.

Notes for ObservationMicroTest

The primary information stored in the test profile is the test id, timing, and references to ObservationMicroOrg

Notes:

• The time stored in fhir, effectiveDateTime, is the charttime from MIMIC. This is the time the specimen was collected
• There are tests with no links to organisms. These tests are kept since they specify why the test could not be completed. The majority of the time this is a simple as no growth occuring. The comments column from microbiologyevents is pulled in as valueString to provide a value for the tests with no organism
• specimen is stored here

Notes for ObservationMicroOrg

The primary information stored in the organism profile is the organism, reference to ObservationMicroSusc and reference back to ObservationMicroTest

Notes:

• The time stored in ObservationMicroOrg is just a repeat of ObservationMicroTest, pulling in microbiologyevents charttime
• references a single ObservationMicroTest the organism is a part of with derivedFrom
• references one to many ObservationMicroSusc as part of hasMember
• There are a small amount of entries that have an organism but no susceptiblity results, these values store a valueString with either the microbiologyevents comments column info if present or a fixed message: 'No susceptibility data present'.

Notes for ObservationMicroSusc

The primary information stored in the susceptibility profile is the antibiotic tested, susceptiblity results, and timing of results available.

Notes:

• The time stored in this profile in effectiveDateTime represents when the result was made available
• The antibiotic tested is stored in the code element
• The susceptibility result for that antibiotic is stored under interpretation