updating after response from FHIR community on how to represent bacterial resistance in FHIR. There are SNOMED codes to represent the specific antibiotic resistance of an identified species of bacteria that would represent the "value" of a FHIR Observation resource.
Creating a FHIR (Fast Healthcare Interoperability Resources) Observation resource for a blood culture that is positive for Vancomycin-resistant Escherichia coli (E. coli) involves specifying several components in the resource to accurately represent the clinical findings. Here’s an example of what such an Observation resource might look like in JSON format, which is commonly used in FHIR:
{
"resourceType": "Observation",
"id": "blood-culture-observation-12345",
"status": "final",
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "600-7",
"display": "Bacteria identified in Blood by Culture"
}
]
},
"subject": {
"reference": "Patient/example"
},
"issued": "2024-02-13T08:03:00Z",
"performer": [
{
"reference": "Practitioner/example"
}
],
"valueCodeableConcept": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "112283007",
"display": "Escherichia coli"
}
],
"text": "Vancomycin-resistant Escherichia coli"
},
"interpretation": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation",
"code": "POS",
"display": "Positive"
}
],
"text": "Positive for Vancomycin-resistant Escherichia coli"
}
],
"note": [
{
"text": "Blood culture positive for Vancomycin-resistant Escherichia coli (VRE)"
}
]
}
Explanation of key elements in this resource:
• resourceType: Identifies the type of the resource, which is “Observation” in this case.
• id: A unique identifier for this particular observation.
• status: The status of the observation (e.g., “final”).
• code: Uses LOINC (Logical Observation Identifiers Names and Codes) to indicate the type of observation, here representing a blood culture.
• subject: Reference to the patient associated with this observation.
• issued: The date and time at which the observation was made available.
• performer: Reference to the practitioner or organization that performed the observation.
• valueCodeableConcept: Uses SNOMED CT to specify the finding, in this case, E. coli, with a note indicating it’s vancomycin-resistant.
• interpretation: Provides an interpretation of the observation, here indicating a positive result for vancomycin-resistant E. coli.
• note: Any additional notes or comments related to the observation.
This is a simplified example and in a real-world scenario, additional details like patient information, encounter data, and more specific coding might be included.
I reached out about the representation of antibiotic resistance in FHIR and received the response below:
here is some debate going on in zulip (www.chat.fhir.org) around that:stream:Orders+and+Observation+WG topic:Micro+/+Culture near:419845077
It is definitely an observation but how the organism and the susceptibilities are tied together is what the debate is about at this time.
OO says using observation.has member in the observation that has the organism name as observation.value and then have each susceptibility is it's own observation - see https://build.fhir.org/diagnostics-module.html#10.0.3.1.1
Jay and several other folks think we should use observation.value and then populate observation.component - one for each antibiotic susceptibility.
Duplicate Patient resources are approached by use of the Patient.link element (the last element in the Patient Resource) . Patient - FHIR v4.0.1 (hl7.org)
See sections 8.1.4 and 8.1.4.1 below Resource Content.