Laboratory Test


NameTypeLinkVersionNumberVersionDateStatus
ObservationObservationhttps://demis.rki.de/fhir/ars/StructureDefinition/Observation1.0.02025-06-13active

This page describes the microbiological diagnostics performed and their results. Only one profile is intended for laboratory testing for ARS. Specific features of different procedures and results are reflected in the codes used; see the Semantics.

For ARS, it is crucial that the diagnostic procedures for pathogen identification, as well as susceptibility and genotypic resistance tests, are transmitted.

This includes all methods that:

  • clearly identify the pathogen phenotypically and genotypically as part of the diagnostics performed;
    • In a diagnostic chain consisting of a negative anaerobic blood culture, a positive aerobic blood culture, Gram stain microscopy, MALDI-TOF, and multiplex PCR, the negative anaerobic blood culture result, the MALDI-TOF result, and the multiplex PCR result must be submitted.
  • are used for phenotypic susceptibility testing.
    • The results of all tested active substances, i.e., the complete resistance profile, must be presented, regardless of the result.
  • are used for genotypic resistance testing.
    • All procedures and results should be submitted to ARS.

Each observation references the Specimen resource, which describes the material underlying the diagnosis.

Observations reference each other via the triggeredBy (FHIR-R5) extension to indicate a sequence of diagnostic steps.

An observation can act as a "bracket resource" by referencing associated observations via hasMember. The bracket resource also contains the reference to the previous diagnostic step via triggeredBy. The observations to be bracketed do not contain a triggeredBy element. An example of a valid use is an observation for the antibiogram, which summarizes the individual observations from the resistance tests. Further valid uses could be defined in the future for panels and in the field of microscopy.


Profile

idS Σ1..1string
id0..0string
extensionC0..0Extension
versionIdΣ0..0id
lastUpdatedΣ0..0instant
sourceΣ0..0uri
arsProfileS Σ1..1canonical(StructureDefinition)Pattern
securityΣ0..0CodingBinding
tagΣ0..0Coding
implicitRulesΣ ?!0..1uri
language0..1codeBinding
text0..1Narrative
contained0..*Resource
id0..1string
id0..1string
extensionC0..0Extension
urlS1..1uriAuto Value
id0..1string
extensionC0..*Extension
referenceS Σ C1..1string
typeΣ0..0uriBinding
identifierΣ0..0Identifier
displayΣ0..0string
id0..1string
extensionC0..0Extension
urlS1..1uriAuto Value
valueCodeS1..1codePattern
urlS1..1uriAuto Value
modifierExtension?! C0..*Extension
identifierΣ0..0Identifier
basedOnΣ0..0Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)
partOfΣ0..0Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)
statusS Σ ?!1..1codeBinding
category0..0CodeableConceptBinding
id0..1string
extensionC0..*Extension
id0..1string
extensionC0..*Extension
systemS Σ1..1uriPattern
versionS Σ1..1string
codeS Σ1..1code
displayΣ0..1string
userSelectedΣ0..1boolean
textS Σ0..1string
id0..1string
extensionC0..*Extension
referenceS Σ C1..1string
typeΣ0..0uriBinding
identifierΣ0..0Identifier
displayΣ0..0string
focusΣ0..0Reference(Resource)
encounterΣ0..0Reference(Encounter)
issuedS Σ1..1instant
performerΣ0..0Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)
id0..1string
extensionC0..*Extension
id0..1string
extensionC0..*Extension
systemS Σ1..1uriPattern
versionS Σ1..1string
codeS Σ1..1code
displayΣ0..1string
userSelectedΣ0..1boolean
textS Σ0..1string
id0..1string
extensionC0..*Extension
valueS Σ1..1decimal
comparatorS Σ ?!0..1codeBinding
unitΣ0..1string
systemS Σ C1..1uriPattern
codeS Σ1..1code
id0..1string
extensionC0..*Extension
id0..1string
extensionC0..*Extension
valueS Σ1..1decimal
comparatorΣ ?!0..1codeBinding
unitΣ0..1string
systemS Σ C0..1uriPattern
codeS Σ0..1code
id0..1string
extensionC0..*Extension
valueS Σ1..1decimal
comparatorΣ ?!0..1codeBinding
unitΣ0..1string
systemS Σ C0..1uriPattern
codeS Σ0..1code
id0..1string
extensionC0..*Extension
id0..1string
extensionC0..*Extension
valueS Σ1..1decimal
comparatorΣ ?!0..0codeBinding
unitΣ0..1string
systemS Σ C1..1uriPattern
codeS Σ1..1code
id0..1string
extensionC0..*Extension
valueS Σ1..1decimal
comparatorΣ ?!0..0codeBinding
unitΣ0..1string
systemS Σ C1..1uriPattern
codeS Σ1..1code
dataAbsentReasonS C0..1CodeableConceptBinding
id0..1string
extensionC0..*Extension
id0..1string
extensionC0..*Extension
systemS Σ1..1uriPattern
versionS Σ1..1string
codeS Σ1..1code
displayΣ0..1string
userSelectedΣ0..1boolean
id0..1string
extensionC0..*Extension
systemS Σ1..1uriPattern
versionS Σ1..1string
codeS Σ1..1code
displayΣ0..1string
userSelectedΣ0..1boolean
textΣ0..1string
note0..0Annotation
bodySite0..0CodeableConcept
id0..1string
extensionC0..*Extension
id0..1string
extensionC0..*Extension
systemS Σ1..1uriPattern
versionS Σ1..1string
codeS Σ1..1code
displayΣ0..1string
userSelectedΣ0..1boolean
textS Σ0..1string
id0..1string
extensionC0..*Extension
referenceS Σ C1..1string
typeΣ0..0uriBinding
identifierΣ0..0Identifier
displayΣ0..0string
device0..0Reference(Device | DeviceMetric)
id0..1string
id0..1string
extensionC0..0Extension
urlS1..1uriAuto Value
id0..1string
extensionC0..*Extension
id0..1string
extensionC0..*Extension
systemS Σ1..1uri
versionS Σ1..1string
codeS Σ1..1code
displayΣ0..1string
userSelectedΣ0..1boolean
textS Σ0..1string
modifierExtensionΣ ?! C0..*Extension
lowC0..1SimpleQuantity
highC0..1SimpleQuantity
type0..1CodeableConceptBinding
appliesTo0..*CodeableConcept
age0..1Range
textS0..1string
id0..1string
extensionC0..*Extension
referenceS Σ C1..1string
typeΣ0..0uriBinding
identifierΣ0..0Identifier
displayΣ0..0string
derivedFromΣ0..0Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)
id0..1string
extensionC0..*Extension
modifierExtensionΣ ?! C0..*Extension
codeΣ1..1CodeableConcept
valueQuantityQuantity
valueCodeableConceptCodeableConcept
valueStringstring
valueBooleanboolean
valueIntegerinteger
valueRangeRange
valueRatioRatio
valueSampledDataSampledData
valueTimetime
valueDateTimedateTime
valuePeriodPeriod
dataAbsentReasonC0..1CodeableConceptBinding
interpretation0..*CodeableConceptBinding
referenceRange0..*see (referenceRange)



Observation.code (Question about the performed test (LOINC))

  • Beschreibt durch einen LOINC-Code die Frage nach dem durchgeführten Test.

Observation.code.text (Original name)

  • Original name from the laboratory information system (LIS) or from the sending system. This information is used for data quality management.

Observation.value[x] (Results of the performed test )

  • The result of the test performed can be described both as a qualitative statement (valueCodeableConcept) and as a quantitative statement (valueQuantity).

Observation.valueCodeableConcept (Results of the performed tests (SNOMED))

  • As a qualitative indication of the result, SNOMED codes are expected that describe the detection or non-detection of an analyte, the pathogen detected, the gene, antigen, toxin, antibody detected, etc.

Observation.valueCodeableConcept.text (Original name )

  • Original name from the laboratory information system (LIS) or from the sending system. This information is used for data quality management.

Observation.valueQuantity (Result of the test performed (quantitative, decimal))

  • A quantitative result with the unit UCUM is expected here. It may be important to specify a reference range for the described values. This can be done using Observation.referenceRange.

Observation.valueRatio (Result of the test performed (quantitative, ratio))

  • Here, a ratio can be given as a quantitative result of microbiological diagnostics.

Observation.valueRange (Result of the test performed (quantitative, range))

  • Here, a range consisting of low and high can be given as a quantitative indication.

Observation.interpretation (Interpretation of the results )

  • An interpretation of the result is always expected. For ordinal qualitative data, this can correspond to the result described under Observation.valueCodeableConcept. However, especially for quantitative data on the result under Observation.valueQuantity, the evaluation of the result can be provided here. The information must be provided as a SNOMED code or by specifying a code according to the FHIR basic standard.

Observation.method (Laboratory method )

  • The laboratory method used is expected as a SNOMED code.

Observation.referenceRange (Reference values and norm)

  • Reference values ​​used to interpret a quantitative test result should be specified. Reference values ​​are often test kit-specific. In particular, the extension 'norm' should also include the norm after the result of the phenotypic susceptibility test has been evaluated.

Observation.referenceRange.extension:norm.value[x].text

  • If breakpoints are missing, e.g. in EUCAST, an evaluation and interpretation of the result can be supplemented textually.

Observation.referenceRange.text

  • A reference range entry must contain at least one of the fields 'low', 'high', or 'text'. If necessary, dummy text can be inserted here for ARS, e.g., 'standard specification only'.




Constraints

none




Bindings

pathstrengthvalueSet
Observation.code.codingextensiblehttps://demis.rki.de/fhir/ars/ValueSet/testLOINC
Observation.value[x].codingextensiblehttps://demis.rki.de/fhir/ars/ValueSet/antwortSNOMED
Observation.interpretation.codingextensiblehttp://hl7.org/fhir/ValueSet/observation-interpretation
Observation.interpretation.codingextensiblehttps://demis.rki.de/fhir/ars/ValueSet/interpretationSNOMED
Observation.method.codingextensiblehttps://demis.rki.de/fhir/ars/ValueSet/methodeSNOMED




Example

Example 1: No microorganism found

Observation
<Observation xmlns="http://hl7.org/fhir">
<id value="f72b3b42-c268-476a-9f81-97045dc60ed3" />
<profile value="https://demis.rki.de/fhir/ars/StructureDefinition/Observation" />
</meta>
<status value="final" />
<system value="http://loinc.org" />
<version value="2.79" />
<code value="41852-5" />
</coding>
</code>
<reference value="Patient/43511fe3-aa5f-73fb-7e59-2313ba0ca76c" />
</subject>
<issued value="2023-06-14T00:00:00.000+01:00" />
<system value="http://snomed.info/sct" />
<version value="http://snomed.info/sct/11000274103/version/20250515" />
<code value="264868006" />
</coding>
<text value="kein Wachstum" />
</valueCodeableConcept>
<system value="http://snomed.info/sct" />
<version value="http://snomed.info/sct/11000274103/version/20250515" />
<code value="260385009" />
</coding>
</interpretation>
<system value="http://snomed.info/sct" />
<version value="http://snomed.info/sct/11000274103/version/20250515" />
<code value="703725008" />
</coding>
<text value="Kultur" />
</method>
<reference value="Specimen/156d0d82-c914-4a13-8796-9270ffa8bb52" />
</specimen>
</Observation>
{
"resourceType": "Observation",
"id": "f72b3b42-c268-476a-9f81-97045dc60ed3",
"meta": {
"profile": [
"https://demis.rki.de/fhir/ars/StructureDefinition/Observation"
]
},
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "41852-5",
"version": "2.79"
}
]
},
"coding": [
{
"system": "http://snomed.info/sct",
"code": "264868006",
"version": "http://snomed.info/sct/11000274103/version/20250515"
}
],
"text": "kein Wachstum"
},
{
"coding": [
{
"system": "http://snomed.info/sct",
"code": "260385009",
"version": "http://snomed.info/sct/11000274103/version/20250515"
}
]
}
],
"method": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "703725008",
"version": "http://snomed.info/sct/11000274103/version/20250515"
}
],
"text": "Kultur"
},
"status": "final",
"subject": {
"reference": "Patient/43511fe3-aa5f-73fb-7e59-2313ba0ca76c"
},
"issued": "2023-06-14T00:00:00.000+01:00",
"reference": "Specimen/156d0d82-c914-4a13-8796-9270ffa8bb52"
}
}

Example 2: Detection of Klebsiella pneumoniae including susceptibility testing

Observation
    
Observation
Observation
<Observation xmlns="http://hl7.org/fhir">
<id value="e5b6d4eb-e055-468a-4d03-96c5fcd9ddf7" />
<profile value="https://demis.rki.de/fhir/ars/StructureDefinition/Observation" />
</meta>
<status value="final" />
<system value="http://loinc.org" />
<version value="2.79" />
<code value="41852-5" />
<display value="Microorganism or agent identified in Specimen" />
</coding>
</code>
<reference value="Patient/43511fe3-aa5f-73fb-7e59-2313ba0ca76c" />
</subject>
<issued value="2023-06-14T00:00:00.000+01:00" />
<system value="http://snomed.info/sct" />
<version value="http://snomed.info/sct/11000274103/version/20250515" />
<code value="56415008" />
</coding>
<text value="Klebsiella pneumoniae" />
</valueCodeableConcept>
<system value="http://snomed.info/sct" />
<version value="http://snomed.info/sct/11000274103/version/20250515" />
<code value="10828004" />
</coding>
</interpretation>
<system value="http://snomed.info/sct" />
<version value="http://snomed.info/sct/11000274103/version/20250515" />
<code value="83581000052107" />
</coding>
<text value="MALDI-TOF" />
</method>
<reference value="Specimen/3a2f563f-a155-498f-a5b2-a2959e2380a1" />
</specimen>
</Observation>
<Observation xmlns="http://hl7.org/fhir">
<id value="baf8fd45-5c3a-b1a2-e221-fee38df64cf5" />
<profile value="https://demis.rki.de/fhir/ars/StructureDefinition/Observation" />
</meta>
<status value="final" />
<system value="http://loinc.org" />
<version value="2.79" />
<code value="18932-4" />
<display value="Imipenem [Susceptibility]" />
</coding>
</code>
<reference value="Patient/43511fe3-aa5f-73fb-7e59-2313ba0ca76c" />
</subject>
<issued value="2023-06-14T00:00:00.000+01:00" />
<value value="5" />
<system value="http://unitsofmeasure.org" />
<code value="mg/L" />
</valueQuantity>
<system value="http://snomed.info/sct" />
<version value="http://snomed.info/sct/11000274103/version/20250515" />
<code value="1306581009" />
<display value="EUCAST-Kategorie 2019 - R (resistent)" />
</coding>
</interpretation>
<system value="http://snomed.info/sct" />
<version value="http://snomed.info/sct/11000274103/version/20250515" />
<code value="263696007" />
</coding>
<text value="Mikrodilution" />
</method>
<reference value="Specimen/3a2f563f-a155-498f-a5b2-a2959e2380a1" />
</specimen>
<extension url="https://demis.rki.de/fhir/ars/StructureDefinition/Norm">
<system value="https://demis.rki.de/fhir/ars/CodeSystem/norm" />
<version value="1.0.0" />
<code value="EUCAST" />
</coding>
<text value="EUCAST (v 13.1)" />
</valueCodeableConcept>
</extension>
<text value="nur Angabe Norm" />
</referenceRange>
</Observation>
<Observation xmlns="http://hl7.org/fhir">
<id value="1c3d4ca4-af8b-4142-b257-f0ec49f7c68f" />
<profile value="https://demis.rki.de/fhir/ars/StructureDefinition/Observation" />
</meta>
<status value="final" />
<system value="http://loinc.org" />
<version value="2.79" />
<code value="18932-4" />
<display value="Imipenem [Susceptibility]" />
</coding>
</code>
<reference value="Patient/43511fe3-aa5f-73fb-7e59-2313ba0ca76c" />
</subject>
<issued value="2023-06-14T00:00:00.000+01:00" />
<system value="http://snomed.info/sct" />
<version value="http://snomed.info/sct/11000274103/version/20250515" />
<code value="1306581009" />
<display value="EUCAST-Kategorie 2019 - R (resistent)" />
</coding>
</valueCodeableConcept>
<system value="http://snomed.info/sct" />
<version value="http://snomed.info/sct/11000274103/version/20250515" />
<code value="1306581009" />
<display value="EUCAST-Kategorie 2019 - R (resistent)" />
</coding>
</interpretation>
<system value="http://snomed.info/sct" />
<version value="http://snomed.info/sct/11000274103/version/20250515" />
<code value="263696007" />
</coding>
<text value="Mikrodilution" />
</method>
<reference value="Specimen/3a2f563f-a155-498f-a5b2-a2959e2380a1" />
</specimen>
<extension url="https://demis.rki.de/fhir/ars/StructureDefinition/Norm">
<system value="https://demis.rki.de/fhir/ars/CodeSystem/norm" />
<version value="1.0.0" />
<code value="EUCAST" />
</coding>
<text value="EUCAST (v 13.1)" />
</valueCodeableConcept>
</extension>
<text value="nur Angabe Norm" />
</referenceRange>
</Observation>
{
"resourceType": "Observation",
"id": "e5b6d4eb-e055-468a-4d03-96c5fcd9ddf7",
"meta": {
"profile": [
"https://demis.rki.de/fhir/ars/StructureDefinition/Observation"
]
},
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "41852-5",
"display": "Microorganism or agent identified in Specimen",
"version": "2.79"
}
]
},
"coding": [
{
"system": "http://snomed.info/sct",
"code": "56415008",
"version": "http://snomed.info/sct/11000274103/version/20250515"
}
],
"text": "Klebsiella pneumoniae"
},
{
"coding": [
{
"system": "http://snomed.info/sct",
"code": "10828004",
"version": "http://snomed.info/sct/11000274103/version/20250515"
}
]
}
],
"method": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "83581000052107",
"version": "http://snomed.info/sct/11000274103/version/20250515"
}
],
"text": "MALDI-TOF"
},
"status": "final",
"subject": {
"reference": "Patient/43511fe3-aa5f-73fb-7e59-2313ba0ca76c"
},
"issued": "2023-06-14T00:00:00.000+01:00",
"reference": "Specimen/3a2f563f-a155-498f-a5b2-a2959e2380a1"
}
}
{
"resourceType": "Observation",
"id": "baf8fd45-5c3a-b1a2-e221-fee38df64cf5",
"meta": {
"profile": [
"https://demis.rki.de/fhir/ars/StructureDefinition/Observation"
]
},
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "18932-4",
"display": "Imipenem [Susceptibility]",
"version": "2.79"
}
]
},
"system": "http://unitsofmeasure.org",
"value": 5,
"code": "mg/L"
},
{
"coding": [
{
"system": "http://snomed.info/sct",
"code": "1306581009",
"version": "http://snomed.info/sct/11000274103/version/20250515",
"display": "EUCAST-Kategorie 2019 - R (resistent)"
}
]
}
],
"method": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "263696007",
"version": "http://snomed.info/sct/11000274103/version/20250515"
}
],
"text": "Mikrodilution"
},
{
{
"url": "https://demis.rki.de/fhir/ars/StructureDefinition/Norm",
"coding": [
{
"system": "https://demis.rki.de/fhir/ars/CodeSystem/norm",
"code": "EUCAST",
"version": "1.0.0"
}
],
"text": "EUCAST (v 13.1)"
}
}
],
"text": "nur Angabe Norm"
}
],
"status": "final",
"subject": {
"reference": "Patient/43511fe3-aa5f-73fb-7e59-2313ba0ca76c"
},
"issued": "2023-06-14T00:00:00.000+01:00",
"reference": "Specimen/3a2f563f-a155-498f-a5b2-a2959e2380a1"
}
}
{
"resourceType": "Observation",
"id": "1c3d4ca4-af8b-4142-b257-f0ec49f7c68f",
"meta": {
"profile": [
"https://demis.rki.de/fhir/ars/StructureDefinition/Observation"
]
},
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "18932-4",
"display": "Imipenem [Susceptibility]",
"version": "2.79"
}
]
},
"coding": [
{
"system": "http://snomed.info/sct",
"code": "1306581009",
"version": "http://snomed.info/sct/11000274103/version/20250515",
"display": "EUCAST-Kategorie 2019 - R (resistent)"
}
]
},
{
"coding": [
{
"system": "http://snomed.info/sct",
"code": "1306581009",
"version": "http://snomed.info/sct/11000274103/version/20250515",
"display": "EUCAST-Kategorie 2019 - R (resistent)"
}
]
}
],
"method": {
"coding": [
{
"system": "http://snomed.info/sct",
"code": "263696007",
"version": "http://snomed.info/sct/11000274103/version/20250515"
}
],
"text": "Mikrodilution"
},
{
{
"url": "https://demis.rki.de/fhir/ars/StructureDefinition/Norm",
"coding": [
{
"system": "https://demis.rki.de/fhir/ars/CodeSystem/norm",
"code": "EUCAST",
"version": "1.0.0"
}
],
"text": "EUCAST (v 13.1)"
}
}
],
"text": "nur Angabe Norm"
}
],
"status": "final",
"subject": {
"reference": "Patient/43511fe3-aa5f-73fb-7e59-2313ba0ca76c"
},
"issued": "2023-06-14T00:00:00.000+01:00",
"reference": "Specimen/3a2f563f-a155-498f-a5b2-a2959e2380a1"
}
}