FHIR Implementation Guide for PUBLIC Testing
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FHIR Implementation Guide for PUBLIC Testing - Local Development build (v0.1.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

Resource Profile: DiagnosticReport Microbiology Profile

Official URL: https://fhir.osbornemj.com/ig/StructureDefinition/diagnosticreport-microbiology Version: 0.1.0
Active as of 2025-10-17 Maturity Level: 0 Computable Name: DiagnosticReportMicrobiology

The DiagnosticReport Microbiology Profile inherits from the AU Base DiagnosticReport AUBaseDiagnosticReport resource; refer to it for scope and usage definitions. Laboratory results are grouped and summarized using the DiagnosticReport resource, which typically references Observation resource(s). Each Observation resource represents an individual laboratory test and result value or component result values or a nested panel (such as a microbial susceptibility panel) that references other observations. Laboratory results can also be presented in report form or as free text.

Usages:

You can also check for usages in the FHIR IG Statistics

Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. DiagnosticReport 0..* AUBaseDiagnosticReport A diagnostic report in an Australian healthcare context
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... Slices for extension Content/Rules for all slices
.... extension:sexParameterForClinicalUse 0..* (Complex) A context-specific sex parameter for clinical use
URL: http://hl7.org/fhir/StructureDefinition/patient-sexParameterForClinicalUse
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... status ?!SΣ 1..1 code registered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required)
... Slices for category SΣ 1..* CodeableConcept Service category
Slice: Unordered, Open by pattern:$this
Binding: DiagnosticServiceSectionCodes (preferred)
.... category:microbiologySlice SΣ 1..1 CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (preferred)

Required Pattern: At least the following
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: MB
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text 0..1 string Plain text representation of the concept
... code Σ 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: OS LAB Microbiology Report (preferred)
... subject SΣ 1..1 Reference(AU Core Patient) The subject of the report - usually, but not always, the patient
... issued SΣ 0..1 instant DateTime this version was made
... result S 1..* Reference(AU Core Pathology Result Observation) Observations

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
DiagnosticReport.status Base required DiagnosticReportStatus 📦4.0.1 FHIR Std.
DiagnosticReport.category Base preferred Diagnostic Service Section Codes 📦4.0.1 FHIR Std.
DiagnosticReport.category:microbiologySlice Base preferred Diagnostic Service Section Codes 📦4.0.1 FHIR Std.
DiagnosticReport.code Base preferred OS LAB Microbiology Report 📦0.1.0 This IG

Constraints

Id Grade Path(s) Description Expression
dom-2 error DiagnosticReport If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error DiagnosticReport If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error DiagnosticReport If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error DiagnosticReport If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice DiagnosticReport A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()

This structure is derived from AUBaseDiagnosticReport

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. DiagnosticReport 0..* AUBaseDiagnosticReport A diagnostic report in an Australian healthcare context
... identifier S 0..* Identifier, AULocalReportIdentifier, AULocalOrderIdentifier, AUAccessionNumber Business identifier for report
... status S 1..1 code registered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required)
... Slices for category S 1..* CodeableConcept Service category
Slice: Unordered, Open by pattern:$this
.... category:microbiologySlice S 1..1 CodeableConcept Service category
Required Pattern: At least the following
..... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: MB
... subject S 1..1 Reference(AU Core Patient) The subject of the report - usually, but not always, the patient
... issued S 0..1 instant DateTime this version was made
... result S 1..* Reference(AU Core Pathology Result Observation) Observations

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
DiagnosticReport.status Base required DiagnosticReportStatus 📦4.0.1 FHIR Std.
DiagnosticReport.code Base preferred OS LAB Microbiology Report 📦0.1.0 This IG
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. DiagnosticReport 0..* AUBaseDiagnosticReport A diagnostic report in an Australian healthcare context
... id Σ 0..1 id Logical id of this artifact
... meta Σ 0..1 Meta Metadata about the resource
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
... contained 0..* Resource Contained, inline Resources
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:sexParameterForClinicalUse 0..* (Complex) A context-specific sex parameter for clinical use
URL: http://hl7.org/fhir/StructureDefinition/patient-sexParameterForClinicalUse
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier SΣ 0..* Identifier, AULocalReportIdentifier, AULocalOrderIdentifier, AUAccessionNumber Business identifier for report
... basedOn 0..* Reference(CarePlan | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest | AU Base ServiceRequest) What was requested
... status ?!SΣ 1..1 code registered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required)
... Slices for category SΣ 1..* CodeableConcept Service category
Slice: Unordered, Open by pattern:$this
Binding: DiagnosticServiceSectionCodes (preferred)
.... category:microbiologySlice SΣ 1..1 CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (preferred)

Required Pattern: At least the following
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: MB
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text 0..1 string Plain text representation of the concept
... code Σ 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: OS LAB Microbiology Report (preferred)
... subject SΣ 1..1 Reference(AU Core Patient) The subject of the report - usually, but not always, the patient
... encounter Σ 0..1 Reference(Encounter) Health care event when test ordered
... effective[x] Σ 0..1 Clinically relevant time/time-period for report
.... effectiveDateTime dateTime
.... effectivePeriod Period
... issued SΣ 0..1 instant DateTime this version was made
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) Responsible Diagnostic Service
... resultsInterpreter Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) Primary result interpreter
... specimen 0..* Reference(AU Base Specimen) Specimens this report is based on
... result S 1..* Reference(AU Core Pathology Result Observation) Observations
... imagingStudy 0..* Reference(ImagingStudy) Reference to full details of imaging associated with the diagnostic report
... media Σ 0..* BackboneElement Key images associated with this report
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... comment 0..1 string Comment about the image (e.g. explanation)
.... link Σ 1..1 Reference(Media) Reference to the image source
... conclusion 0..1 string Clinical conclusion (interpretation) of test results
... conclusionCode 0..* CodeableConcept Codes for the clinical conclusion of test results
Binding: Clinical Finding . (preferred)
... presentedForm 0..* Attachment Entire report as issued

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
DiagnosticReport.language Base preferred Common Languages 📍4.0.1 FHIR Std.
DiagnosticReport.status Base required DiagnosticReportStatus 📦4.0.1 FHIR Std.
DiagnosticReport.category Base preferred Diagnostic Service Section Codes 📦4.0.1 FHIR Std.
DiagnosticReport.category:microbiologySlice Base preferred Diagnostic Service Section Codes 📦4.0.1 FHIR Std.
DiagnosticReport.code Base preferred OS LAB Microbiology Report 📦0.1.0 This IG
DiagnosticReport.conclusionCode Base preferred Clinical Finding . ⏿1.0.2 tx.hl7.org.au

Constraints

Id Grade Path(s) Description Expression
dom-2 error DiagnosticReport If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error DiagnosticReport If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error DiagnosticReport If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error DiagnosticReport If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice DiagnosticReport A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()

This structure is derived from AUBaseDiagnosticReport

Summary

Mandatory: 4 elements
Must-Support: 7 elements

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element 1 is sliced based on the value of DiagnosticReport.category

Maturity: 0

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. DiagnosticReport 0..* AUBaseDiagnosticReport A diagnostic report in an Australian healthcare context
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... Slices for extension Content/Rules for all slices
.... extension:sexParameterForClinicalUse 0..* (Complex) A context-specific sex parameter for clinical use
URL: http://hl7.org/fhir/StructureDefinition/patient-sexParameterForClinicalUse
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... status ?!SΣ 1..1 code registered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required)
... Slices for category SΣ 1..* CodeableConcept Service category
Slice: Unordered, Open by pattern:$this
Binding: DiagnosticServiceSectionCodes (preferred)
.... category:microbiologySlice SΣ 1..1 CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (preferred)

Required Pattern: At least the following
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: MB
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text 0..1 string Plain text representation of the concept
... code Σ 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: OS LAB Microbiology Report (preferred)
... subject SΣ 1..1 Reference(AU Core Patient) The subject of the report - usually, but not always, the patient
... issued SΣ 0..1 instant DateTime this version was made
... result S 1..* Reference(AU Core Pathology Result Observation) Observations

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
DiagnosticReport.status Base required DiagnosticReportStatus 📦4.0.1 FHIR Std.
DiagnosticReport.category Base preferred Diagnostic Service Section Codes 📦4.0.1 FHIR Std.
DiagnosticReport.category:microbiologySlice Base preferred Diagnostic Service Section Codes 📦4.0.1 FHIR Std.
DiagnosticReport.code Base preferred OS LAB Microbiology Report 📦0.1.0 This IG

Constraints

Id Grade Path(s) Description Expression
dom-2 error DiagnosticReport If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error DiagnosticReport If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error DiagnosticReport If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error DiagnosticReport If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice DiagnosticReport A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()

Differential View

This structure is derived from AUBaseDiagnosticReport

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. DiagnosticReport 0..* AUBaseDiagnosticReport A diagnostic report in an Australian healthcare context
... identifier S 0..* Identifier, AULocalReportIdentifier, AULocalOrderIdentifier, AUAccessionNumber Business identifier for report
... status S 1..1 code registered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required)
... Slices for category S 1..* CodeableConcept Service category
Slice: Unordered, Open by pattern:$this
.... category:microbiologySlice S 1..1 CodeableConcept Service category
Required Pattern: At least the following
..... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: MB
... subject S 1..1 Reference(AU Core Patient) The subject of the report - usually, but not always, the patient
... issued S 0..1 instant DateTime this version was made
... result S 1..* Reference(AU Core Pathology Result Observation) Observations

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
DiagnosticReport.status Base required DiagnosticReportStatus 📦4.0.1 FHIR Std.
DiagnosticReport.code Base preferred OS LAB Microbiology Report 📦0.1.0 This IG

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. DiagnosticReport 0..* AUBaseDiagnosticReport A diagnostic report in an Australian healthcare context
... id Σ 0..1 id Logical id of this artifact
... meta Σ 0..1 Meta Metadata about the resource
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
... contained 0..* Resource Contained, inline Resources
... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:sexParameterForClinicalUse 0..* (Complex) A context-specific sex parameter for clinical use
URL: http://hl7.org/fhir/StructureDefinition/patient-sexParameterForClinicalUse
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier SΣ 0..* Identifier, AULocalReportIdentifier, AULocalOrderIdentifier, AUAccessionNumber Business identifier for report
... basedOn 0..* Reference(CarePlan | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest | AU Base ServiceRequest) What was requested
... status ?!SΣ 1..1 code registered | partial | preliminary | final +
Binding: DiagnosticReportStatus (required)
... Slices for category SΣ 1..* CodeableConcept Service category
Slice: Unordered, Open by pattern:$this
Binding: DiagnosticServiceSectionCodes (preferred)
.... category:microbiologySlice SΣ 1..1 CodeableConcept Service category
Binding: DiagnosticServiceSectionCodes (preferred)

Required Pattern: At least the following
..... id 0..1 string Unique id for inter-element referencing
..... extension 0..* Extension Additional content defined by implementations
..... coding 1..* Coding Code defined by a terminology system
Fixed Value: (Complex)
...... id 0..1 string Unique id for inter-element referencing
...... extension 0..* Extension Additional content defined by implementations
...... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
...... version 0..1 string Version of the system - if relevant
...... code 1..1 code Symbol in syntax defined by the system
Fixed Value: MB
...... display 0..1 string Representation defined by the system
...... userSelected 0..1 boolean If this coding was chosen directly by the user
..... text 0..1 string Plain text representation of the concept
... code Σ 1..1 CodeableConcept Name/Code for this diagnostic report
Binding: OS LAB Microbiology Report (preferred)
... subject SΣ 1..1 Reference(AU Core Patient) The subject of the report - usually, but not always, the patient
... encounter Σ 0..1 Reference(Encounter) Health care event when test ordered
... effective[x] Σ 0..1 Clinically relevant time/time-period for report
.... effectiveDateTime dateTime
.... effectivePeriod Period
... issued SΣ 0..1 instant DateTime this version was made
... performer Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) Responsible Diagnostic Service
... resultsInterpreter Σ 0..* Reference(Practitioner | PractitionerRole | Organization | CareTeam) Primary result interpreter
... specimen 0..* Reference(AU Base Specimen) Specimens this report is based on
... result S 1..* Reference(AU Core Pathology Result Observation) Observations
... imagingStudy 0..* Reference(ImagingStudy) Reference to full details of imaging associated with the diagnostic report
... media Σ 0..* BackboneElement Key images associated with this report
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... comment 0..1 string Comment about the image (e.g. explanation)
.... link Σ 1..1 Reference(Media) Reference to the image source
... conclusion 0..1 string Clinical conclusion (interpretation) of test results
... conclusionCode 0..* CodeableConcept Codes for the clinical conclusion of test results
Binding: Clinical Finding . (preferred)
... presentedForm 0..* Attachment Entire report as issued

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
DiagnosticReport.language Base preferred Common Languages 📍4.0.1 FHIR Std.
DiagnosticReport.status Base required DiagnosticReportStatus 📦4.0.1 FHIR Std.
DiagnosticReport.category Base preferred Diagnostic Service Section Codes 📦4.0.1 FHIR Std.
DiagnosticReport.category:microbiologySlice Base preferred Diagnostic Service Section Codes 📦4.0.1 FHIR Std.
DiagnosticReport.code Base preferred OS LAB Microbiology Report 📦0.1.0 This IG
DiagnosticReport.conclusionCode Base preferred Clinical Finding . ⏿1.0.2 tx.hl7.org.au

Constraints

Id Grade Path(s) Description Expression
dom-2 error DiagnosticReport If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error DiagnosticReport If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error DiagnosticReport If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error DiagnosticReport If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice DiagnosticReport A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()

This structure is derived from AUBaseDiagnosticReport

Summary

Mandatory: 4 elements
Must-Support: 7 elements

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element 1 is sliced based on the value of DiagnosticReport.category

Maturity: 0

 

Other representations of profile: CSV, Excel, Schematron