PATH-R4-18b: Bundle Example - Urine Microscopy, Culture and Sensitivity Report (Structured)

path-mockup-MCS-01-report

  • This is an example of a complex report.
  • The results are represented using a set of structured, coded Observations.
  • It contains multiple levels of test group Observations and test result Observations. Two of the test groups are nested ("Urine Culture" and "Antimicrobial sensitivity").
  • The report includes a range of numeric, semi-quantitative and qualitative results.
  • In this example, the specimen (urine) was collected after the request was made. The specimen is linked to the request within the Bundle using Specimen.request.
  • A clinical interpretation/summary of the test results is carried in DiagnosticReport.conclusion.

The following is a simplified logical data model that illustrates the key references between the FHIR profiles in the example message bundle. To aid clarity, not all of the references are shown. For a detailed description of the relationships between the FHIR profiles, and how they may be used, refer to How to Construct a Pathology Test Report Bundle.


path-data-model-MCS-01-report
<Bundle xmlns="http://hl7.org/fhir">
    <id value="Pathology-Bundle-Urine-MCS-01-Report-Example" />
    <meta>
        <lastUpdated value="2022-02-25T13:47:00+00:00" />
        <profile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Bundle" />
    </meta>
    <identifier>
        <system value="https://tools.ietf.org/html/rfc4122" />
        <value value="86834956-dc57-4b90-8f1b-6174a887ca27" />
    </identifier>
    <type value="message" />
    <entry>
        <fullUrl value="urn:uuid:f18a2226-c0ab-480d-b80a-b6561fe8f9c4" />
        <resource>
            <MessageHeader>
                <!--  TBC Review content of MessageHeader  -->
                <id value="f18a2226-c0ab-480d-b80a-b6561fe8f9c4" />
                <meta>
                    <profile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-MessageHeader" />
                </meta>
                <eventCoding>
                    <system value="http://snomed.info/sct" />
                    <code value="371528001" />
                    <display value="Pathology report" />
                </eventCoding>
                <destination>
                    <name value="PICKERING MEDICAL PRACTICE" />
                    <!--  TBC Update endpoint address  -->
                    <endpoint value="TBC" />
                    <!--  Requesting Organisation  -->
                    <receiver>
                        <reference value="urn:uuid:3c43b5b3-06d6-445f-ae9a-48d5f05df434" />
                    </receiver>
                </destination>
                <sender>
                    <!--  Performing Laboratory  -->
                    <reference value="urn:uuid:8a6d85b8-9837-4fed-a257-4cf207988338" />
                </sender>
                <source>
                    <!--  TBC Update endpoint address  -->
                    <endpoint value="TBC" />
                </source>
                <focus>
                    <!--  DiagnosticReport  -->
                    <reference value="urn:uuid:35d46ca1-f253-4c97-b7ee-fb5fccdf6c20" />
                </focus>
                <definition value="https://fhir.nhs.uk/England/MessageDefinition/England-Pathology-Report" />
            </MessageHeader>
        </resource>
    </entry>
    <entry>
        <fullUrl value="urn:uuid:8a6d85b8-9837-4fed-a257-4cf207988338" />
        <resource>
            <Organization>
                <!--  Performing Laboratory  -->
                <id value="8a6d85b8-9837-4fed-a257-4cf207988338" />
                <meta>
                    <profile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization" />
                </meta>
                <identifier>
                    <system value="https://fhir.nhs.uk/Id/ods-organization-code" />
                    <value value="Y8J7D" />
                </identifier>
                <name value="TD008362 PATH LAB 001" />
                <address>
                    <line value="PATHOLOGY LAB" />
                    <line value="7-8 WELLINGTON PLACE" />
                    <city value="LEEDS" />
                    <district value="WEST YORKSHIRE" />
                    <postalCode value="LS1 4AP" />
                </address>
            </Organization>
        </resource>
    </entry>
    <entry>
        <fullUrl value="urn:uuid:3c43b5b3-06d6-445f-ae9a-48d5f05df434" />
        <resource>
            <Organization>
                <!--  Requesting Organisation  -->
                <id value="3c43b5b3-06d6-445f-ae9a-48d5f05df434" />
                <meta>
                    <profile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Organization" />
                </meta>
                <identifier>
                    <system value="https://fhir.nhs.uk/Id/ods-organization-code" />
                    <value value="B82033" />
                </identifier>
                <name value="PICKERING MEDICAL PRACTICE" />
                <address>
                    <line value="SOUTHGATE" />
                    <city value="PICKERING" />
                    <district value="NORTH YORKSHIRE" />
                    <postalCode value="YO18 8BL" />
                </address>
            </Organization>
        </resource>
    </entry>
    <entry>
        <fullUrl value="urn:uuid:9a835acf-d715-4d84-8dcf-a8435f6417fe" />
        <resource>
            <Practitioner>
                <!--  Requesting Practitioner  -->
                <id value="9a835acf-d715-4d84-8dcf-a8435f6417fe" />
                <meta>
                    <profile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Practitioner" />
                </meta>
                <identifier>
                    <system value="https://fhir.hl7.org.uk/Id/gmc-number" />
                    <value value="C1008215" />
                </identifier>
                <name>
                    <use value="official" />
                    <family value="GASKELL" />
                    <given value="Gale" />
                    <prefix value="Dr" />
                </name>
            </Practitioner>
        </resource>
    </entry>
    <entry>
        <fullUrl value="urn:uuid:ab87a3f8-1d37-44a9-804e-5e962598a6e4" />
        <resource>
            <Patient>
                <id value="ab87a3f8-1d37-44a9-804e-5e962598a6e4" />
                <meta>
                    <profile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient" />
                </meta>
                <identifier>
                    <extension url="https://fhir.hl7.org.uk/StructureDefinition/Extension-UKCore-NHSNumberVerificationStatus">
                        <valueCodeableConcept>
                            <coding>
                                <system value="https://fhir.hl7.org.uk/CodeSystem/UKCore-NHSNumberVerificationStatusEngland" />
                                <code value="01" />
                                <display value="Number present and verified" />
                            </coding>
                        </valueCodeableConcept>
                    </extension>
                    <system value="https://fhir.nhs.uk/Id/nhs-number" />
                    <value value="9727710859" />
                </identifier>
                <name>
                    <use value="official" />
                    <family value="MOXEY" />
                    <given value="Judy" />
                </name>
                <gender value="female" />
                <birthDate value="2004-05-06" />
                <address>
                    <line value="1 CASTLEGATE" />
                    <city value="PICKERING" />
                    <district value="NORTH YORKSHIRE" />
                    <postalCode value="YO18 7AY" />
                </address>
            </Patient>
        </resource>
    </entry>
    <entry>
        <fullUrl value="urn:uuid:1c38d507-9ad7-4b49-ba91-7da204842cac" />
        <resource>
            <ServiceRequest>
                <id value="1c38d507-9ad7-4b49-ba91-7da204842cac" />
                <meta>
                    <profile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-ServiceRequest-Lab" />
                </meta>
                <identifier>
                    <system value="http://B82033-pickeringmedicalpractice.com/labrequest" />
                    <value value="REQ-20220221-000018" />
                </identifier>
                <status value="active" />
                <intent value="order" />
                <code>
                    <coding>
                        <!--  From PaLM procedure reference set  -->
                        <system value="http://snomed.info/sct" />
                        <code value="401324008" />
                        <display value="Urinary microscopy, culture and sensitivities" />
                    </coding>
                </code>
                <subject>
                    <reference value="urn:uuid:ab87a3f8-1d37-44a9-804e-5e962598a6e4" />
                    <display value="MOXEY, Judy" />
                </subject>
                <authoredOn value="2022-02-21T10:29:00+00:00" />
                <requester>
                    <reference value="urn:uuid:9a835acf-d715-4d84-8dcf-a8435f6417fe" />
                    <display value="GASKELL, Dr Gale" />
                </requester>
                <performer>
                    <reference value="urn:uuid:8a6d85b8-9837-4fed-a257-4cf207988338" />
                    <display value="TD008362 PATH LAB 001" />
                </performer>
            </ServiceRequest>
        </resource>
    </entry>
    <entry>
        <fullUrl value="urn:uuid:35d46ca1-f253-4c97-b7ee-fb5fccdf6c20" />
        <resource>
            <DiagnosticReport>
                <id value="35d46ca1-f253-4c97-b7ee-fb5fccdf6c20" />
                <meta>
                    <profile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport-Lab" />
                </meta>
                <identifier>
                    <system value="http://Y8J7D-pathlab001.com/report" />
                    <value value="REP-20220225-006301" />
                </identifier>
                <basedOn>
                    <reference value="urn:uuid:1c38d507-9ad7-4b49-ba91-7da204842cac" />
                </basedOn>
                <status value="final" />
                <category>
                    <coding>
                        <system value="http://terminology.hl7.org/CodeSystem/v2-0074" />
                        <code value="LAB" />
                        <display value="Laboratory" />
                    </coding>
                </category>
                <code>
                    <coding>
                        <system value="http://snomed.info/sct" />
                        <code value="721981007" />
                        <display value="Diagnostic studies report" />
                    </coding>
                </code>
                <subject>
                    <reference value="urn:uuid:ab87a3f8-1d37-44a9-804e-5e962598a6e4" />
                    <display value="MOXEY, Judy" />
                </subject>
                <issued value="2022-02-25T13:47:00+00:00" />
                <performer>
                    <reference value="urn:uuid:8a6d85b8-9837-4fed-a257-4cf207988338" />
                    <display value="TD008362 PATH LAB 001" />
                </performer>
                <specimen>
                    <reference value="urn:uuid:bde5b0a5-4fb3-4655-acf0-215b93aee006" />
                </specimen>
                <result>
                    <!--  Urine microscopy, culture and sensitivities group  -->
                    <reference value="urn:uuid:724714a1-c3a3-48c0-87a3-8d3f6740d24c" />
                </result>
                <conclusion value="Likely to be clinically significant." />
            </DiagnosticReport>
        </resource>
    </entry>
    <entry>
        <fullUrl value="urn:uuid:724714a1-c3a3-48c0-87a3-8d3f6740d24c" />
        <resource>
            <Observation>
                <!--  Urine microscopy, culture and sensitivities group  -->
                <id value="724714a1-c3a3-48c0-87a3-8d3f6740d24c" />
                <meta>
                    <profile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Observation-Group-Lab" />
                </meta>
                <identifier>
                    <system value="https://tools.ietf.org/html/rfc4122" />
                    <value value="7ba81e08-8099-4fdb-9b50-a3c11afb6c0b" />
                </identifier>
                <status value="final" />
                <category>
                    <coding>
                        <system value="http://terminology.hl7.org/CodeSystem/observation-category" />
                        <code value="laboratory" />
                        <display value="Laboratory" />
                    </coding>
                </category>
                <code>
                    <coding>
                        <!--  From PaLM procedure reference set  -->
                        <system value="http://snomed.info/sct" />
                        <code value="401324008" />
                        <display value="Urinary microscopy, culture and sensitivities" />
                    </coding>
                </code>
                <subject>
                    <reference value="urn:uuid:ab87a3f8-1d37-44a9-804e-5e962598a6e4" />
                    <display value="MOXEY, Judy" />
                </subject>
                <issued value="2022-02-25T13:47:00+00:00" />
                <performer>
                    <reference value="urn:uuid:8a6d85b8-9837-4fed-a257-4cf207988338" />
                    <display value="TD008362 PATH LAB 001" />
                </performer>
                <hasMember>
                    <!--  Microscopy group  -->
                    <reference value="urn:uuid:bd867909-49ca-4a4b-b02f-162790b6800f" />
                </hasMember>
                <hasMember>
                    <!--  Staphylococcus aureus - culture and sensitivities group  -->
                    <reference value="urn:uuid:70af0ca7-a77a-4daa-8aa2-1740433b1c3e" />
                </hasMember>
            </Observation>
        </resource>
    </entry>
    <entry>
        <fullUrl value="urn:uuid:bd867909-49ca-4a4b-b02f-162790b6800f" />
        <resource>
            <Observation>
                <!--  Microscopy group  -->
                <id value="bd867909-49ca-4a4b-b02f-162790b6800f" />
                <meta>
                    <profile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Observation-Group-Lab" />
                </meta>
                <identifier>
                    <system value="https://tools.ietf.org/html/rfc4122" />
                    <value value="02875aea-9815-4d1d-b34e-f9f29b859d02" />
                </identifier>
                <status value="final" />
                <category>
                    <coding>
                        <system value="http://terminology.hl7.org/CodeSystem/observation-category" />
                        <code value="laboratory" />
                        <display value="Laboratory" />
                    </coding>
                </category>
                <code>
                    <coding>
                        <!--  From PaLM procedure reference set  -->
                        <system value="http://snomed.info/sct" />
                        <code value="127800008" />
                        <display value="Microscopic urinalysis" />
                    </coding>
                </code>
                <subject>
                    <reference value="urn:uuid:ab87a3f8-1d37-44a9-804e-5e962598a6e4" />
                    <display value="MOXEY, Judy" />
                </subject>
                <issued value="2022-02-25T13:47:00+00:00" />
                <performer>
                    <reference value="urn:uuid:8a6d85b8-9837-4fed-a257-4cf207988338" />
                    <display value="TD008362 PATH LAB 001" />
                </performer>
                <hasMember>
                    <!--  Casts in urine  -->
                    <reference value="urn:uuid:17ec651c-1b6f-43e9-9033-cbb49dbac3db" />
                </hasMember>
                <hasMember>
                    <!--  White blood cell count in urine  -->
                    <reference value="urn:uuid:3dc8d5d8-90ef-485c-ad67-d2e3c83ed83f" />
                </hasMember>
                <hasMember>
                    <!--  Red blood cell count in urine  -->
                    <reference value="urn:uuid:fce26593-20ee-45b6-b805-7eb7d0f0a3fa" />
                </hasMember>
                <hasMember>
                    <!--  Epithelial cells in urine  -->
                    <reference value="urn:uuid:a4b0fa1f-8679-45bb-82a2-85e4e1bd519a" />
                </hasMember>
            </Observation>
        </resource>
    </entry>
    <entry>
        <fullUrl value="urn:uuid:17ec651c-1b6f-43e9-9033-cbb49dbac3db" />
        <resource>
            <Observation>
                <!--  Casts in urine  -->
                <id value="17ec651c-1b6f-43e9-9033-cbb49dbac3db" />
                <meta>
                    <profile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Observation-Lab" />
                </meta>
                <identifier>
                    <system value="https://tools.ietf.org/html/rfc4122" />
                    <value value="eab75d90-ce08-40a4-8247-34aad0d58873" />
                </identifier>
                <status value="final" />
                <category>
                    <coding>
                        <system value="http://terminology.hl7.org/CodeSystem/observation-category" />
                        <code value="laboratory" />
                        <display value="Laboratory" />
                    </coding>
                </category>
                <code>
                    <coding>
                        <!--  From PaLM observable entity reference set  -->
                        <system value="http://snomed.info/sct" />
                        <code value="51761000237101" />
                        <display value="Hyaline casts in mid-stream urine microscopy qualitative result" />
                    </coding>
                </code>
                <subject>
                    <reference value="urn:uuid:ab87a3f8-1d37-44a9-804e-5e962598a6e4" />
                    <display value="MOXEY, Judy" />
                </subject>
                <issued value="2022-02-25T13:47:00+00:00" />
                <performer>
                    <reference value="urn:uuid:8a6d85b8-9837-4fed-a257-4cf207988338" />
                    <display value="TD008362 PATH LAB 001" />
                </performer>
                <valueCodeableConcept>
                    <coding>
                        <system value="http://snomed.info/sct" />
                        <code value="47492008" />
                        <display value="Not seen" />
                    </coding>
                </valueCodeableConcept>
                <specimen>
                    <reference value="urn:uuid:bde5b0a5-4fb3-4655-acf0-215b93aee006" />
                </specimen>
            </Observation>
        </resource>
    </entry>
    <entry>
        <fullUrl value="urn:uuid:3dc8d5d8-90ef-485c-ad67-d2e3c83ed83f" />
        <resource>
            <Observation>
                <!--  White blood cell count in urine  -->
                <id value="3dc8d5d8-90ef-485c-ad67-d2e3c83ed83f" />
                <meta>
                    <profile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Observation-Lab" />
                </meta>
                <identifier>
                    <system value="https://tools.ietf.org/html/rfc4122" />
                    <value value="e644abd4-2587-486b-b6fe-ea3be866df29" />
                </identifier>
                <status value="final" />
                <category>
                    <coding>
                        <system value="http://terminology.hl7.org/CodeSystem/observation-category" />
                        <code value="laboratory" />
                        <display value="Laboratory" />
                    </coding>
                </category>
                <code>
                    <coding>
                        <!--  From PaLM observable entity reference set  -->
                        <system value="http://snomed.info/sct" />
                        <code value="42331000237103" />
                        <display value="White blood cell count in urine" />
                    </coding>
                </code>
                <subject>
                    <reference value="urn:uuid:ab87a3f8-1d37-44a9-804e-5e962598a6e4" />
                    <display value="MOXEY, Judy" />
                </subject>
                <issued value="2022-02-25T13:47:00+00:00" />
                <performer>
                    <reference value="urn:uuid:8a6d85b8-9837-4fed-a257-4cf207988338" />
                    <display value="TD008362 PATH LAB 001" />
                </performer>
                <valueQuantity>
                    <value value="35" />
                    <comparator value="&gt;" />
                    <unit value="x10*6/L" />
                    <system value="http://unitsofmeasure.org" />
                    <code value="10^6/L" />
                </valueQuantity>
                <specimen>
                    <reference value="urn:uuid:bde5b0a5-4fb3-4655-acf0-215b93aee006" />
                </specimen>
            </Observation>
        </resource>
    </entry>
    <entry>
        <fullUrl value="urn:uuid:fce26593-20ee-45b6-b805-7eb7d0f0a3fa" />
        <resource>
            <Observation>
                <!--  Red blood cell count in urine  -->
                <id value="fce26593-20ee-45b6-b805-7eb7d0f0a3fa" />
                <meta>
                    <profile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Observation-Lab" />
                </meta>
                <identifier>
                    <system value="https://tools.ietf.org/html/rfc4122" />
                    <value value="fc9d8f93-5cc7-43e8-8816-f4f438221b9f" />
                </identifier>
                <status value="final" />
                <category>
                    <coding>
                        <system value="http://terminology.hl7.org/CodeSystem/observation-category" />
                        <code value="laboratory" />
                        <display value="Laboratory" />
                    </coding>
                </category>
                <code>
                    <coding>
                        <!--  From PaLM observable entity reference set  -->
                        <system value="http://snomed.info/sct" />
                        <code value="43331000237105" />
                        <display value="Red blood cell count in urine" />
                    </coding>
                </code>
                <subject>
                    <reference value="urn:uuid:ab87a3f8-1d37-44a9-804e-5e962598a6e4" />
                    <display value="MOXEY, Judy" />
                </subject>
                <issued value="2022-02-25T13:47:00+00:00" />
                <performer>
                    <reference value="urn:uuid:8a6d85b8-9837-4fed-a257-4cf207988338" />
                    <display value="TD008362 PATH LAB 001" />
                </performer>
                <valueRange>
                    <low>
                        <value value="10" />
                        <unit value="x10*6/L" />
                        <system value="http://unitsofmeasure.org" />
                        <code value="10^6/L" />
                    </low>
                    <high>
                        <value value="35" />
                        <unit value="x10*6/L" />
                        <system value="http://unitsofmeasure.org" />
                        <code value="10^6/L" />
                    </high>
                </valueRange>
                <specimen>
                    <reference value="urn:uuid:bde5b0a5-4fb3-4655-acf0-215b93aee006" />
                </specimen>
            </Observation>
        </resource>
    </entry>
    <entry>
        <fullUrl value="urn:uuid:a4b0fa1f-8679-45bb-82a2-85e4e1bd519a" />
        <resource>
            <Observation>
                <!--  Epithelial cells in urine  -->
                <id value="a4b0fa1f-8679-45bb-82a2-85e4e1bd519a" />
                <meta>
                    <profile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Observation-Lab" />
                </meta>
                <identifier>
                    <system value="https://tools.ietf.org/html/rfc4122" />
                    <value value="db372648-314a-481a-a793-736b0ec3be76" />
                </identifier>
                <status value="final" />
                <category>
                    <coding>
                        <system value="http://terminology.hl7.org/CodeSystem/observation-category" />
                        <code value="laboratory" />
                        <display value="Laboratory" />
                    </coding>
                </category>
                <code>
                    <coding>
                        <!--  From PaLM observable entity reference set  -->
                        <system value="http://snomed.info/sct" />
                        <code value="49941000237104" />
                        <display value="Epithelial cells in mid-stream urine microscopy qualitative result" />
                    </coding>
                </code>
                <subject>
                    <reference value="urn:uuid:ab87a3f8-1d37-44a9-804e-5e962598a6e4" />
                    <display value="MOXEY, Judy" />
                </subject>
                <issued value="2022-02-25T13:47:00+00:00" />
                <performer>
                    <reference value="urn:uuid:8a6d85b8-9837-4fed-a257-4cf207988338" />
                    <display value="TD008362 PATH LAB 001" />
                </performer>
                <valueCodeableConcept>
                    <coding>
                        <system value="http://snomed.info/sct" />
                        <code value="260347006" />
                        <display value="Present + out of ++++" />
                    </coding>
                </valueCodeableConcept>
                <specimen>
                    <reference value="urn:uuid:bde5b0a5-4fb3-4655-acf0-215b93aee006" />
                </specimen>
            </Observation>
        </resource>
    </entry>
    <entry>
        <fullUrl value="urn:uuid:70af0ca7-a77a-4daa-8aa2-1740433b1c3e" />
        <resource>
            <Observation>
                <!--  Staphylococcus aureus - culture and sensitivities group  -->
                <id value="70af0ca7-a77a-4daa-8aa2-1740433b1c3e" />
                <meta>
                    <profile value="https://fhir.hl7.org.uk/StructureDefinition/UKCore-Observation-Group-Lab" />
                </meta>
                <identifier>
                    <system value="https://tools.ietf.org/html/rfc4122" />
                    <value value="147dbdea-22e1-4327-8407-b92bf362e115" />
                </identifier>
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                </category>
                <code>
                    <coding>
                        <!--  From PaLM procedure reference set  -->
                        <system value="http://snomed.info/sct" />
                        <code value="117010004" />
                        <display value="Urine culture" />
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                <subject>
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                    <!--  Staphylococcus aureus - culture result  -->
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                    <!--  Staphylococcus aureus - sensitivities group  -->
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    <entry>
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                        <!--  From PaLM observable entity reference set  -->
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    <entry>
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                        <!--  From PaLM procedure reference set  -->
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                <code>
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                        <!--  From PaLM observable entity reference set  -->
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    <entry>
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                        <!--  From PaLM observable entity reference set  -->
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