CH ELM (R4)
1.5.0 - release Switzerland flag

This page is part of the Observations of notifiable communicable infectious diseases (v1.5.0: Release) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version. For a full list of available versions, see the Directory of published versions

FHIR Document (Bundle)

The CH ELM exchange format defines a FHIR document representing a coherent set of information specific to the transmission of laboratory data. This FHIR document is based on the CH Lab report document which is part of the CH LAB-Report Project.

The exchange format expects a separate FHIR document per patient, organism and test performed.

The FHIR document consists of a bundle-resource of type "document" (the terms "FHIR document" and "Bundle" are synonymous in the context of the CH ELM project).

The bundle resource contains a consistent set of entries representing FHIR resources specific for the transmission of laboratory data:

{
"resourceType": "Bundle",
"entry": [
    {
        "resourceType": "Composition"
    },
parameters like date, language, title, author, and referring to the different resources
    {
        "resourceType": "DiagnosticReport"
    },
represents the laboratory report as a result of a lab order, with references to all other resources
    {
        "resourceType": "Patient"
    },
the person from whom the specimen was taken
    {
        "resourceType": "Observation"
    },
defines the analyzed organism with the laboratory test result-values, interpretation, and test execution date
    {
        "resourceType": "Specimen"
    },
the specimen material with collection date
    {
        "resourceType": "ServiceRequest"
    },
the lab order with the laboratory order ID, the requester, and performer of the laboratory test
    {
        "resourceType": "PractitionerRole"
    },
the orderer of the laboratory test containing a practitioner and/or organization
    {
        "resourceType": "Practitioner"
    },
the person ordering the laboratory test
    {
        "resourceType": "Organization"
    },
the organization ordering the laboratory test
    {
        "resourceType": "Organization"
    }
the performing laboratory
]
}

The FHIR document is generic and applicable for all types of organisms and reporting scenarios (use cases). For each resource within the FHIR document, a resource profile is defined to meet specific data needs depending on the context and use case.

Resource profiles

Resource profiles are a way to customize and constrain FHIR resources to meet specific requirements depending on a particular context. These rules might restrict the allowable values for certain elements, specify additional mandatory elements, or define extensions to capture additional data beyond the standard FHIR resources. In the CH ELM Implementation Guide multiple profiles can exist based on the same FHIR resource.

Example: the FHIR resource «organization» is used to map the sender of the FHIR Document, the performing laboratory and the orderer of the laboratory test – each of which having its own profile.

The diagram “Resource Overview” illustrates the connections between the individual resource-profiles of a FHIR document.

See the examples in chapter 2.2 to learn how to use the resource profiles for different use cases and data requirements.

Example FHIR documents

Default scenario

Examples of basic FHIR documents (no additional codes for organism or specimen)
Disease observation.code display LOINC observation.code
(leading code)
FHIR Document
Campylobacteriosis Campylobacter coli DNA [Presence] in Stool by NAA with probe detection 101552-8 JSON, XML
Chikungunya fever Chikungunya virus RNA [Presence] in Urine by NAA with probe detection 86515-4 JSON, XML
Cholera Vibrio cholerae toxin ctx gene [Presence] in Specimen by NAA with probe detection 53942-9 JSON, XML
Covid-19 SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory system specimen by NAA with probe detection 94500-6 JSON, XML
Dengue - reporting of high-level titer result Dengue virus IgG Ab [Titer] in Serum 6811-4 JSON, XML
Diphtheria Corynebacterium diphtheriae DNA [Presence] in Specimen by NAA with probe detection 67561-1 JSON, XML
Gonorrhoea Neisseria gonorrhoeae [Presence] in Urethra by Organism specific culture 697-3 JSON, XML
Haemophilus influenzae disease Haemophilus influenzae B DNA [Presence] in Blood by NAA with probe detection 53607-8 JSON, XML
Hepatitis A Hepatitis A virus IgM Ab [Presence] in Serum 22314-9 JSON, XML
Hepatitis B Hepatitis B virus core IgM Ab [Presence] in Serum 31204-1 JSON, XML
Hepatitis C Hepatitis C virus Ab [Presence] in Serum by Immunoblot 5199-5 JSON, XML
Hepatitis E Hepatitis E virus RNA [Presence] in Stool by NAA with probe detection 91071-1 JSON, XML
Influenza Influenza virus A RNA [Presence] in Nasopharynx by NAA with probe detection 76078-5 JSON, XML
Listeriosis Listeria monocytogenes DNA [Presence] in Cerebral spinal fluid by NAA with non-probe detection 82184-3 JSON, XML
Malaria Plasmodium knowlesi DNA [Presence] in Blood by NAA with probe detection 70568-1 JSON, XML
Measles - reporting of a seroconversion Measles virus IgG and IgM [Interpretation] in Serum 44012-3 JSON, XML
Pneumococcal disease Streptococcus pneumoniae Ag [Presence] in Cerebral spinal fluid 20489-1 JSON, XML
Rubella - reporting of a seroconversion Rubella virus IgG Ab [Interpretation] in Serum 20458-6 JSON, XML
Tick - borne encephalitis Tick - borne encephalitis virus RNA [Presence] in Specimen by NAA with probe detection 97920-3 JSON, XML
Example of a SNOMED CT code instead of a LOINC code in observation.code
Disease observation.code display SNOMED CT observation.code
(leading code)
FHIR Document
Syphilis Treponema pallidum (organism) 72904005 JSON, XML
Example of an organism specification
Disease observation.code display LOINC observation.code
(leading code)
FHIR Document
Carbapenemase - producing enterobacteriaceae (CPE) Carbapenem resistance bla OXA-48-like gene [Presence] by Molecular method 85827-4 JSON, XML
Legionellosis Legionella sp Ag [Presence] in Urine 32781-7 JSON, XML
Shigellosis Shigella sp DNA [Presence] in Stool by NAA with probe detection 101427-3 JSON, XML
Tularaemia - with optional organism specification Francisella tularensis Ag [Presence] in Serum 31828-7 JSON, XML
Example of a specimen specification
Disease observation.code display LOINC observation.code
(leading code)
FHIR Document
Chlamydiosis Chlamydia trachomatis [Presence] in Specimen by Organism specific culture 6349-5 JSON, XML
Monkeypox Monkeypox virus DNA [Presence] in Specimen by NAA with probe detection 100383-9 JSON, XML
Example of a VCT Patient with specimen specification
Disease observation.code display LOINC observation.code
(leading code)
FHIR Document
Chlamydiosis Chlamydia trachomatis [Presence] in Specimen by Organism specific culture 6349-5 JSON, XML

Broker scenario

Disease observation.code display LOINC observation.code
(leading code)
FHIR Document
Gonorrhoea Neisseria gonorrhoeae [Presence] in Urethra by Organism specific culture 697-3 JSON, XML

Scenario for confirmation tests

Disease observation.code display LOINC observation.code
(leading code)
FHIR Document
Meningococcal disease - initial observation by primary laboratory Microscopic observation [Identifier] in Cerebral spinal fluid by Gram stain 14357-8 JSON, XML
Meningococcal disease - confirmation test by reference laboratory Neisseria meningitidis [Presence] in Cerebral spinal fluid by Organism specific culture 86581-6 JSON, XML