CH ELM (R4)
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This page is part of the Observations of notifiable communicable infectious diseases (v1.7.0: Release) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version in its permanent home (it will always be available at this URL). 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
Anthrax Bacillus anthracis Ag [Presence] in Specimen 31726-3 JSON, XML
Botulisms Clostridium botulinum toxin [Presence] in Specimen by Mouse bioassay 33696-6 JSON, XML
Brucellosis Brucella sp IgA Ab [Presence] in Serum 101802-7 JSON, XML
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
Crimean-Congo Crimean-Congo hemorrhagic fever virus RNA [Presence] in Serum by NAA with probe detection 88192-0 JSON, XML
Creutzfeldt-Jakob Disease (CJD) 14-3-3 Ag [Presence] in Cerebral spinal fluid 31989-7 JSON, XML
Dengue - reporting of high-level titer result Dengue virus IgG Ab [Titer] in Serum 6811-4 JSON, XML
Ebola Ebola virus RNA [Presence] in Blood by NAA with probe detection 86518-8 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
Lassa fever Lassa virus RNA [Presence] in Specimen by NAA with probe detection 97646-4 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
Marburg fever Marburg virus RNA [Presence] in Blood by NAA with probe detection 86574-1 JSON, XML
Measles - reporting of a seroconversion Measles virus IgG and IgM [Interpretation] in Serum 44012-3 JSON, XML
MERS Middle East respiratory syndrome coronavirus (MERS-CoV) RNA [Presence] in Respiratory system specimen by NAA with probe detection 94501-4 JSON, XML
Plague Yersinia pestis [Presence] in Specimen by Organism specific culture 33685-9 JSON, XML
Pneumococcal disease Streptococcus pneumoniae Ag [Presence] in Cerebral spinal fluid 20489-1 JSON, XML
Poliomyelitis Polio virus identified in Specimen by Organism specific culture 73907-8 JSON, XML
Rabies Rabies virus neutralizing antibody [Presence] in Serum by Neutralization test 70858-6 JSON, XML
Rubella - reporting of a seroconversion Rubella virus IgG Ab [Interpretation] in Serum 20458-6 JSON, XML
Rubella - reporting of an avidity Rubella virus IgG Ab avidity [Ratio] in Serum by Immunoassay 52986-7 JSON, XML
SARS SARS coronavirus RNA [Presence] in Specimen by NAA with probe detection 41458-1 JSON, XML
Smallpox Variola virus DNA [Presence] in Specimen by NAA with probe detection 41856-6 JSON, XML
Tick - borne encephalitis Tick - borne encephalitis virus RNA [Presence] in Specimen by NAA with probe detection 97920-3 JSON, XML
Trichinellosis Trichinella spiralis [Presence] in Tissue by Light microscopy 23499-7 JSON, XML
Yellow fever Yellow fever virus IgM Ab [Presence] in Serum 41216-3 JSON, XML
Zika fever Zika virus IgM Ab [Presence] in Serum by Immunofluorescence 82731-1 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
HIV Human immunodeficiency virus type I (organism) 89293008 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
Hanta fever Hantavirus RNA [Presence] in Blood by NAA with probe detection 18725-2 <a href="Bundle-52Doc-Hantavirus.json.html"">JSON</a>, <a href="Bundle-52Doc-Hantavirus.xml.html"">XML</a>
Influenza A new subtype Influenza virus A hemagglutinin type RNA [Identifier] in Specimen by NAA with probe detection 59423-4 JSON, XML
Legionellosis Legionella sp Ag [Presence] in Urine 32781-7 JSON, XML
Paratyphoid fever Salmonella sp [Presence] in Stool by Culture 82301-3 JSON, XML
Salmonellosis Salmonella sp DNA [Presence] in Specimen by NAA with probe detection 49612-5 JSON, XML
Shigellosis Shigella sp [Presence] in Specimen by Organism specific culture 46454-5 JSON, XML
Tularaemia - with optional organism specification Francisella tularensis Ag [Presence] in Serum 31828-7 JSON, XML
West-Nile-Fever Virus identified in Specimen by Culture 6584-7 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
Example of quantity, ratio or text observation values (non-coded)
Disease observation.code display LOINC observation.code
(leading code)
FHIR Document
Salmonellosis Salmonella sp antigenic formula [Identifier] in Isolate by Agglutination 56475-7 JSON, XML
Monkeypox Monkeypox virus clade [Type] in Specimen by Sequencing 101003-2 JSON, XML
HIV HIV 1 RNA [Units/volume] (viral load) in Serum or Plasma by NAA with probe detection 62469-2 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