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PROTECT-CHILD Pediatric Transplant Data Implementation Guide
0.1.0-ci-build -

PROTECT-CHILD Pediatric Transplant Data Implementation Guide
0.1.0-ci-build - ci-build

PROTECT-CHILD Pediatric Transplant Data Implementation Guide, published by Protect Child. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/hl7-eu/protect-child/ and changes regularly. See the Directory of published versions

Microbiology

Microbiology profile Microbiology DiagnosticReport + Observations Microbiology ID M Visit ID M Donor ID O VIRAL SEROLOGY EBV Positive R EBV (copies/mL) R CMV Positive R CMV (copies/mL) R BKV Positive R BKV (copies/mL) R Parvovirus B19 Pos. R Parvovirus B19 (copies/mL) R HSV Positive R VZV Positive R Adenovirus Positive R CULTURE Culture Result R Other Microbiology R EBV Hepatitis (Liver) R Evidence BKVaN R

Each result profile below derives from MicrobiologyResult.

Concept map: MicrobiologyLmToFhir

Cardinality key — M = Mandatory (1..1) · R = Recommended (0..1) · O = Optional (0..1)

DM field Card. FHIR Code Value Notes
microbiology_id M MicrobiologyReport — identifier  
visit_id M MicrobiologyReport and each result — encounter The recipient's Visit, also for donor results
donor_id O MicrobiologyReport and each result — subject Reference(Donor) for donor results; otherwise Reference(PatientTransplant)
ebv_dna R MicrobiologyNucleicAcid LOINC 5002-1 — Epstein Barr virus DNA [Presence] in Blood by NAA with probe detection Detected / Not detected  
ebv_dna_copies R MicrobiologyViralLoad LOINC 36923-1 — Epstein Barr virus DNA [#/volume] (viral load) in Blood by NAA with probe detection Quantity Alternatives: 93840-7, 47982-4, 43730-1
ebv_igm_anti_ea R MicrobiologySerology MicrobiologyCS#ebv-ea-igm — EBV early antigen IgM Ab [Presence] in Serum Positive / Negative LOINC has no IgM-specific EBV early-antigen code; 7882-4 (early Ab, any isotype) is broader.
ebv_igm_anti_vca R MicrobiologySerology LOINC 30340-4 — Epstein Barr virus capsid IgM Ab [Presence] in Serum Positive / Negative Alternatives: 24115-8, 40751-0, 93714-4; the OMOP sheet maps this to 3012732 (EBNA IgM, LOINC 7884-0), which is a different antigen.
ebv_igg_anti_vca R MicrobiologySerology LOINC 30339-6 — Epstein Barr virus capsid IgG Ab [Presence] in Serum Positive / Negative Alternatives: 93713-6
ebv_igg_ebna R MicrobiologySerology LOINC 7883-2 — Epstein Barr virus nuclear IgG Ab [Presence] in Serum Positive / Negative  
cmv_dna R MicrobiologyNucleicAcid LOINC 4996-5 — Cytomegalovirus DNA [Presence] in Blood by NAA with probe detection Detected / Not detected  
cmv_dna_copies R MicrobiologyViralLoad LOINC 29604-6 — Cytomegalovirus DNA [#/volume] (viral load) in Blood by NAA with probe detection Quantity Alternatives: 100675-8, 30247-1, 72493-0
cmv_igm R MicrobiologySerology LOINC 30325-5 — Cytomegalovirus IgM Ab [Presence] in Serum or Plasma Positive / Negative Alternatives: 87725-8
cmv_igg R MicrobiologySerology LOINC 13949-3 — Cytomegalovirus IgG Ab [Presence] in Serum or Plasma by Immunoassay Positive / Negative Alternatives: 22244-8, 87726-6
parvovirus_b19_dna R MicrobiologyNucleicAcid LOINC 50348-2 — Parvovirus B19 DNA [Presence] in Blood by NAA with probe detection Detected / Not detected Alternatives: 75543-9
parvovirus_b19_dna_copies R MicrobiologyViralLoad LOINC 49431-0 — Parvovirus B19 DNA [#/volume] (viral load) in Blood by NAA with probe detection Quantity Alternatives: 49434-4, 74420-1
parvovirus_b19_igg R MicrobiologySerology LOINC 29675-6 — Parvovirus B19 IgG Ab [Presence] in Serum Positive / Negative  
parvovirus_b19_igm R MicrobiologySerology LOINC 7981-4 — Parvovirus B19 IgM Ab [Presence] in Serum Positive / Negative  
hsv_igg R MicrobiologySerology LOINC 19106-4 — Herpes simplex virus IgG Ab [Presence] in Serum Positive / Negative  
hsv_igm R MicrobiologySerology LOINC 25435-9 — Herpes simplex virus IgM Ab [Presence] in Serum Positive / Negative  
adenovirus_igg R MicrobiologySerology LOINC 41162-9 — Adenovirus IgG Ab [Presence] in Serum Positive / Negative  
adenovirus_igm R MicrobiologySerology LOINC 21054-2 — Adenovirus IgM Ab [Presence] in Serum Positive / Negative  
blood_adenovirus_dna R MicrobiologyNucleicAcid LOINC 86511-3 — Adenovirus DNA [Presence] in Blood by NAA with probe detection Detected / Not detected  
blood_adenovirus_dna_copies R MicrobiologyViralLoad LOINC 49341-1 — Adenovirus DNA [#/volume] (viral load) in Blood by NAA with probe detection Quantity Alternatives: 49334-6, 106727-1
vzv_igg R MicrobiologySerology LOINC 19162-7 — Varicella zoster virus IgG Ab [Presence] in Serum Positive / Negative  
vzv_igm R MicrobiologySerology LOINC 21597-0 — Varicella zoster virus IgM Ab [Presence] in Serum Positive / Negative  
blood_bkv_dna R MicrobiologyNucleicAcid LOINC 63475-8 — BK virus DNA [Presence] in Blood Detected / Not detected  
blood_bkv_dna_copies R MicrobiologyViralLoad LOINC 49345-2 — BK virus DNA [#/volume] (viral load) in Blood by NAA with probe detection Quantity Alternatives: 101341-6, 41479-7, 32284-2
urine_bkv_dna R MicrobiologyNucleicAcid LOINC 33978-8 — BK virus DNA [Presence] in Urine by NAA with probe detection Detected / Not detected  
bkv_dna_kidney_biopsy R MicrobiologyNucleicAcid LOINC 47251-4 — BK virus DNA [Presence] in Specimen by NAA with probe detection Detected / Not detected Generic-specimen code; Observation.specimen identifies the kidney biopsy tissue. Kidney only
bkv_fish_kidney_biopsy R MicrobiologyNucleicAcid MicrobiologyCS#bkv-dna-ish-tissue — BK virus DNA [Presence] in Tissue by in situ hybridization Detected / Not detected LOINC has no in-situ hybridisation code for BK virus in tissue. Kidney only
blood_colture R MicrobiologyCulture LOINC 600-7 — Bacteria identified in Blood by Culture Organism, or Positive / Negative Kidney only
urine_colture R MicrobiologyCulture LOINC 630-4 — Bacteria identified in Urine by Culture Organism, or Positive / Negative Kidney only
other_positivity R MicrobiologyReport — conclusion (free text) Kidney only
ebv_hepatitis_liver R MicrobiologyDiagnosis (Condition) SNOMED 302919001 Epstein-Barr virus hepatitis presence = positive Liver only. MicrobiologyDiagnosis (Condition). false → the same Condition with verificationStatus = #refuted; blank → no Condition.
evidence_bkvan R MicrobiologyDiagnosis (Condition) SNOMED 713886006 BK virus nephropathy presence = positive MicrobiologyDiagnosis (Condition). No → the same Condition with verificationStatus = #refuted; Unknown or blank → no Condition.