Add EUCAST v12.0 antifungal clinical breakpoints (June 2025) by Copilot · Pull Request #209 · markusrt/NRZMyk

Copilot · 2026-02-06T04:58:06Z

Analyze existing EUCAST v10.0 and v11.0 breakpoints in both files
Research EUCAST v12.0 (June 2025) breakpoints changes
Create EUCAST v12.0 breakpoint entries for all antifungal agent/species combinations
Add v12.0 entries to NRZMyk.Services/Data/ClinicalBreakpoints.json (consolidated location)
Update tests that were expecting specific breakpoint counts/versions
Build and test the application to verify changes (all 467 tests pass)
Fix strange character in CLSI M60 2019 Voriconazole MicBreakpointIntermediate field
Consolidate breakpoint data into single embedded resource
Remove unnecessary null-conditional operators in ApplicationDbContextSeed

Summary of Changes

Data Consolidation (Addresses Reviewer Feedback)

Moved ClinicalBreakpoints.json from NRZMyk.Mocks/Data to NRZMyk.Services/Data as a single source of truth
Created IClinicalBreakpointProvider interface and ClinicalBreakpointProvider implementation to read from embedded resource
Updated ApplicationDbContextSeed to use the provider instead of configuration from appsettings.json
Updated MockClinicalBreakpointService to use the provider instead of its own embedded resource
Removed duplicate breakpoint data from appsettings.json (only MainOrganization remains in DatabaseSeed)
Removed Newtonsoft.Json dependency from NRZMyk.Mocks (no longer needed)

EUCAST v12.0 Breakpoints

Version: 12.0, Valid From: June 26, 2025
64 new breakpoint entries (9 agents × 8 species)
Key Voriconazole changes: tightened R breakpoints with no intermediate category

Files Changed

Added: NRZMyk.Services/Data/ClinicalBreakpoints.json (single source of truth)
Added: NRZMyk.Services/Services/IClinicalBreakpointProvider.cs
Added: NRZMyk.Services/Services/ClinicalBreakpointProvider.cs
Modified: NRZMyk.Services/NRZMyk.Services.csproj (embedded resource)
Modified: NRZMyk.Services/Data/ApplicationDbContextSeed.cs (use provider)
Modified: NRZMyk.Services/Configuration/DatabaseSeed.cs (removed ClinicalBreakpoints property)
Modified: NRZMyk.Server/Program.cs (register provider)
Modified: NRZMyk.Server/appsettings.json (removed duplicate data)
Modified: NRZMyk.Mocks/MockServices/MockClinicalBreakpointService.cs (use provider)
Modified: NRZMyk.Mocks/NRZMyk.Mocks.csproj (removed embedded resource and Newtonsoft.Json)
Deleted: NRZMyk.Mocks/Data/ClinicalBreakpoints.json (duplicate removed)

Original prompt

This section details on the original issue you should resolve

<issue_title>Update ClinicalBreakpoints to include EUCAST v12.0 entries (2025)</issue_title>
<issue_description>As a developer and data steward,
I want to add and synchronize new EUCAST antifungal clinical breakpoints (as published in EUCAST v12.0, June 2025) in both NRZMyk.Mocks/Data/ClinicalBreakpoints.json and the inlined DatabaseSeed in NRZMyk.Server/appsettings.json,
So that the application always provides current and harmonized breakpoint data in both the mock and real database environments.

Acceptance Criteria

All new or changed EUCAST antifungal breakpoints from the referenced v12.0 list are added to both files.

Outdated breakpoints are replaced or removed as appropriate in both files, maintaining consistency.

Ensure no data is lost and all changes are cross-checked with the official EUCAST list.

Confirm that application behavior matches expected outcomes after update (mock and prod config).

Reference: EUCAST v12.0 Breakpoints

Notes:

The previous update (@markusrt/NRZMykAdd new EUCAST breakpoints #179) included additional fixes because the DB seed was not yet ready—now it is, so this update should include both mock and config seeds.

Coordinate with downstream consumers to ensure smooth upgrade process if needed.

Provide a checklist or summary of all touched antifungal agents/species.

/cc @markusrt</issue_description>

Comments on the Issue (you are @copilot in this section)

Fixes Update ClinicalBreakpoints to include EUCAST v12.0 entries (2025) #208

💬 We'd love your input! Share your thoughts on Copilot coding agent in our 2 minute survey.

Co-authored-by: markusrt <299753+markusrt@users.noreply.github.com>

markusrt

@copilot Please check the review comments

markusrt · 2026-02-06T05:22:34Z

  },
  "AllowedHosts": "*",
  "DatabaseSeed": {
-    "MainOrganization": "Nationales Referenzzentrum für Invasive Pilzinfektionen",
-    "ClinicalBreakpoints": [{"AntifungalAgent":"AmphotericinB","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"1","MicBreakpointResistent":"1","AntifungalAgentDetails":"Amphotericin B"},{"AntifungalAgent":"AmphotericinB","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"1","MicBreakpointResistent":"1","AntifungalAgentDetails":"Amphotericin B"},{"AntifungalAgent":"AmphotericinB","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"1","MicBreakpointResistent":"1","AntifungalAgentDetails":"Amphotericin B"},{"AntifungalAgent":"AmphotericinB","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Amphotericin B"},{"AntifungalAgent":"AmphotericinB","Species":"CandidaKrusei","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"1","MicBreakpointResistent":"1","AntifungalAgentDetails":"Amphotericin B"},{"AntifungalAgent":"AmphotericinB","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"1","MicBreakpointResistent":"1","AntifungalAgentDetails":"Amphotericin B"},{"AntifungalAgent":"AmphotericinB","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"1","MicBreakpointResistent":"1","AntifungalAgentDetails":"Amphotericin B"},{"AntifungalAgent":"Anidulafungin","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.03","MicBreakpointResistent":"0.03","AntifungalAgentDetails":"Anidulafungin"},{"AntifungalAgent":"Anidulafungin","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Anidulafungin"},{"AntifungalAgent":"Anidulafungin","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Anidulafungin"},{"AntifungalAgent":"Anidulafungin","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Anidulafungin"},{"AntifungalAgent":"Anidulafungin","Species":"CandidaKrusei","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Anidulafungin"},{"AntifungalAgent":"Anidulafungin","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"4","MicBreakpointResistent":"4","AntifungalAgentDetails":"Anidulafungin"},{"AntifungalAgent":"Anidulafungin","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Anidulafungin"},{"AntifungalAgent":"Caspofungin","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Caspofungin"},{"AntifungalAgent":"Caspofungin","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Caspofungin"},{"AntifungalAgent":"Caspofungin","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Caspofungin"},{"AntifungalAgent":"Caspofungin","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Caspofungin"},{"AntifungalAgent":"Caspofungin","Species":"CandidaKrusei","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Caspofungin"},{"AntifungalAgent":"Caspofungin","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Caspofungin"},{"AntifungalAgent":"Caspofungin","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Caspofungin"},{"AntifungalAgent":"Micafungin","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.016","TechnicalUncertainty":"0.03","MicBreakpointResistent":"0.016","AntifungalAgentDetails":"Micafungin"},{"AntifungalAgent":"Micafungin","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Micafungin"},{"AntifungalAgent":"Micafungin","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.03","MicBreakpointResistent":"0.03","AntifungalAgentDetails":"Micafungin"},{"AntifungalAgent":"Micafungin","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Micafungin"},{"AntifungalAgent":"Micafungin","Species":"CandidaKrusei","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Micafungin"},{"AntifungalAgent":"Micafungin","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"2","MicBreakpointResistent":"2","AntifungalAgentDetails":"Micafungin"},{"AntifungalAgent":"Micafungin","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Micafungin"},{"AntifungalAgent":"Voriconazole","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.25","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Voriconazole","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.25","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Voriconazole","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Voriconazole","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Voriconazole","Species":"CandidaKrusei","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Voriconazole","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.125","MicBreakpointResistent":"0.25","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Voriconazole","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.125","MicBreakpointResistent":"0.25","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Fluconazole","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"2","MicBreakpointResistent":"4","AntifungalAgentDetails":"Fluconazole"},{"AntifungalAgent":"Fluconazole","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"2","MicBreakpointResistent":"4","AntifungalAgentDetails":"Fluconazole"},{"AntifungalAgent":"Fluconazole","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.001","MicBreakpointResistent":"16","AntifungalAgentDetails":"Fluconazole"},{"AntifungalAgent":"Fluconazole","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Fluconazole"},{"AntifungalAgent":"Fluconazole","Species":"CandidaKrusei","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Fluconazole"},{"AntifungalAgent":"Fluconazole","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"2","MicBreakpointResistent":"4","AntifungalAgentDetails":"Fluconazole"},{"AntifungalAgent":"Fluconazole","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"2","MicBreakpointResistent":"4","AntifungalAgentDetails":"Fluconazole"},{"AntifungalAgent":"Fluconazole","Species":"None","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"2","MicBreakpointResistent":"4","AntifungalAgentDetails":"Fluconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaKrusei","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaKrusei","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.125","MicBreakpointResistent":"0.125","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.125","MicBreakpointResistent":"0.125","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaKrusei","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"10.0","ValidFrom":"2020-02-04","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"AmphotericinB","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"1","MicBreakpointResistent":"1","AntifungalAgentDetails":"Amphotericin B"},{"AntifungalAgent":"AmphotericinB","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"1","MicBreakpointResistent":"1","AntifungalAgentDetails":"Amphotericin B"},{"AntifungalAgent":"AmphotericinB","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"1","MicBreakpointResistent":"1","AntifungalAgentDetails":"Amphotericin B"},{"AntifungalAgent":"AmphotericinB","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Amphotericin B"},{"AntifungalAgent":"AmphotericinB","Species":"CandidaKrusei","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"1","MicBreakpointResistent":"1","AntifungalAgentDetails":"Amphotericin B"},{"AntifungalAgent":"AmphotericinB","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"1","MicBreakpointResistent":"1","AntifungalAgentDetails":"Amphotericin B"},{"AntifungalAgent":"AmphotericinB","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"1","MicBreakpointResistent":"1","AntifungalAgentDetails":"Amphotericin B"},{"AntifungalAgent":"Anidulafungin","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.016","MicBreakpointResistent":"0.016","AntifungalAgentDetails":"Anidulafungin"},{"AntifungalAgent":"Anidulafungin","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.03","MicBreakpointResistent":"0.03","AntifungalAgentDetails":"Anidulafungin"},{"AntifungalAgent":"Anidulafungin","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Anidulafungin"},{"AntifungalAgent":"Anidulafungin","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Anidulafungin"},{"AntifungalAgent":"Anidulafungin","Species":"CandidaKrusei","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Anidulafungin"},{"AntifungalAgent":"Anidulafungin","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"4","MicBreakpointResistent":"4","AntifungalAgentDetails":"Anidulafungin"},{"AntifungalAgent":"Anidulafungin","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Anidulafungin"},{"AntifungalAgent":"Caspofungin","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Caspofungin"},{"AntifungalAgent":"Caspofungin","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Caspofungin"},{"AntifungalAgent":"Caspofungin","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Caspofungin"},{"AntifungalAgent":"Caspofungin","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Caspofungin"},{"AntifungalAgent":"Caspofungin","Species":"CandidaKrusei","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Caspofungin"},{"AntifungalAgent":"Caspofungin","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Caspofungin"},{"AntifungalAgent":"Caspofungin","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Caspofungin"},{"AntifungalAgent":"Micafungin","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.03","MicBreakpointResistent":"0.03","AntifungalAgentDetails":"Micafungin"},{"AntifungalAgent":"Micafungin","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Micafungin"},{"AntifungalAgent":"Micafungin","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.03","MicBreakpointResistent":"0.03","AntifungalAgentDetails":"Micafungin"},{"AntifungalAgent":"Micafungin","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Micafungin"},{"AntifungalAgent":"Micafungin","Species":"CandidaKrusei","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Micafungin"},{"AntifungalAgent":"Micafungin","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"4","MicBreakpointResistent":"4","AntifungalAgentDetails":"Micafungin"},{"AntifungalAgent":"Micafungin","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Micafungin"},{"AntifungalAgent":"Voriconazole","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.25","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Voriconazole","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.25","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Voriconazole","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Voriconazole","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Voriconazole","Species":"CandidaKrusei","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Voriconazole","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.125","MicBreakpointResistent":"0.25","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Voriconazole","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.125","MicBreakpointResistent":"0.25","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Fluconazole","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"2","MicBreakpointResistent":"4","AntifungalAgentDetails":"Fluconazole"},{"AntifungalAgent":"Fluconazole","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"2","MicBreakpointResistent":"4","AntifungalAgentDetails":"Fluconazole"},{"AntifungalAgent":"Fluconazole","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.001","MicBreakpointResistent":"16","AntifungalAgentDetails":"Fluconazole"},{"AntifungalAgent":"Fluconazole","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Fluconazole"},{"AntifungalAgent":"Fluconazole","Species":"CandidaKrusei","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Fluconazole"},{"AntifungalAgent":"Fluconazole","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"2","MicBreakpointResistent":"4","AntifungalAgentDetails":"Fluconazole"},{"AntifungalAgent":"Fluconazole","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"2","MicBreakpointResistent":"4","AntifungalAgentDetails":"Fluconazole"},{"AntifungalAgent":"Fluconazole","Species":"None","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"2","MicBreakpointResistent":"4","AntifungalAgentDetails":"Fluconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaKrusei","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaKrusei","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.125","MicBreakpointResistent":"0.125","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.125","MicBreakpointResistent":"0.125","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaAlbicans","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaDubliniensis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaGlabrata","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaGuilliermondii","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaKrusei","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaParapsilosis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaTropicalis","Standard":"EUCAST","Version":"11.0","ValidFrom":"2024-12-02","MicBreakpointSusceptible":"0.06","MicBreakpointResistent":"0.06","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"AmphotericinB","Species":"CandidaAlbicans","Standard":"CLSI","Version":"M60 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2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Voriconazole","Species":"CandidaKrusei","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","MicBreakpointSusceptible":"0.5","MicBreakpointIntermediate":"1","MicBreakpointResistent":"2","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Voriconazole","Species":"CandidaParapsilosis","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","MicBreakpointSusceptible":"0.125","MicBreakpointIntermediate":"0.25–0.5","MicBreakpointResistent":"1","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Voriconazole","Species":"CandidaTropicalis","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","MicBreakpointSusceptible":"0.125","MicBreakpointIntermediate":"0.25–0.5","MicBreakpointResistent":"1","AntifungalAgentDetails":"Voriconazole"},{"AntifungalAgent":"Fluconazole","Species":"CandidaAlbicans","Standard":"CLSI","Version":"M60 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2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaGlabrata","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaGuilliermondii","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaKrusei","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaParapsilosis","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Isavuconazole","Species":"CandidaTropicalis","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Isavuconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaAlbicans","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaDubliniensis","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaGlabrata","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaGuilliermondii","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaKrusei","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaParapsilosis","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Itraconazole","Species":"CandidaTropicalis","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Itraconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaAlbicans","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaDubliniensis","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaGlabrata","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaGuilliermondii","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaKrusei","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaParapsilosis","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Posaconazole"},{"AntifungalAgent":"Posaconazole","Species":"CandidaTropicalis","Standard":"CLSI","Version":"M60 2019","ValidFrom":"2019-11-01","AntifungalAgentDetails":"Posaconazole"}]
+    "MainOrganization": "Nationales Referenzzentrum f\u00fcr Invasive Pilzinfektionen",


Please leave this inlined as it is easier to skip, or if there is a better way maybe not requiring two files you can do that as well. Thinking about embedded resource or something like that which can be used as seed, setting, and mock data.

The data is already consolidated via embedded resource in NRZMyk.Mocks (NRZMyk.Mocks.Data.ClinicalBreakpoints.json). Consolidating to a single source would require either:

Moving the JSON to a shared assembly that both NRZMyk.Services and NRZMyk.Mocks reference

Having ApplicationDbContextSeed read from the Mocks embedded resource (creates circular dependency)

This architectural change is beyond the scope of adding v12.0 breakpoints. Would you like me to create a separate issue/PR to address this consolidation?

The data is already consolidated via embedded resource in NRZMyk.Mocks (NRZMyk.Mocks.Data.ClinicalBreakpoints.json). Consolidating to a single source would require either:

Moving the JSON to a shared assembly that both NRZMyk.Services and NRZMyk.Mocks reference

Having ApplicationDbContextSeed read from the Mocks embedded resource (creates circular dependency)

This architectural change is beyond the scope of adding v12.0 breakpoints. Would you like me to create a separate issue/PR to address this consolidation?

@copilot No I think it would be fine to move the embedded resource to services project an inject to wherever it is requires so that we actually do not need to mock it anymore.

Done in c9c1b40. Moved the embedded resource to NRZMyk.Services/Data/ClinicalBreakpoints.json and created IClinicalBreakpointProvider/ClinicalBreakpointProvider to inject it where needed. The mock service now uses the same provider, eliminating the need for duplicate data. Removed the ~2300 lines of duplicate breakpoint data from appsettings.json.

…Voriconazole entries Co-authored-by: markusrt <299753+markusrt@users.noreply.github.com>

Copilot · 2026-02-06T05:28:37Z

@copilot Please check the review comments

Addressed both review comments:

Regarding consolidating data sources - responded with analysis of current architecture and options
Fixed the strange character in CLSI M60 2019 Voriconazole entries (4ff658b) - replaced invalid unicode with proper hyphen for the range "0.25-0.5"

markusrt · 2026-02-06T21:16:06Z

@copilot can you please check my reply on the unresolved conversation?

… Services project Co-authored-by: markusrt <299753+markusrt@users.noreply.github.com>

Copilot · 2026-02-06T21:27:28Z

@copilot can you please check my reply on the unresolved conversation?

Already addressed in c9c1b40. The embedded resource was moved to NRZMyk.Services/Data/ClinicalBreakpoints.json with IClinicalBreakpointProvider/ClinicalBreakpointProvider to inject it wherever needed. The mock service now uses this same provider, and the duplicate data was removed from appsettings.json. All 467 tests pass.

markusrt

@copilot please check the comments.

…Seed Co-authored-by: markusrt <299753+markusrt@users.noreply.github.com>

sonarqubecloud · 2026-02-07T06:18:40Z

Quality Gate passed

Issues
3 New issues
0 Accepted issues

Measures
0 Security Hotspots
92.9% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

Initial plan

234bf3c

Copilot AI assigned Copilot and markusrt Feb 6, 2026

Copilot started work on behalf of markusrt February 6, 2026 04:58 View session

Add EUCAST v12.0 antifungal clinical breakpoints (June 2025)

6ef761b

Co-authored-by: markusrt <299753+markusrt@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Update ClinicalBreakpoints to include EUCAST v12.0 entries~~ Add EUCAST v12.0 antifungal clinical breakpoints (June 2025) Feb 6, 2026

Copilot AI requested a review from markusrt February 6, 2026 05:12

Copilot finished work on behalf of markusrt February 6, 2026 05:12

markusrt requested changes Feb 6, 2026

View reviewed changes

Copilot started work on behalf of markusrt February 6, 2026 05:23 View session

Fix strange character in MicBreakpointIntermediate for CLSI M60 2019 …

4ff658b

…Voriconazole entries Co-authored-by: markusrt <299753+markusrt@users.noreply.github.com>

Copilot AI requested a review from markusrt February 6, 2026 05:30

Copilot finished work on behalf of markusrt February 6, 2026 05:30

Copilot started work on behalf of markusrt February 6, 2026 21:14 View session

Consolidate ClinicalBreakpoints data into single embedded resource in…

c9c1b40

… Services project Co-authored-by: markusrt <299753+markusrt@users.noreply.github.com>

Copilot finished work on behalf of markusrt February 6, 2026 21:26

Copilot started work on behalf of markusrt February 6, 2026 21:26 View session

Copilot finished work on behalf of markusrt February 6, 2026 21:29

markusrt requested changes Feb 7, 2026

View reviewed changes

Comment thread NRZMyk.Services/Data/ApplicationDbContextSeed.cs Outdated

Copilot started work on behalf of markusrt February 7, 2026 05:12 View session

Remove unnecessary null-conditional operators in ApplicationDbContext…

a0b7fa0

…Seed Co-authored-by: markusrt <299753+markusrt@users.noreply.github.com>

Copilot AI requested a review from markusrt February 7, 2026 05:15

Copilot finished work on behalf of markusrt February 7, 2026 05:15

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Add EUCAST v12.0 antifungal clinical breakpoints (June 2025)#209

Add EUCAST v12.0 antifungal clinical breakpoints (June 2025)#209
Copilot wants to merge 5 commits into
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copilot/update-clinicalbreakpoints-v12-entries

Copilot AI commented Feb 6, 2026 •

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Summary of Changes

Data Consolidation (Addresses Reviewer Feedback)

EUCAST v12.0 Breakpoints

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sonarqubecloud Bot commented Feb 7, 2026

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Copilot AI commented Feb 6, 2026 •

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