Shipped analyzer clinical defaults

Bridge profiles define the instrument codes and runtime behavior; OpenELIS resolves those codes to its local clinical catalog. The core configuration in src/main/resources/configuration/ ships the analyzer result options, for example dictionaries/analyzer-result-options.csv. The analyzer harness adds its molecular tests and their result choices from projects/analyzer-harness/config-templates/, loaded through OpenELIS's normal configuration loader by the harness-catalog-init service. Those harness CSVs are test configuration, not part of the catalog every site receives.

Xpert rifampin-resistance outcomes

The harness Xpert RIF Resistance test uses the Analyzer GeneXpert RIF Results choices DETECTED, NOT DETECTED and Indeterminate. The GeneXpert profile reports the raw values DETECTED, NOT DETECTED and INDETERMINATE; the generic resolver handles the difference in capitalization.

These are molecular resistance-detection outcomes. They must not be translated by a global detected-to-resistant or not-detected-to-susceptible rule. The Cepheid instructions, 303-0942 Rev. B, Results describe presence, absence or an indeterminate call for resistance-associated mutations. CDC interpretation guidance also distinguishes these calls from growth-based susceptibility testing.

The detected and not-detected choices have their own dictionary identities. Previously stored Resistant/Susceptible choices and historical clinical results are not renamed or deleted, and existing local bindings are not silently rewritten. Site-uploaded catalog overrides remain site-owned.

AnalyzerCatalogIdentityIntegrationTest exercises the production catalog handlers and default resolver, including repeat loading with stable option IDs. The GeneXpert harness workflow sends native ASTM messages for each outcome and checks the saved value, patient, order, test and specimen.

COVID answer wording and specimen selection

The respiratory COVID test already has SARS-CoV-2 RNA DETECTED and SARS-COV-2 RNA NOT DETECTED choices, so adding a Positive/Negative pair would duplicate clinical answers. Instead, the profile contract supplies optional result_value_hints, keyed by exact reported values. Resolution uses an exact raw label first, then the hinted equivalent label if no exact match exists. Ambiguous matches stay unresolved, and the raw value is kept.

GeneXpert profile revision 7 (Bridge 3.2.4) supplies these hints together with a Respiratory Swab specimen hint. The specimen hint is needed because the catalog also contains COVID tests for other specimens.

The Cepheid instructions, 302-3562 Rev G, section 16 support the positive/negative detection meanings and distinguish INVALID, ERROR and NO RESULT. The profile does not equate ERROR with Invalid or invent an INDETERMINATE translation.

The test's primary result is that categorical overall call. Its only numeric components are the non-primary N2 and E cycle-threshold values that 055-seed-molecular-components.xml adds with the Ct unit, which stay blank when an instrument does not transmit per-target Ct.

What remains to be qualified is tracked in the analyzer roadmap.