Update data/rag/knowledge_base/Cryptococcus/gattii.json

data/rag/knowledge_base/Cryptococcus/gattii.json

@@ -1,52 +1,125 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Cryptococcus",
   "species": "gattii",
-  "full_name": "Cryptococcus gattii",
-  "clinical_significance": "A highly virulent Cryptococcus species complex that infects immunocompetent hosts. Often causes large pulmonary or CNS cryptococcomas, and outbreaks have occurred in Canada, the U.S. Pacific Northwest, and Australia.",
-  "phenotype_profile": {
-    "morphology": "Encapsulated yeast; often features a larger and more robust capsule than C. neoformans.",
-    "culture": "Mucoid colonies; blue coloration on CGB (L-canavanine–glycine–bromothymol blue) medium due to ability to utilize glycine.",
-    "biochemical": [
-      "Urease positive",
-      "Phenol oxidase positive",
-      "Grows at 37 °C",
-      "Positive on CGB agar (turns medium blue)",
-      "No pseudohyphae",
-      "Strong melanin production"
-    ]
+
+  "overview": {
+    "short": "Cryptococcus gattii is an encapsulated yeast capable of causing pulmonary and CNS disease, including in immunocompetent hosts.",
+    "clinical_context": "Associated with pulmonary masses (cryptococcomas) and meningoencephalitis; classically linked to environmental exposure."
   },
-  "differentiation": {
-    "from close species": [
-      "Blue color change on CGB agar is highly specific for C. gattii.",
-      "More frequent disease in immunocompetent hosts vs. C. neoformans.",
-      "Associated with tree habitats (eucalyptus, rainforest species)."
+
+  "expected_fields": {
+    "Gram Stain": "Variable",
+    "Shape": "Yeast",
+    "Motility": "Negative",
+    "Capsule": "Positive",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Sabouraud Dextrose Agar",
+      "Blood Agar"
     ],
-    "from other genera": [
-      "Melanin-producing, encapsulated, but CGB-positive profile is unique."
-    ]
+    "Colony Morphology": [
+      "Mucoid",
+      "Cream",
+      "Smooth"
+    ],
+    "Oxygen Requirement": "Aerobe",
+    "Growth Temperature": "25//37",
+    "Catalase": "Positive",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Positive",
+    "Citrate": "Negative",
+    "Methyl Red": "Unknown",
+    "VP": "Unknown",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Negative",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Negative",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Negative",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Negative",
+    "Maltose Fermentation": "Negative",
+    "Mannitol Fermentation": "Negative",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Negative",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Negative",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Negative",
+    "Inositol Fermentation": "Positive",
+    "Gas Production": "Negative",
+    "TSI Pattern": "Unknown",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "None"
   },
-  "virulence_factors": [
-    "Large polysaccharide capsule",
-    "Melanin production",
-    "Ability to form large cryptococcomas",
-    "Survival and replication in macrophages",
-    "Enhanced resistance to oxidative stress"
+
+  "species_markers": [
+    {
+      "field": "Capsule",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Encapsulation is expected and clinically important."
+    },
+    {
+      "field": "Urease",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Supports Cryptococcus identification."
+    },
+    {
+      "field": "Growth Temperature",
+      "value": "25//37",
+      "importance": "medium",
+      "notes": "Growth at 37°C supports pathogenic Cryptococcus species."
+    }
   ],
-  "confirmation_methods": [
-    "CGB agar",
-    "MALDI-TOF MS",
-    "MLST / molecular typing",
-    "ITS sequencing"
+
+  "common_confusions": [
+    {
+      "species": "Cryptococcus neoformans",
+      "reason": "Very similar phenotype; routine biochemical fields often overlap."
+    },
+    {
+      "genus": "Rhodotorula",
+      "reason": "Some species are urease-positive yeasts; pigmentation differences help but may be subtle."
+    }
   ],
-  "treatment_notes": [
-    "Requires longer antifungal therapy than C. neoformans",
-    "Amphotericin B + flucytosine induction",
-    "Prolonged fluconazole consolidation phase",
-    "Surgical resection sometimes required for cryptococcomas"
+
+  "when_to_question_identification": [
+    "Capsule not demonstrated argues against Cryptococcus gattii.",
+    "Urease negativity suggests a different yeast genus.",
+    "A strong carbohydrate fermentation profile is inconsistent with Cryptococcus."
   ],
-  "notes": "Major outbreak pathogen with environmental reservoirs in western Canada and the Pacific Northwest.",
-  "references": [
-    "C. gattii outbreak epidemiology",
-    "Treatment outcomes literature"
+
+  "recommended_next_tests": [
+    {
+      "test": "India ink preparation",
+      "reason": "Demonstrates characteristic capsule.",
+      "api_kit": "Not applicable"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Practical route to species-level ID vs C. neoformans complex.",
+      "api_kit": "Not applicable"
+    },
+    {
+      "test": "Molecular identification",
+      "reason": "Useful for complex-level discrimination where phenotype overlaps.",
+      "api_kit": "Not applicable"
+    }
   ]
-}
+}