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

data/rag/knowledge_base/Cryptococcus/genus.json

@@ -1,75 +1,136 @@
 {
+  "schema_version": "1.0",
+  "level": "genus",
   "genus": "Cryptococcus",
-  "taxonomy": {
-    "family": "Cryptococcaceae",
-    "order": "Tremellales",
-    "class": "Tremellomycetes",
-    "phylum": "Basidiomycota"
+
+  "overview": {
+    "short": "Cryptococcus species are encapsulated, yeast-form fungi primarily affecting immunocompromised hosts.",
+    "clinical_context": "Most commonly associated with pulmonary infections and meningoencephalitis, especially in HIV/AIDS and other immunosuppressed patients."
   },
-  "overview": "Cryptococcus is a genus of encapsulated, budding yeasts with worldwide distribution. Several species are human pathogens, most notably Cryptococcus neoformans and Cryptococcus gattii. The polysaccharide capsule, melanin production, and ability to survive in macrophages are major virulence determinants. Infections range from pulmonary colonization to life-threatening meningitis.",
-  "key_traits": [
-    "Encapsulated budding yeasts",
-    "Phenol oxidase positive (melanin production on birdseed agar)",
-    "Urease positive (important discriminator from Candida)",
-    "Growth at 37 °C (species dependent)",
-    "Non-fermentative yeast",
-    "India ink shows thick capsule",
-    "Can survive intracellularly in macrophages",
-    "No pseudohyphae (differentiates from Candida)"
-  ],
-  "ecology": "Found in soil, decaying wood, tree hollows, and avian droppings (especially pigeon droppings for C. neoformans). C. gattii is associated with eucalyptus and tropical/subtropical trees but has expanded into temperate regions.",
-  "pathogenicity": "Major causes of cryptococcosis. C. neoformans causes meningitis predominantly in immunocompromised individuals, especially HIV/AIDS patients. C. gattii causes infections in immunocompetent hosts and can form large cryptococcomas. Non-neoformans species, such as C. laurentii, rarely cause disease but may cause fungemia or peritonitis in immunosuppressed patients.",
-  "genus_level_biochemistry": {
-    "general_tendencies": [
-      "Urease positive.",
-      "Phenol oxidase positive (brown/black colonies on caffeic acid agar).",
-      "Spherical budding yeasts with prominent capsule.",
-      "Do not form pseudohyphae.",
-      "Different species have different thermotolerance."
+
+  "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"
     ],
-    "non_definitive_tests": [
-      "Carbohydrate assimilation patterns vary and often require molecular confirmation.",
-      "India ink sensitivity is high but not perfect."
-    ]
-  },
-  "genus_differentiation": {
-    "from_close_genera": [
-      "Candida produces pseudohyphae/hyphae; Cryptococcus does not.",
-      "Rhodotorula produce pink/red pigment; Cryptococcus is non-pigmented on routine media.",
-      "Trichosporon produce arthroconidia; Cryptococcus does not.",
-      "Histoplasma and Blastomyces form molds at 25 °C; Cryptococcus does not dimorph."
+    "Colony Morphology": [
+      "Mucoid",
+      "Cream",
+      "Smooth"
     ],
-    "key_rag_filters": [
-      "Encapsulated urease-positive yeast → strongly suggests Cryptococcus.",
-      "Melanin production on birdseed agar → Cryptococcus-specific.",
-      "HIV/AIDS patient + meningitis → C. neoformans overwhelmingly likely.",
-      "Immunocompetent + brain mass → C. gattii top differential."
-    ]
+    "Oxygen Requirement": "Aerobe",
+    "Growth Temperature": "20//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"
   },
-  "diagnostics": {
-    "typical_lab_findings": [
-      "Capsulated budding yeasts on India ink",
-      "Positive cryptococcal antigen (CrAg)",
-      "Brown/black colonies on birdseed agar (melanin)",
-      "Urease positive"
-    ],
-    "important_tests": [
-      "CrAg latex or lateral flow assay",
-      "India ink preparation",
-      "MALDI-TOF MS",
-      "Culture on Sabouraud agar",
-      "PCR for species complexes"
-    ],
-    "confirmation_methods": [
-      "Cryptococcal antigen test",
-      "MALDI-TOF MS",
-      "ITS or multilocus sequencing for species"
-    ]
+
+  "field_notes": {
+    "Capsule": "Prominent polysaccharide capsule is a defining feature and key virulence factor.",
+    "Urease": "Urease positivity is consistent across clinically relevant Cryptococcus species.",
+    "Inositol Fermentation": "Positive reaction is characteristic and aids differentiation from other yeasts."
   },
-  "notes": "Cryptococcus species differ dramatically in virulence; species-level identification has clinical importance.",
-  "references": [
-    "Cryptococcus global surveillance literature",
-    "Manual of Clinical Microbiology",
-    "WHO cryptococcal meningitis guidelines"
+
+  "key_differentiators": [
+    {
+      "field": "Capsule",
+      "expected": "Positive",
+      "distinguishes_from": ["Candida"],
+      "notes": "Encapsulation separates Cryptococcus from most Candida species."
+    },
+    {
+      "field": "Urease",
+      "expected": "Positive",
+      "distinguishes_from": ["Candida"],
+      "notes": "Urease activity is a key screening test for Cryptococcus."
+    },
+    {
+      "field": "Inositol Fermentation",
+      "expected": "Positive",
+      "distinguishes_from": ["Candida"],
+      "notes": "Inositol utilization supports Cryptococcus identification."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Candida",
+      "reason": "Both are yeast-form fungi, but Candida lacks a capsule and is urease negative."
+    },
+    {
+      "genus": "Rhodotorula",
+      "reason": "Some species share urease positivity but differ in pigmentation and capsule presence."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Absence of capsule argues against Cryptococcus.",
+    "Urease negativity suggests alternative yeast genera.",
+    "Strong carbohydrate fermentation profile is inconsistent with Cryptococcus."
+  ],
+
+  "recommended_next_tests": [
+    {
+      "test": "India ink preparation",
+      "reason": "Demonstrates the characteristic polysaccharide capsule.",
+      "api_kit": "Not applicable"
+    },
+    {
+      "test": "Urease test",
+      "reason": "Rapid screening test for Cryptococcus.",
+      "api_kit": "Christensen Urea Agar"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Accurate species-level identification.",
+      "api_kit": "Not applicable"
+    }
+  ],
+
+  "supported_species": [
+    "neoformans",
+    "gattii",
+    "laurentii"
   ]
-}
+}