Update data/rag/knowledge_base/Chromobacterium/aquaticum.json

data/rag/knowledge_base/Chromobacterium/aquaticum.json

@@ -1,45 +1,90 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Chromobacterium",
   "species": "aquaticum",
-  "full_name": "Chromobacterium aquaticum",
-  "clinical_significance": "Primarily an environmental freshwater organism with low documented pathogenicity. Rare clinical isolations include contaminated wounds and occasional bacteremia, typically in immunocompromised patients.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative motile rods.",
-    "culture": "Non-pigmented to weakly pigmented colonies; smooth and glistening. No violacein production.",
-    "biochemical": [
-      "Oxidase positive",
-      "Catalase positive",
-      "Indole negative",
-      "ONPG negative",
-      "Nitrate reduction positive",
-      "Motile",
-      "No growth in 6.5% NaCl"
-    ]
+
+  "overview": {
+    "short": "Chromobacterium aquaticum is a Gram-negative, motile rod primarily isolated from freshwater environments.",
+    "clinical_context": "Considered environmental with no established role in human disease."
   },
-  "differentiation": {
-    "from close species": [
-      "Non-pigmented and non-hemolytic (differs from haemolyticum and violaceum).",
-      "Less virulent; typically environmental contaminant.",
-      "Requires MALDI-TOF for accurate identification."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Unknown",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Nutrient Agar",
+      "Blood Agar"
     ],
-    "from other genera": [
-      "Oxidase-positive environmental rod → must be distinguished from Aeromonas, Shewanella, and Pseudomonas.",
-      "Lack of pigment excludes C. violaceum."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Convex"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "15//30",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Positive",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Positive",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Negative",
+    "Maltose Fermentation": "Positive",
+    "Mannitol Fermentation": "Negative",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Negative",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Negative",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Positive",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Negative",
+    "TSI Pattern": "A/A",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Peritrichous"
   },
-  "virulence_factors": [
-    "Environmental enzymes enabling survival (low human virulence)",
-    "Occasional biofilm formation"
-  ],
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "16S rRNA sequencing",
-    "Biochemical profile (non-pigmented, oxidase positive)"
+
+  "species_markers": [
+    {
+      "field": "Growth Temperature",
+      "value": "15//30",
+      "importance": "medium",
+      "notes": "Lower optimal growth temperature supports environmental origin."
+    },
+    {
+      "field": "Pigment",
+      "value": "None",
+      "importance": "medium",
+      "notes": "Lack of violacein helps separate from C. violaceum."
+    }
   ],
-  "treatment_notes": "Often susceptible to fluoroquinolones and TMP-SMX. Low-level clinical relevance requires susceptibility-guided therapy.",
-  "notes": "Most isolates represent colonization or contamination unless repeatedly recovered.",
-  "references": [
-    "Environmental Chromobacterium reports",
-    "Rare freshwater organism clinical case documentation"
+
+  "when_to_question_identification": [
+    "Recovery from a normally sterile clinical site.",
+    "Presence of violacein pigment.",
+    "Growth at elevated temperatures above 37°C."
   ]
-}
+}