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

data/rag/knowledge_base/Chromobacterium/genus.json

@@ -1,79 +1,127 @@
 {
+  "schema_version": "1.0",
+  "level": "genus",
   "genus": "Chromobacterium",
-  "taxonomy": {
-    "family": "Neisseriaceae",
-    "order": "Neisseriales",
-    "class": "Gammaproteobacteria",
-    "phylum": "Proteobacteria"
+
+  "overview": {
+    "short": "Chromobacterium species are Gram-negative, facultatively anaerobic rods commonly found in soil and aquatic environments, notable for pigment production.",
+    "clinical_context": "Rare but potentially severe opportunistic infections including septicemia, particularly in tropical regions."
   },
-  "overview": "Chromobacterium is a genus of motile, aerobic or facultatively anaerobic Gram-negative rods commonly found in soil and freshwater environments of tropical and subtropical regions. Some species produce a striking violet pigment (violacein). While many species are environmental, Chromobacterium violaceum and Chromobacterium haemolyticum can cause severe human infections, including bacteremia, skin and soft tissue infection, sepsis, and visceral abscesses.",
-  "key_traits": [
-    "Gram-negative rods",
-    "Motile (polar flagella)",
-    "Oxidase positive",
-    "Catalase positive",
-    "Nitrate reduction positive",
-    "Pigment production species-dependent (violacein)",
-    "Grow on routine media",
-    "Do not require NaCl and do not tolerate high salt",
-    "ONPG negative",
-    "Some species β-hemolytic"
-  ],
-  "ecology": "Found in tropical/subtropical water, soil, stagnant ponds, and occasionally drinking-water systems. Infections usually follow exposure of wounds to contaminated water or soil.",
-  "pathogenicity": "C. violaceum and C. haemolyticum cause severe systemic infections with high mortality. C. aquaticum is rarely pathogenic. Infections may include necrotizing skin infections, abscesses (especially liver), bacteremia, and septic shock. Rapid progression is common due to virulence enzymes and innate resistance to multiple antibiotics.",
-  "genus_level_biochemistry": {
-    "general_tendencies": [
-      "Oxidase positive (key Enterobacterales discriminator).",
-      "Motile Gram-negative rods.",
-      "Pigmentation (violacein) in some species such as C. violaceum.",
-      "Hemolysis variable depending on species.",
-      "Nitrate reduction positive.",
-      "Do not grow in 6.5% NaCl."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Unknown",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Variable",
+    "Haemolysis Type": "Unknown",
+    "Media Grown On": [
+      "Blood Agar",
+      "Nutrient Agar"
     ],
-    "non_definitive_tests": [
-      "Pigmentation alone cannot definitively identify species.",
-      "Some non-violacein-producing isolates may be misidentified as Aeromonas or Pseudomonas."
-    ]
-  },
-  "genus_differentiation": {
-    "from_close_genera": [
-      "Aeromonas are also oxidase positive but show different carbohydrate profiles and indole positivity in some species.",
-      "Pseudomonas are typically non-fermenters but often pigment differently and have different antibiotic profiles.",
-      "Burkholderia pseudomallei has wrinkled colonies and different epidemiology.",
-      "Shewanella produce H2S and tolerate salt; Chromobacterium does not."
+    "Colony Morphology": [
+      "Smooth",
+      "Purple",
+      "Convex"
     ],
-    "key_rag_filters": [
-      "Freshwater/soil exposure + rapidly progressive sepsis → Chromobacterium or Aeromonas; pigment suggests Chromobacterium.",
-      "Purple/violet colonies → strong indicator of C. violaceum.",
-      "β-hemolytic oxidase-positive rod → consider C. haemolyticum.",
-      "Non-pigmented Chromobacterium isolates should trigger caution due to high virulence."
-    ]
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "20//37",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Variable",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Variable",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Variable",
+    "Lysine Decarboxylase": "Positive",
+    "Ornithine Decarboxylase": "Variable",
+    "Ornitihine Decarboxylase": "Variable",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Variable",
+    "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": "Purple",
+    "Motility Type": "Peritrichous"
   },
-  "diagnostics": {
-    "typical_lab_findings": [
-      "Smooth colonies; may be violet (violacein producers)",
-      "Oxidase positive",
-      "Motile rods",
-      "Growth on blood and MacConkey agar",
-      "β-hemolysis in some species"
-    ],
-    "important_tests": [
-      "Oxidase test",
-      "Pigment evaluation (violacein)",
-      "Nitrate reduction",
-      "Hemolysis pattern",
-      "MALDI-TOF MS"
-    ],
-    "confirmation_methods": [
-      "MALDI-TOF MS",
-      "16S rRNA or multilocus sequencing",
-      "Pigment profile (supportive only)"
-    ]
+
+  "field_notes": {
+    "Pigment": "Violacein pigment is a hallmark feature but may be absent in some species.",
+    "Oxidase": "Oxidase positivity supports differentiation from Enterobacterales."
   },
-  "notes": "Incorrectly assumed to be benign environmental bacteria; however, infections—especially with C. violaceum or C. haemolyticum—can be rapidly fatal.",
-  "references": [
-    "Manual of Clinical Microbiology",
-    "Chromobacterium case reports",
-    "Freshwater pathogen epidemiology"
+
+  "key_differentiators": [
+    {
+      "field": "Pigment",
+      "expected": "Purple",
+      "distinguishes_from": ["Aeromonas", "Vibrio"],
+      "notes": "Violacein production is strongly suggestive of Chromobacterium."
+    },
+    {
+      "field": "Oxidase",
+      "expected": "Positive",
+      "distinguishes_from": ["Enterobacter", "Escherichia"],
+      "notes": "Oxidase positivity helps exclude Enterobacterales."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Aeromonas",
+      "reason": "Shared aquatic habitat and oxidase positivity."
+    },
+    {
+      "genus": "Vibrio",
+      "reason": "Motile, oxidase-positive Gram-negative rods."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Absence of pigment in a suspected Chromobacterium isolate.",
+    "Oxidase-negative result obtained.",
+    "Growth only under strict anaerobic conditions."
+  ],
+
+  "recommended_next_tests": [
+    {
+      "test": "Oxidase test",
+      "reason": "Confirms oxidase-positive non-Enterobacterales.",
+      "api_kit": "API 20 NE"
+    },
+    {
+      "test": "Pigment assessment",
+      "reason": "Violacein supports Chromobacterium identification."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Definitive confirmation for rare but clinically significant isolates."
+    }
+  ],
+
+  "supported_species": [
+    "violaceum",
+    "haemolyticum",
+    "aquaticum"
   ]
-}
+}