Update data/rag/knowledge_base/Bartonella/bacilliformis.json

data/rag/knowledge_base/Bartonella/bacilliformis.json

@@ -1,46 +1,108 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Bartonella",
   "species": "bacilliformis",
-  "full_name": "Bartonella bacilliformis",
-  "clinical_significance": "Causes Carrión disease, consisting of an acute hemolytic phase (Oroya fever) and a chronic vasoproliferative phase (verruga peruana). Endemic to the Andes and transmitted by sandflies (Lutzomyia spp.). High mortality in the acute phase if untreated.",
-  "phenotype_profile": {
-    "morphology": "Small curved Gram-negative rods; invade and deform erythrocytes.",
-    "culture": "More fastidious than other Bartonella; slow growth on blood-enriched media at 25–30°C; enhanced by CO₂.",
-    "biochemical": [
-      "Oxidase negative",
-      "Catalase negative",
-      "Motile by peritrichous flagella",
-      "ONPG negative",
-      "Does not grow in 6.5% NaCl",
-      "Non-fermentative"
-    ]
+
+  "overview": {
+    "short": "Bartonella bacilliformis is a fastidious Gram-negative bacillus responsible for Carrion’s disease.",
+    "clinical_context": "Causes Oroya fever and verruga peruana, endemic to regions of South America."
   },
-  "differentiation": {
-    "from_close_species": [
-      "Only Bartonella that produces severe hemolytic anemia.",
-      "Prefers cooler temperatures (25–30°C), unlike B. henselae or B. quintana.",
-      "Causes intracellular erythrocyte invasion with characteristic deformation."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Negative",
+    "Capsule": "Negative",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "Chocolate Agar"
     ],
-    "from_other_genera": [
-      "Intracellular erythrocyte invasion is distinct from Brucella or Coxiella.",
-      "Geographical restriction to Andes strongly aids identification."
-    ]
+    "Colony Morphology": [
+      "Small",
+      "Grey",
+      "Rough"
+    ],
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "25//30",
+    "Catalase": "Negative",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "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": "Negative",
+    "Gas Production": "Negative",
+    "TSI Pattern": "Unknown",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "None"
   },
-  "virulence_factors": [
-    "Deformation hemolysin",
-    "Erythrocyte invasion factors",
-    "VirB T4SS–like secretion system"
+
+  "species_markers": [
+    {
+      "field": "Growth Temperature",
+      "value": "25–30°C",
+      "importance": "high",
+      "notes": "Lower optimal temperature than other Bartonella species."
+    },
+    {
+      "field": "Geographic Association",
+      "value": "South America",
+      "importance": "high",
+      "notes": "Endemic to Andean regions."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Brucella",
+      "reason": "Small Gram-negative rods with limited biochemical reactivity."
+    }
   ],
-  "confirmation_methods": [
-    "PCR from blood (best method)",
-    "Wright or Giemsa stain showing intraerythrocytic bacteria",
-    "Culture at 25–30°C with prolonged incubation",
-    "Serology in chronic phase"
+
+  "when_to_question_identification": [
+    "No travel or exposure to endemic regions.",
+    "Growth at 37°C only.",
+    "Positive biochemical reactions detected."
   ],
-  "treatment_notes": "Fluoroquinolones, chloramphenicol, or β-lactams. Acute Oroya fever phase requires urgent therapy.",
-  "notes": "Highly region-specific; rarely isolated outside Andean countries.",
-  "references": [
-    "Carrión disease clinical guidelines",
-    "Vector-borne Bartonella research"
+
+  "recommended_next_tests": [
+    {
+      "test": "PCR",
+      "reason": "Most reliable method for species-level identification."
+    },
+    {
+      "test": "Serology",
+      "reason": "Supportive in endemic regions."
+    }
   ]
-}
+}