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

data/rag/knowledge_base/Bartonella/quintana.json

@@ -1,45 +1,102 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Bartonella",
   "species": "quintana",
-  "full_name": "Bartonella quintana",
-  "clinical_significance": "Causes trench fever (relapsing fever with shin pain), chronic bacteremia, culture-negative endocarditis, and bacillary angiomatosis. Transmitted by the human body louse and strongly associated with homelessness and poor hygiene.",
-  "phenotype_profile": {
-    "morphology": "Small Gram-negative rods; intracellular in erythrocytes and endothelial cells.",
-    "culture": "Slow-growing on chocolate agar (2–4 weeks). Growth enhanced in CO₂.",
-    "biochemical": [
-      "Oxidase negative",
-      "Catalase negative",
-      "Non-motile",
-      "ONPG negative",
-      "Non-fermentative"
-    ]
+
+  "overview": {
+    "short": "Bartonella quintana is a fastidious Gram-negative bacillus historically associated with trench fever.",
+    "clinical_context": "Causes trench fever, chronic bacteremia, and culture-negative endocarditis, particularly in vulnerable populations."
   },
-  "differentiation": {
-    "from_close_species": [
-      "Associated with homelessness and lice exposure (key epidemiological clue).",
-      "More commonly causes chronic bacteremia and endocarditis than B. henselae.",
-      "Less associated with cat exposure than B. henselae."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Negative",
+    "Capsule": "Negative",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Chocolate Agar",
+      "Blood Agar"
     ],
-    "from_other_genera": [
-      "Intracellular persistence distinguishes from fastidious GNRs.",
-      "Louse transmission distinguishes from Brucella and Coxiella."
-    ]
+    "Colony Morphology": [
+      "Small",
+      "Grey",
+      "Rough"
+    ],
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "30//37",
+    "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": [
-    "Trw type IV secretion system",
-    "Endothelial adhesion factors",
-    "Immune evasion within erythrocytes"
+
+  "species_markers": [
+    {
+      "field": "Clinical Association",
+      "value": "Louse-borne infection",
+      "importance": "high",
+      "notes": "Strong association with body lice and trench fever."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Bartonella henselae",
+      "reason": "Similar growth characteristics and biochemical inactivity."
+    }
   ],
-  "confirmation_methods": [
-    "PCR from blood or tissue",
-    "Serology (paired titers)",
-    "Prolonged culture with CO₂",
-    "Warthin–Starry or Steiner stain"
+
+  "when_to_question_identification": [
+    "No history of homelessness or lice exposure.",
+    "Positive biochemical reactions detected.",
+    "Growth within 48 hours on standard media."
   ],
-  "treatment_notes": "Doxycycline ± gentamicin for endocarditis. Erythromycin or doxycycline for trench fever.",
-  "notes": "Common cause of culture-negative endocarditis in vulnerable populations.",
-  "references": [
-    "Trench fever reviews",
-    "Bartonella endocarditis case literature"
+
+  "recommended_next_tests": [
+    {
+      "test": "Serology",
+      "reason": "Commonly used for diagnosis of trench fever."
+    },
+    {
+      "test": "PCR",
+      "reason": "Detection from blood in chronic bacteremia."
+    }
   ]
-}
+}