Update data/rag/knowledge_base/Clostridium/botulinum.json

data/rag/knowledge_base/Clostridium/botulinum.json

@@ -1,51 +1,120 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Clostridium",
   "species": "botulinum",
-  "full_name": "Clostridium botulinum",
-  "clinical_significance": "Producer of botulinum neurotoxins (BoNT types A–G), the most potent toxins known. Causes foodborne, infant, and wound botulism, resulting in flaccid paralysis. Spores ubiquitously found in soil, sediments, and foods.",
-  "phenotype_profile": {
-    "morphology": "Large Gram-positive rods; subterminal spores giving a 'tennis-racket' appearance. May appear Gram-variable.",
-    "culture": "Lipase-positive iridescent sheen on egg-yolk agar (for proteolytic strains). Slow anaerobic growth.",
-    "biochemical": [
-      "Strict anaerobe",
-      "Catalase negative",
-      "Lipase positive (type A and B strains)",
-      "Proteolytic strains digest gelatin and casein",
-      "Non-proteolytic strains grow at low temperatures",
-      "Indole negative",
-      "No growth in 6.5% NaCl"
-    ]
+
+  "overview": {
+    "short": "Clostridium botulinum is a Gram-positive, anaerobic, spore-forming rod that produces botulinum neurotoxin.",
+    "clinical_context": "Responsible for botulism, a severe neuroparalytic illness caused by toxin ingestion or production in vivo."
   },
-  "differentiation": {
-    "from close species": [
-      "Lipase-positive sheen separates proteolytic botulinum strains from many Clostridia.",
-      "Toxin production is the essential identifying characteristic.",
-      "Non-proteolytic strains can grow at refrigeration temperatures."
+
+  "expected_fields": {
+    "Gram Stain": "Positive",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Negative",
+    "Spore Formation": "Positive",
+    "Haemolysis": "Variable",
+    "Haemolysis Type": "Variable",
+    "Media Grown On": [
+      "Blood Agar",
+      "Egg Yolk Agar"
     ],
-    "from other genera": [
-      "BoNT-mediated flaccid paralysis is unique.",
-      "ANAEROBIC + spore-forming + toxin = Clostridium botulinum or related groups."
-    ]
+    "Colony Morphology": [
+      "Irregular",
+      "Spreading"
+    ],
+    "Oxygen Requirement": "Anaerobic",
+    "Growth Temperature": "10//48",
+    "Catalase": "Negative",
+    "Oxidase": "Negative",
+    "Indole": "Variable",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Variable",
+    "VP": "Negative",
+    "H2S": "Variable",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Positive",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Variable",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Positive",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Variable",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Variable",
+    "Maltose Fermentation": "Variable",
+    "Mannitol Fermentation": "Negative",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Variable",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Variable",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Variable",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Variable",
+    "TSI Pattern": "Unknown",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Peritrichous"
   },
-  "virulence_factors": [
-    "Botulinum neurotoxins (A–G)",
-    "Spore formation",
-    "Proteolytic enzymes (strain dependent)"
+
+  "species_markers": [
+    {
+      "field": "Lipase Test",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Supports identification of proteolytic C. botulinum groups."
+    },
+    {
+      "field": "Motility",
+      "value": "Positive",
+      "importance": "medium",
+      "notes": "Helps differentiate from non-motile clostridia such as C. perfringens."
+    },
+    {
+      "field": "Glucose Fermentation",
+      "value": "Variable",
+      "importance": "medium",
+      "notes": "Reflects heterogeneity across toxin groups."
+    }
   ],
-  "confirmation_methods": [
-    "Mouse bioassay (gold standard)",
-    "PCR for BoNT genes",
-    "Toxin neutralization assays",
-    "MALDI-TOF (organism ID only)"
+
+  "common_confusions": [
+    {
+      "species": "Clostridium sporogenes",
+      "reason": "Genetically related with overlapping biochemical and enzymatic traits."
+    }
   ],
-  "treatment_notes": [
-    "Botulinum antitoxin (e.g., BIG-IV for infants)",
-    "Supportive care including ventilation",
-    "For wound botulism: penicillin or metronidazole"
+
+  "when_to_question_identification": [
+    "Lipase negativity argues against proteolytic C. botulinum.",
+    "Strong carbohydrate fermentation suggests another clostridial species.",
+    "Non-spore-forming phenotype is inconsistent."
   ],
-  "notes": "BoNT production does NOT require organism viability—foodborne intoxication is due to preformed toxin.",
-  "references": [
-    "CDC Botulism Guidelines",
-    "Botulinum neurotoxin structure-function research"
+
+  "recommended_next_tests": [
+    {
+      "test": "Botulinum toxin detection",
+      "reason": "Definitive identification and clinical relevance.",
+      "api_kit": "Not applicable"
+    },
+    {
+      "test": "Lipase activity on Egg Yolk Agar",
+      "reason": "Supports differentiation of proteolytic strains.",
+      "api_kit": "API 20A"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Species-level identification when databases are appropriate.",
+      "api_kit": "Not applicable"
+    }
   ]
-}
+}