Update data/rag/knowledge_base/Bacillus/cereus.json

data/rag/knowledge_base/Bacillus/cereus.json

@@ -1,48 +1,118 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Bacillus",
   "species": "cereus",
-  "full_name": "Bacillus cereus",
-  "clinical_significance": "A major cause of foodborne illness, including emetic and diarrheal syndromes. Also causes opportunistic infections such as bacteremia, endophthalmitis, wound infections, and pneumonia, particularly in immunocompromised individuals.",
-  "phenotype_profile": {
-    "morphology": "Large Gram-positive rods; central spores; motile; β-hemolytic.",
-    "culture": "Large, flat, spreading colonies on blood agar with β-hemolysis. Lecithinase positive on egg-yolk agar.",
-    "biochemical": [
-      "Motile",
-      "β-hemolytic",
-      "Catalase positive",
-      "ONPG negative",
-      "Nitrate reduction positive",
-      "Lecithinase positive",
-      "Grows in 6.5% NaCl variably"
-    ]
+
+  "overview": {
+    "short": "Bacillus cereus is a motile, beta-haemolytic, Gram-positive spore-forming rod associated with foodborne illness and opportunistic infections.",
+    "clinical_context": "Common cause of toxin-mediated gastroenteritis and occasional invasive disease."
   },
-  "differentiation": {
-    "from_close_species": [
-      "Motility and β-hemolysis distinguish B. cereus from B. anthracis.",
-      "Lecithinase positivity helps separate from B. thuringiensis (variable) and B. mycoides.",
-      "Parasporal crystals absent (unlike B. thuringiensis)."
+
+  "expected_fields": {
+    "Gram Stain": "Positive",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Negative",
+    "Spore Formation": "Positive",
+    "Haemolysis": "Positive",
+    "Haemolysis Type": "Beta",
+    "Media Grown On": [
+      "Blood Agar"
     ],
-    "from_other_genera": [
-      "Spore formation distinguishes from Listeria.",
-      "Aerobic growth differentiates from Clostridium."
-    ]
+    "Colony Morphology": [
+      "Large",
+      "Flat",
+      "Irregular"
+    ],
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "10//45",
+    "Catalase": "Positive",
+    "Oxidase": "Variable",
+    "Indole": "Negative",
+    "Urease": "Variable",
+    "Citrate": "Variable",
+    "Methyl Red": "Variable",
+    "VP": "Positive",
+    "H2S": "Negative",
+    "DNase": "Positive",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Positive",
+    "Esculin Hydrolysis": "Variable",
+    "Nitrate Reduction": "Variable",
+    "NaCl Tolerant (>=6%)": "Variable",
+    "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": "Variable",
+    "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": "Variable",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Peritrichous"
   },
-  "virulence_factors": [
-    "Cereulide (emetic toxin)",
-    "Enterotoxins (Hbl, Nhe, CytK)",
-    "Phospholipases",
-    "Hemolysins"
+
+  "species_markers": [
+    {
+      "field": "Haemolysis",
+      "value": "Beta",
+      "importance": "high",
+      "notes": "Strong beta-haemolysis distinguishes B. cereus from B. anthracis."
+    },
+    {
+      "field": "Motility",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Motility is absent in B. anthracis."
+    },
+    {
+      "field": "DNase",
+      "value": "Positive",
+      "importance": "medium",
+      "notes": "Supports identification within the B. cereus group."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Bacillus thuringiensis",
+      "reason": "Genetically very similar; requires specialized testing."
+    }
   ],
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "Lecithinase test",
-    "PCR for toxin genes",
-    "Motility and hemolysis patterns"
+
+  "when_to_question_identification": [
+    "Non-haemolytic isolate suggests B. anthracis.",
+    "Non-motile isolate argues against B. cereus.",
+    "Capsule presence suggests B. anthracis."
   ],
-  "treatment_notes": "Many isolates resistant to β-lactams (β-lactamases). Fluoroquinolones, carbapenems, and vancomycin usually effective.",
-  "notes": "Indistinguishable from B. thuringiensis and B. anthracis by 16S rRNA alone.",
-  "references": [
-    "Foodborne disease literature",
-    "Bacillus cereus enterotoxin research"
+
+  "recommended_next_tests": [
+    {
+      "test": "Motility testing",
+      "reason": "Key discriminator from B. anthracis."
+    },
+    {
+      "test": "API 50 CHB",
+      "reason": "Carbohydrate utilization profile supports Bacillus species differentiation.",
+      "api_kit": "API 50 CHB"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable identification within the Bacillus cereus group."
+    }
   ]
-}
+}