Update data/rag/knowledge_base/Capnocytophaga/sputigena.json

data/rag/knowledge_base/Capnocytophaga/sputigena.json

@@ -1,45 +1,98 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Capnocytophaga",
   "species": "sputigena",
-  "full_name": "Capnocytophaga sputigena",
-  "clinical_significance": "A human oral species associated with periodontal disease, dental plaque, and opportunistic infections. More frequently implicated in bacteremia in neutropenic patients compared with C. ochracea.",
-  "phenotype_profile": {
-    "morphology": "Fusiform Gram-negative rods; strong gliding motility.",
-    "culture": "Slow-growing spreading colonies; may produce weak β-hemolysis; requires CO₂.",
-    "biochemical": [
-      "Oxidase negative",
-      "Catalase weak or negative",
-      "Indole negative",
-      "ONPG negative",
-      "Non-fermentative",
-      "No growth in 6.5% NaCl"
-    ]
+
+  "overview": {
+    "short": "Capnocytophaga sputigena is a Gram-negative, capnophilic rod found in the human oral cavity.",
+    "clinical_context": "Primarily associated with periodontal disease and oral infections, rarely causing systemic disease."
   },
-  "differentiation": {
-    "from close species": [
-      "More hemolytic than C. ochracea.",
-      "More commonly associated with neutropenic bacteremia.",
-      "Minor biochemical differences; identification requires MALDI-TOF."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Negative",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "Chocolate Agar"
     ],
-    "from other genera": [
-      "Fusiform shape + gliding motility highly characteristic.",
-      "Failure to grow anaerobically helps exclude Fusobacterium."
-    ]
+    "Colony Morphology": [
+      "Spreading",
+      "Thin",
+      "Grey"
+    ],
+    "Oxygen Requirement": "Capnophilic",
+    "Growth Temperature": "30//37",
+    "Catalase": "Negative",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "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": "Positive",
+    "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": "Negative",
+    "TSI Pattern": "Unknown",
+    "Colony Pattern": "Spreading",
+    "Pigment": "None",
+    "Motility Type": "Gliding"
   },
-  "virulence_factors": [
-    "Sialidase production",
-    "Adhesion to oral surfaces",
-    "Gliding motility aiding tissue invasion"
+
+  "species_markers": [
+    {
+      "field": "Catalase",
+      "value": "Negative",
+      "importance": "medium",
+      "notes": "Consistent with human oral Capnocytophaga species."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Capnocytophaga ochracea",
+      "reason": "Very similar biochemical and ecological profiles."
+    }
   ],
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "16S sequencing",
-    "CO₂-dependent growth pattern"
+
+  "when_to_question_identification": [
+    "Catalase positivity.",
+    "Animal exposure history.",
+    "Indole positivity."
   ],
-  "treatment_notes": "Generally susceptible to β-lactam/β-lactamase inhibitors, carbapenems, tetracyclines. Variable susceptibility to clindamycin and macrolides.",
-  "notes": "Important in immunocompromised hosts, especially those with mucositis.",
-  "references": [
-    "Capnocytophaga bacteremia studies",
-    "Oral anaerobe clinical microbiology reports"
+
+  "recommended_next_tests": [
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable species differentiation."
+    }
   ]
-}
+}