Update data/rag/knowledge_base/Aggregatibacter/aphrophilus.json

data/rag/knowledge_base/Aggregatibacter/aphrophilus.json

@@ -1,43 +1,102 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Aggregatibacter",
   "species": "aphrophilus",
-  "full_name": "Aggregatibacter aphrophilus",
-  "clinical_significance": "Previously known as Haemophilus aphrophilus. A significant cause of infective endocarditis as part of the HACEK group. Also associated with brain abscesses, sinus infections, and bacteremia.",
-  "phenotype_profile": {
-    "morphology": "Small Gram-negative coccobacilli.",
-    "culture": "Better growth on chocolate agar but can grow on blood agar without X or V factors. Fastidious and slow-growing.",
-    "biochemical": [
-      "Catalase variable",
-      "Oxidase positive or weakly positive",
-      "Ferments glucose",
-      "ONPG negative",
-      "Does not grow in 6.5% NaCl",
-      "Reduces nitrate",
-      "Indole negative"
-    ]
+
+  "overview": {
+    "short": "Aggregatibacter aphrophilus is a Gram-negative, fastidious coccobacillus commonly isolated from the oral cavity and associated with endocarditis.",
+    "clinical_context": "A member of the HACEK group, frequently implicated in culture-negative endocarditis."
   },
-  "differentiation": {
-    "from_close_species": [
-      "Oxidase positivity more common than in A. actinomycetemcomitans.",
-      "Not associated with star-shaped colonies.",
-      "More strongly linked to HACEK endocarditis than A. actinomycetemcomitans."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Short Rods",
+    "Motility": "Negative",
+    "Capsule": "Negative",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "Chocolate Agar"
     ],
-    "from_other_genera": [
-      "Does not require V factor, distinguishing it from Haemophilus species.",
-      "Coccobacillary morphology and fastidious growth differentiate from Enterobacterales.",
-      "Less rod-like and less oxidase-negative than A. segnis."
-    ]
+    "Colony Morphology": [
+      "Small",
+      "Smooth",
+      "Grey"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "35//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": "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": "Positive",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Variable",
+    "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"
   },
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "16S rRNA sequencing",
-    "Growth without X/V factors",
-    "Oxidase positivity"
+
+  "species_markers": [
+    {
+      "field": "Catalase",
+      "value": "Negative",
+      "importance": "high",
+      "notes": "Differentiates A. aphrophilus from A. actinomycetemcomitans."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Aggregatibacter actinomycetemcomitans",
+      "reason": "Shared habitat and similar growth characteristics."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Catalase positivity suggests A. actinomycetemcomitans.",
+    "Star-shaped colonies suggest A. actinomycetemcomitans.",
+    "Growth on MacConkey Agar argues against Aggregatibacter."
   ],
-  "treatment_notes": "Typically susceptible to third-generation cephalosporins, fluoroquinolones, and β-lactams.",
-  "notes": "A well-recognized cause of HACEK endocarditis.",
-  "references": [
-    "HACEK endocarditis literature",
-    "Manual of Clinical Microbiology"
+
+  "recommended_next_tests": [
+    {
+      "test": "Catalase test",
+      "reason": "Key discriminator within Aggregatibacter species."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Accurate identification of HACEK organisms."
+    }
   ]
-}
+}