Update data/rag/knowledge_base/Alcaligenes/denitrificans.json

data/rag/knowledge_base/Alcaligenes/denitrificans.json

@@ -1,41 +1,100 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Alcaligenes",
   "species": "denitrificans",
-  "full_name": "Alcaligenes denitrificans",
-  "clinical_significance": "Primarily an environmental species associated with soil and aquatic ecosystems. Human infection is rare but can occur in immunocompromised individuals, typically presenting as bacteremia or device-associated infections.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative rods, motile.",
-    "culture": "Non-lactose fermenting colonies on MacConkey. No pigment production.",
-    "biochemical": [
-      "Oxidase positive",
-      "Catalase positive",
-      "Asaccharolytic",
-      "ONPG negative",
-      "Does not grow in 6.5% NaCl",
-      "Strong nitrate reduction (defining trait)",
-      "Motile",
-      "Indole negative"
-    ]
+
+  "overview": {
+    "short": "Alcaligenes denitrificans is an aerobic, oxidase-positive, non-fermentative Gram-negative rod capable of nitrate reduction.",
+    "clinical_context": "Rarely isolated from clinical specimens but may be encountered in environmental or hospital settings."
   },
-  "differentiation": {
-    "from_close_species": [
-      "Strong nitrate reduction distinguishes A. denitrificans from A. faecalis.",
-      "More environmental and less commonly pathogenic.",
-      "Still strictly asaccharolytic unlike Achromobacter spp."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Negative",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "Nutrient Agar"
     ],
-    "from_other_genera": [
-      "Pigment absence separates from Delftia.",
-      "Weak biochemical reactivity differentiates from Comamonas."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey-White"
+    ],
+    "Oxygen Requirement": "Aerobe",
+    "Growth Temperature": "20//42",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "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": "Positive",
+    "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": "K/K",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Peritrichous"
   },
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "Strong nitrate reduction",
-    "16S rRNA sequencing"
+
+  "species_markers": [
+    {
+      "field": "Nitrate Reduction",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Primary distinguishing feature of A. denitrificans."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Alcaligenes faecalis",
+      "reason": "Shared oxidase positivity and non-fermentative profile."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Negative nitrate reduction suggests A. faecalis.",
+    "Glucose fermentation suggests another genus."
   ],
-  "treatment_notes": "Limited data; susceptibility should be guided by testing.",
-  "notes": "Environmental organism rarely implicated in disease.",
-  "references": [
-    "Manual of Clinical Microbiology"
+
+  "recommended_next_tests": [
+    {
+      "test": "Nitrate reduction",
+      "reason": "Defining test for this species."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Accurate species-level confirmation."
+    }
   ]
-}
+}