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

data/rag/knowledge_base/Achromobacter/denitrificans.json

@@ -1,43 +1,99 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Achromobacter",
   "species": "denitrificans",
-  "full_name": "Achromobacter denitrificans",
-  "clinical_significance": "Occasionally associated with opportunistic infections such as bacteremia, pneumonia, and urinary tract infections, especially in immunocompromised patients. Historically misidentified as A. xylosoxidans in some systems.",
-  "phenotype_profile": {
-    "morphology": "Motile Gram-negative rods; non-fermenting.",
-    "culture": "Grows as smooth, grey, non-lactose-fermenting colonies on blood and MacConkey agar.",
-    "biochemical": [
-      "Oxidase positive",
-      "Catalase positive",
-      "Non-fermenter",
-      "ONPG negative",
-      "Does not grow in 6.5% NaCl",
-      "Nitrate reduction strongly positive (defining trait)",
-      "Usually does not oxidize xylose",
-      "Motile"
-    ]
+
+  "overview": {
+    "short": "Achromobacter denitrificans is a Gram-negative, aerobic, non-fermenting rod characterized by strong nitrate reduction and denitrification capability.",
+    "clinical_context": "Rarely associated with human infection and more commonly encountered in environmental samples."
   },
-  "differentiation": {
-    "from_close_species": [
-      "Strong nitrate reduction differentiates A. denitrificans from A. inosolitus and some xylosoxidans strains.",
-      "Lack of xylose oxidation separates it from A. xylosoxidans.",
-      "More robust oxidative metabolism compared to A. inosolitus."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Unknown",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar"
     ],
-    "from_other_genera": [
-      "Oxidase positivity and motility rule out Bordetella and some Alcaligenes species.",
-      "No pigment production differentiates it from Delftia.",
-      "Nitrate positivity helps differentiate from Ralstonia species."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey"
+    ],
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "20//37",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Variable",
+    "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": "Positive",
+    "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": "Polar"
   },
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "Nitrate reduction test",
-    "16S rRNA sequencing"
+
+  "species_markers": [
+    {
+      "field": "Nitrate Reduction",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Denitrification capability is characteristic of A. denitrificans."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Achromobacter xylosoxidans",
+      "reason": "Shared oxidase positivity and non-fermentative metabolism."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Absence of nitrate reduction argues against A. denitrificans.",
+    "Clinical isolation should prompt confirmation due to rarity."
   ],
-  "treatment_notes": "Often resistant to aminoglycosides and some beta-lactams. Susceptibility testing essential.",
-  "notes": "Historically confused with xylosoxidans complex; modern MALDI-TOF systems achieve accurate separation.",
-  "references": [
-    "Manual of Clinical Microbiology, 12th Edition.",
-    "Studies on differentiation of Achromobacter species in clinical labs."
+
+  "recommended_next_tests": [
+    {
+      "test": "Nitrate reduction and denitrification testing",
+      "reason": "Defining feature of this species."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Required for reliable species-level identification."
+    }
   ]
-}
+}