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

data/rag/knowledge_base/Alcaligenes/faecalis.json

@@ -1,44 +1,106 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Alcaligenes",
   "species": "faecalis",
-  "full_name": "Alcaligenes faecalis",
-  "clinical_significance": "Alcaligenes faecalis is an environmental organism occasionally causing opportunistic infections including bacteremia, urinary tract infections, peritonitis, and wound infections. It is commonly associated with contamination of fluids and equipment in healthcare settings.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative rods; may appear slightly curved.",
-    "culture": "Non-lactose fermenting colonies on MacConkey agar, often with a fruity or sweet odor. Growth occurs on routine aerobic media.",
-    "biochemical": [
-      "Oxidase positive",
-      "Catalase positive",
-      "Asaccharolytic (non-fermenter)",
-      "ONPG negative",
-      "Does not grow in 6.5% NaCl",
-      "Motile",
-      "Nitrate reduction positive or variable",
-      "Indole negative"
-    ]
+
+  "overview": {
+    "short": "Alcaligenes faecalis is an aerobic, oxidase-positive, non-fermentative Gram-negative rod commonly isolated from environmental and clinical specimens.",
+    "clinical_context": "Occasionally associated with opportunistic infections, including bacteremia and respiratory infections."
   },
-  "differentiation": {
-    "from_close_species": [
-      "More common in clinical isolates than A. denitrificans.",
-      "Strongly asaccharolytic, unlike Achromobacter xylosoxidans.",
-      "Characteristic fruity odor may help differentiate."
+
+  "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": [
-      "Oxidase positivity distinguishes from Stenotrophomonas.",
-      "Strict asaccharolytic profile separates from Achromobacter.",
-      "No pigment differentiates from Delftia acidovorans."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey-White"
+    ],
+    "Oxygen Requirement": "Aerobe",
+    "Growth Temperature": "20//42",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Negative",
+    "Urease": "Variable",
+    "Citrate": "Negative",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Positive",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Negative",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Positive",
+    "Ornitihine Decarboxylase": "Positive",
+    "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",
-    "Asaccharolytic metabolism",
-    "Oxidase positivity",
-    "16S rRNA sequencing"
+
+  "species_markers": [
+    {
+      "field": "Ornithine Decarboxylase",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Useful discriminator within Alcaligenes species."
+    },
+    {
+      "field": "Gelatin Hydrolysis",
+      "value": "Positive",
+      "importance": "medium",
+      "notes": "Helps distinguish A. faecalis from A. denitrificans."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Alcaligenes denitrificans",
+      "reason": "Shared oxidase positivity and non-fermentative metabolism."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Nitrate reduction positivity suggests A. denitrificans.",
+    "Non-motility argues against A. faecalis."
   ],
-  "treatment_notes": "Often resistant to many β-lactams including ampicillin. Susceptibility testing required as resistance patterns vary.",
-  "notes": "A common environmental contaminant; clinical significance must be interpreted carefully.",
-  "references": [
-    "Manual of Clinical Microbiology",
-    "Clinical reports of Alcaligenes infections"
+
+  "recommended_next_tests": [
+    {
+      "test": "Nitrate reduction",
+      "reason": "Key test to differentiate from A. denitrificans."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable species-level identification."
+    }
   ]
-}
+}