Update data/rag/knowledge_base/Citrobacter/braakii.json

data/rag/knowledge_base/Citrobacter/braakii.json

@@ -1,48 +1,89 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Citrobacter",
   "species": "braakii",
-  "full_name": "Citrobacter braakii",
-  "clinical_significance": "A member of the Citrobacter freundii complex. Causes opportunistic infections similar to C. freundii including UTIs, wound infections, and bacteremia. Often isolated from hospital settings and may carry AmpC β-lactamases.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative motile rods.",
-    "culture": "Non-lactose fermenting or weakly lactose fermenting colonies on MacConkey.",
-    "biochemical": [
-      "Indole negative",
-      "Citrate positive",
-      "ONPG positive",
-      "H2S positive (typical of C. freundii complex)",
-      "Lysine decarboxylase negative",
-      "Motile",
-      "Oxidase negative",
-      "Urease negative or weak"
-    ]
+
+  "overview": {
+    "short": "Citrobacter braakii is a Gram-negative, facultatively anaerobic rod recovered from environmental and clinical sources.",
+    "clinical_context": "Occasionally implicated in opportunistic infections, but less frequently than other Citrobacter species."
   },
-  "differentiation": {
-    "from close species": [
-      "Indole negative distinguishes from C. koserii (indole positive).",
-      "H2S positive → aligns with C. freundii complex.",
-      "Requires MALDI-TOF MS for confident differentiation from C. freundii."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "MacConkey Agar",
+      "Blood Agar"
     ],
-    "from other genera": [
-      "Citrate + ONPG + H2S combination strongly suggests Citrobacter.",
-      "Motility and lysine-negative profile separates from Enterobacter."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Moist"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "10//45",
+    "Catalase": "Positive",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Variable",
+    "Citrate": "Positive",
+    "Methyl Red": "Positive",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Positive",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Variable",
+    "Nitrate Reduction": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Variable",
+    "Ornitihine Decarboxylase": "Variable",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Variable",
+    "Sucrose Fermentation": "Variable",
+    "Maltose Fermentation": "Positive",
+    "Mannitol Fermentation": "Variable",
+    "Sorbitol Fermentation": "Variable",
+    "Xylose Fermentation": "Positive",
+    "Rhamnose Fermentation": "Positive",
+    "Arabinose Fermentation": "Positive",
+    "Raffinose Fermentation": "Variable",
+    "Trehalose Fermentation": "Positive",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Variable",
+    "TSI Pattern": "A/A",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Peritrichous"
   },
-  "virulence_factors": [
-    "AmpC β-lactamase production",
-    "Adhesins for urinary and biliary tract surfaces",
-    "Biofilm formation"
-  ],
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "H2S positivity",
-    "Biochemical panels",
-    "Sequencing when needed"
+
+  "species_markers": [
+    {
+      "field": "Rhamnose Fermentation",
+      "value": "Positive",
+      "importance": "medium",
+      "notes": "Helps differentiate C. braakii from other Citrobacter species."
+    }
   ],
-  "treatment_notes": "Often shows multidrug resistance due to AmpC. Use carbapenems, cefepime, or fluoroquinolones based on susceptibility.",
-  "notes": "Part of the C. freundii complex; clinically behaves similarly to freundii.",
-  "references": [
-    "Citrobacter taxonomy literature",
-    "Hospital-associated Citrobacter infection reports"
+
+  "recommended_next_tests": [
+    {
+      "test": "Carbohydrate fermentation profile",
+      "reason": "Supports separation from closely related Citrobacter species."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Confirms species-level identification."
+    }
   ]
-}
+}