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

data/rag/knowledge_base/Citrobacter/freundii.json

@@ -1,50 +1,106 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Citrobacter",
   "species": "freundii",
-  "full_name": "Citrobacter freundii",
-  "clinical_significance": "The most common Citrobacter species isolated clinically. Causes UTIs, pneumonia, intra-abdominal infections, wound infections, bacteremia, and healthcare-associated outbreaks. Frequently carries inducible AmpC β-lactamase, conferring resistance to many β-lactams.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative motile rods.",
-    "culture": "Lactose variable: slow fermenter or NLF. Colonies may appear yellowish or colorless on MacConkey.",
-    "biochemical": [
-      "Indole variable (often negative)",
-      "Citrate positive",
-      "ONPG positive",
-      "H2S positive (important differentiator)",
-      "Lysine decarboxylase negative",
-      "Urease negative or weak",
-      "Motile",
-      "Oxidase negative"
-    ]
+
+  "overview": {
+    "short": "Citrobacter freundii is a Gram-negative, facultatively anaerobic rod commonly isolated from the intestinal tract and environment.",
+    "clinical_context": "Associated with opportunistic infections including urinary tract, bloodstream, and intra-abdominal infections."
   },
-  "differentiation": {
-    "from close species": [
-      "H2S production is typical of the C. freundii complex, unlike C. koserii and C. braakii.",
-      "Indole variable but commonly negative.",
-      "Higher frequency of AmpC β-lactamase production than koserii or braakii."
+
+  "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": [
-      "ONPG positive but H2S positive distinguishes from Salmonella.",
-      "Motile and citrate positive differentiates from Klebsiella.",
-      "Lysine decarboxylase negative distinguishes 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": "Positive",
+    "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": "Variable",
+    "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": [
-    "Inducible AmpC β-lactamase (major clinical issue)",
-    "Biofilm formation",
-    "Adhesins enabling urinary tract infection",
-    "Endotoxin-mediated inflammation"
+
+  "species_markers": [
+    {
+      "field": "H2S",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Commonly produces H2S, helping differentiate from other Citrobacter species."
+    },
+    {
+      "field": "Indole",
+      "value": "Negative",
+      "importance": "medium",
+      "notes": "Indole negativity helps separate from C. koseri."
+    }
   ],
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "H2S positivity",
-    "AmpC phenotypic tests",
-    "Molecular assays"
+
+  "common_confusions": [
+    {
+      "genus": "Salmonella",
+      "reason": "Shared H2S production and Enterobacterales profile."
+    }
   ],
-  "treatment_notes": "Often resistant to penicillins and cephalosporins due to AmpC. Carbapenems, cefepime, fluoroquinolones, and aminoglycosides may be effective depending on susceptibility.",
-  "notes": "Important nosocomial pathogen; may cause outbreaks in ICUs and nursing facilities.",
-  "references": [
-    "Citrobacter freundii outbreak reports",
-    "AmpC resistance literature"
+
+  "recommended_next_tests": [
+    {
+      "test": "H2S production",
+      "reason": "Supports differentiation from non-H2S-producing Enterobacterales."
+    },
+    {
+      "test": "API 20E",
+      "reason": "Standard biochemical identification for Enterobacterales."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Accurate species-level identification."
+    }
   ]
-}
+}