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

data/rag/knowledge_base/Citrobacter/koseri.json

@@ -1,49 +1,104 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Citrobacter",
-  "species": "koserii",
-  "full_name": "Citrobacter koserii",
-  "clinical_significance": "Commonly associated with neonatal meningitis and brain abscesses, with high morbidity. Also causes UTIs, wound infections, and bacteremia in adults but with lower frequency than C. freundii.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative motile rods.",
-    "culture": "Slow lactose fermenter or NLF on MacConkey; gray colonies on blood agar.",
-    "biochemical": [
-      "Indole positive (key differentiator)",
-      "Citrate positive",
-      "ONPG positive",
-      "H2S negative",
-      "Lysine decarboxylase negative",
-      "Urease weak or negative",
-      "Motile",
-      "Oxidase negative"
-    ]
+  "species": "koseri",
+
+  "overview": {
+    "short": "Citrobacter koseri is a Gram-negative, facultatively anaerobic rod notable for its association with neonatal infections.",
+    "clinical_context": "Strongly associated with neonatal meningitis and brain abscess formation."
   },
-  "differentiation": {
-    "from close species": [
-      "Indole positive differentiates from most C. freundii and C. braakii, which are typically indole negative.",
-      "Does not produce H2S (unlike C. freundii group).",
-      "Strong association with CNS disease sets it apart clinically."
+
+  "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 positive + ONPG positive distinguishes from Salmonella.",
-      "Motile unlike Klebsiella.",
-      "Lysine decarboxylase negative excludes Enterobacter."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Moist"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "10//45",
+    "Catalase": "Positive",
+    "Oxidase": "Negative",
+    "Indole": "Positive",
+    "Urease": "Negative",
+    "Citrate": "Positive",
+    "Methyl Red": "Positive",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Positive",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Negative",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Positive",
+    "Ornitihine Decarboxylase": "Positive",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Variable",
+    "Sucrose Fermentation": "Negative",
+    "Maltose Fermentation": "Positive",
+    "Mannitol Fermentation": "Negative",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Positive",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Positive",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Positive",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Negative",
+    "TSI Pattern": "A/A",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Peritrichous"
   },
-  "virulence_factors": [
-    "Ability to invade neonatal CNS tissues",
-    "Biofilm formation on medical devices",
-    "Lipopolysaccharide-mediated inflammation"
+
+  "species_markers": [
+    {
+      "field": "Indole",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Key discriminator separating C. koseri from C. freundii and C. braakii."
+    },
+    {
+      "field": "Ornithine Decarboxylase",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Supports identification within Citrobacter species."
+    }
   ],
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "Indole positivity",
-    "Biochemical panels",
-    "PCR or sequencing if needed"
+
+  "when_to_question_identification": [
+    "H2S production suggests another Citrobacter species.",
+    "Indole negativity argues against C. koseri."
   ],
-  "treatment_notes": "Often susceptible to third-generation cephalosporins, carbapenems, fluoroquinolones, and aminoglycosides. Resistance via AmpC less common than in C. freundii but possible.",
-  "notes": "A leading cause of neonatal brain abscess; high suspicion needed when isolated from neonatal blood/CSF.",
-  "references": [
-    "Neonatal meningitis case series",
-    "Citrobacter koserii clinical reviews"
+
+  "recommended_next_tests": [
+    {
+      "test": "Indole test",
+      "reason": "Critical for species confirmation."
+    },
+    {
+      "test": "API 20E",
+      "reason": "Biochemical differentiation of Enterobacterales."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable identification in neonatal cases."
+    }
   ]
-}
+}