Update data/rag/knowledge_base/Enterobacter/asburiae.json

data/rag/knowledge_base/Enterobacter/asburiae.json

@@ -1,52 +1,136 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Enterobacter",
   "species": "asburiae",
-  "full_name": "Enterobacter asburiae",
-  "clinical_significance": "A member of the Enterobacter cloacae complex. Causes opportunistic infections including UTIs, wound infections, pneumonia, and bacteremia. Less frequently associated with hospital outbreaks compared to E. hormaechei.",
-  "phenotype_profile": {
-    "morphology": "Motile Gram-negative rod.",
-    "culture": "Lactose fermenting on MacConkey; colonies similar to E. cloacae.",
-    "biochemical": [
-      "Indole variable (some strains weakly positive)",
-      "Citrate positive",
-      "ONPG positive",
-      "Lysine decarboxylase positive",
-      "Ornithine decarboxylase positive",
-      "Gas from glucose variable",
-      "Urease negative or weak",
-      "Motile"
-    ]
+
+  "overview": {
+    "short": "Enterobacter asburiae is a Gram-negative, facultatively anaerobic rod within the Enterobacter cloacae complex, less commonly isolated than E. cloacae or E. hormaechei.",
+    "clinical_context": "Typically associated with opportunistic infections, including urinary tract, wound, and bloodstream infections, primarily in immunocompromised or hospitalised patients."
   },
-  "differentiation": {
-    "from close species": [
-      "Indole variable—unlike E. cloacae which is typically indole negative.",
-      "Less associated with AmpC hyperproduction compared to E. cloacae or E. hormaechei.",
-      "MALDI-TOF MS or WGS required for definitive differentiation from ECC species."
+
+  "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": [
-      "Motile LF organism excludes Klebsiella.",
-      "Lysine positive excludes Citrobacter.",
-      "DNase negative excludes Serratia."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Moist"
+    ],
+    "Oxygen Requirement": "Facultative Anaerobe",
+    "Growth Temperature": "10//45",
+    "Catalase": "Positive",
+    "Oxidase": "Negative",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Positive",
+    "Methyl Red": "Negative",
+    "VP": "Positive",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Positive",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Positive",
+    "Esculin Hydrolysis": "Positive",
+    "Nitrate Reduction": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "Glucose Fermentation": "Positive",
+    "Lactose Fermentation": "Variable",
+    "Sucrose Fermentation": "Positive",
+    "Maltose Fermentation": "Positive",
+    "Mannitol Fermentation": "Positive",
+    "Sorbitol Fermentation": "Variable",
+    "Xylose Fermentation": "Positive",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Positive",
+    "Raffinose Fermentation": "Negative",
+    "Trehalose Fermentation": "Positive",
+    "Inositol Fermentation": "Negative",
+    "Gas Production": "Variable",
+    "TSI Pattern": "A/A",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Peritrichous"
   },
-  "virulence_factors": [
-      "Biofilm formation",
-      "Inducible AmpC β-lactamase (less active than in E. hormaechei)",
-      "Efflux pump systems"
+
+  "species_markers": [
+    {
+      "field": "Lysine Decarboxylase",
+      "value": "Negative",
+      "importance": "high",
+      "notes": "Helps distinguish E. asburiae from lysine-positive Enterobacter species."
+    },
+    {
+      "field": "Ornithine Decarboxylase",
+      "value": "Negative",
+      "importance": "high",
+      "notes": "Key discriminator separating E. asburiae from E. hormaechei."
+    },
+    {
+      "field": "Rhamnose Fermentation",
+      "value": "Negative",
+      "importance": "high",
+      "notes": "Differentiates E. asburiae from rhamnose-positive E. hormaechei."
+    },
+    {
+      "field": "Gelatin Hydrolysis",
+      "value": "Positive",
+      "importance": "medium",
+      "notes": "More consistently positive in E. asburiae than in some other complex members."
+    }
   ],
-  "confirmation_methods": [
-      "MALDI-TOF MS",
-      "Genomic sequencing within ECC framework",
-      "Biochemical indole variability"
+
+  "common_confusions": [
+    {
+      "species": "Enterobacter cloacae",
+      "reason": "Shared general biochemical profile and overlapping sugar fermentation patterns."
+    },
+    {
+      "species": "Enterobacter hormaechei",
+      "reason": "Overlapping colony morphology and growth characteristics within the E. cloacae complex."
+    }
   ],
-  "treatment_notes": [
-      "Management similar to other ECC species.",
-      "Cefepime, piperacillin–tazobactam, or carbapenems depending on susceptibility.",
-      "Avoid 3rd-gen cephalosporins due to AmpC inducibility."
+
+  "when_to_question_identification": [
+    "Ornithine decarboxylase positivity argues against E. asburiae.",
+    "Rhamnose positivity suggests E. hormaechei rather than E. asburiae.",
+    "Lysine decarboxylase positivity is inconsistent with E. asburiae."
   ],
-  "notes": "Often misidentified as E. cloacae without molecular tools.",
-  "references": [
-      "ECC diagnostic and genomic studies",
-      "Clinical reports involving Enterobacter asburiae"
+
+  "recommended_next_tests": [
+    {
+      "test": "Ornithine decarboxylase",
+      "reason": "Primary discriminator from E. hormaechei."
+    },
+    {
+      "test": "Lysine decarboxylase",
+      "reason": "Helpful in separating E. asburiae from other Enterobacter species."
+    },
+    {
+      "test": "Rhamnose fermentation",
+      "reason": "Supports differentiation within the E. cloacae complex."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Preferred routine method for accurate species-level identification."
+    },
+    {
+      "test": "Whole genome sequencing",
+      "reason": "Definitive resolution when species-level precision is clinically critical."
+    }
   ]
-}
+}