Update data/rag/knowledge_base/Cupriavidus/pauculus.json

data/rag/knowledge_base/Cupriavidus/pauculus.json

@@ -1,49 +1,102 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Cupriavidus",
   "species": "pauculus",
-  "full_name": "Cupriavidus pauculus",
-  "clinical_significance": "An opportunistic pathogen associated with contaminated water systems, hemodialysis fluids, and medical devices. Causes bacteremia, peritonitis, and respiratory infections, especially in immunocompromised patients or ICU settings.",
-  "phenotype_profile": {
-    "morphology": "Motile Gram-negative rods.",
-    "culture": "Non-pigmented colonies on blood and MacConkey agar (NLF).",
-    "biochemical": [
-      "Oxidase weak or negative",
-      "Catalase positive",
-      "Non-fermentative",
-      "Nitrate positive",
-      "Urease negative",
-      "Motile",
-      "No distinctive pigment"
-    ]
+
+  "overview": {
+    "short": "Cupriavidus pauculus is a Gram-negative, aerobic, non-fermentative rod associated with environmental and occasional clinical isolates.",
+    "clinical_context": "Reported in sporadic opportunistic infections and from contaminated water sources."
   },
-  "differentiation": {
-    "from close species": [
-      "More strongly associated with water-system related outbreaks than C. gilardii.",
-      "Less resistant than C. gilardii; typically more antibiotic susceptible.",
-      "MALDI-TOF essential for accurate speciation."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Negative",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar"
     ],
-    "from other genera": [
-      "Contaminated water association differentiates from Burkholderia.",
-      "Weak oxidase reaction helps rule out Ralstonia."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Non-pigmented"
+    ],
+    "Oxygen Requirement": "Aerobe",
+    "Growth Temperature": "20//37",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Negative",
+    "Urease": "Variable",
+    "Citrate": "Positive",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Positive",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Variable",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Positive",
+    "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": "Polar"
   },
-  "virulence_factors": [
-      "Biofilm formation in water systems",
-      "Environmental resilience",
-      "Ability to persist in nutrient-poor fluids"
+
+  "species_markers": [
+    {
+      "field": "Nitrate Reduction",
+      "value": "Positive",
+      "importance": "medium",
+      "notes": "Differentiates from some other Cupriavidus species."
+    }
   ],
-  "confirmation_methods": [
-      "MALDI-TOF MS",
-      "16S rRNA or rpoB sequencing",
-      "Environmental source tracing"
+
+  "common_confusions": [
+    {
+      "genus": "Burkholderia",
+      "reason": "Shared non-fermentative, oxidase-positive phenotype."
+    }
   ],
-  "treatment_notes": [
-      "Often susceptible to carbapenems, fluoroquinolones, and TMP-SMX.",
-      "β-lactam resistance occasionally observed but less severe than in C. gilardii."
+
+  "when_to_question_identification": [
+    "Glucose fermentation is inconsistent with C. pauculus.",
+    "Anaerobic growth suggests an alternative genus."
   ],
-  "notes": "Frequently involved in pseudobacteremia events from contaminated water or fluid systems.",
-  "references": [
-      "Water-system contamination outbreak literature",
-      "Cupriavidus pauculus case reports"
+
+  "recommended_next_tests": [
+    {
+      "test": "Nitrate reduction",
+      "reason": "Useful for species-level support.",
+      "api_kit": "API 20 NE"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Confirms species-level identity.",
+      "api_kit": "Not applicable"
+    }
   ]
-}
+}