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

data/rag/knowledge_base/Cupriavidus/gilardii.json

@@ -1,47 +1,114 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Cupriavidus",
   "species": "gilardii",
-  "full_name": "Cupriavidus gilardii",
-  "clinical_significance": "An emerging opportunistic pathogen increasingly recovered from clinical specimens including blood, respiratory secretions, wounds, and catheter-associated infections. Notable for multidrug resistance and misidentification as Ralstonia or Burkholderia in older systems.",
-  "phenotype_profile": {
-    "morphology": "Slender, motile Gram-negative rods.",
-    "culture": "Smooth, non-pigmented colonies on routine media; NLF on MacConkey.",
-    "biochemical": [
-      "Oxidase weak or negative (important discriminator)",
-      "Catalase positive",
-      "Non-fermentative oxidative metabolism",
-      "Nitrate reduction positive",
-      "Urease negative",
-      "Motile",
-      "No pigment production"
-    ]
+
+  "overview": {
+    "short": "Cupriavidus gilardii is a Gram-negative, aerobic, non-fermentative rod increasingly recognised as an opportunistic human pathogen.",
+    "clinical_context": "Associated with bloodstream, respiratory, and device-related infections, particularly in immunocompromised patients."
   },
-  "differentiation": {
-    "from close species": [
-      "More commonly isolated from human clinical specimens than C. metallidurans or C. pauculus.",
-      "Oxidase weaker than typical Burkholderia.",
-      "MALDI-TOF MS required for reliable identification due to phenotypic overlap.",
-      "Often exhibits multidrug resistance patterns not seen in C. pauculus."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Negative",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "Chocolate Agar"
     ],
-    "from other genera": [
-      "Distinguishable from Ralstonia by oxidase variability and MALDI-TOF profile.",
-      "No DNase activity distinguishes from Delftia acidovorans."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Non-pigmented"
+    ],
+    "Oxygen Requirement": "Aerobe",
+    "Growth Temperature": "20//37",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Negative",
+    "Urease": "Variable",
+    "Citrate": "Negative",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Negative",
+    "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": [
-      "Ability to colonize catheters and biofilm formation",
-      "Intrinsic antibiotic resistance mechanisms",
-      "Environmental persistence"
+
+  "species_markers": [
+    {
+      "field": "Citrate",
+      "value": "Negative",
+      "importance": "medium",
+      "notes": "Helps separate C. gilardii from other citrate-positive Cupriavidus species."
+    },
+    {
+      "field": "Nitrate Reduction",
+      "value": "Negative",
+      "importance": "medium",
+      "notes": "Differentiates from denitrifying environmental relatives."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Burkholderia",
+      "reason": "Shared oxidase positivity and non-fermentative metabolism."
+    },
+    {
+      "genus": "Ralstonia",
+      "reason": "Phylogenetic similarity and overlapping biochemical profile."
+    }
   ],
-  "confirmation_methods": [
-      "MALDI-TOF MS",
-      "16S rRNA or rpoB sequencing",
-      "Antibiotic susceptibility patterns"
+
+  "when_to_question_identification": [
+    "Oxidase negativity argues against C. gilardii.",
+    "Any glucose fermentation suggests misidentification.",
+    "Anaerobic growth is inconsistent."
   ],
-  "treatment_notes": "Resistance to β-lactams, aminoglycosides, and some fluoroquinolones possible. TMP-SMX, piperacillin-tazobactam, and carbapenems may be active depending on susceptibility results.",
-  "notes": "Often misidentified before MALDI-TOF adoption; caution recommended in clinical interpretation.",
-  "references": [
-      "Cupriavidus gilardii case reports",
-      "Burkholderiales non-fermenter clinical literature"
+
+  "recommended_next_tests": [
+    {
+      "test": "Arginine dihydrolase",
+      "reason": "Supports placement among Cupriavidus species.",
+      "api_kit": "API 20 NE"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable discrimination from Burkholderia and Ralstonia.",
+      "api_kit": "Not applicable"
+    }
   ]
-}
+}