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

data/rag/knowledge_base/Cupriavidus/genus.json

@@ -1,77 +1,136 @@
 {
+  "schema_version": "1.0",
+  "level": "genus",
   "genus": "Cupriavidus",
-  "taxonomy": {
-    "family": "Burkholderiaceae",
-    "order": "Burkholderiales",
-    "class": "Betaproteobacteria",
-    "phylum": "Proteobacteria"
+
+  "overview": {
+    "short": "Cupriavidus species are Gram-negative, aerobic, non-fermentative rods within the Betaproteobacteria, notable for environmental resilience and metal resistance.",
+    "clinical_context": "Occasionally isolated from opportunistic infections, particularly in immunocompromised patients or from contaminated medical devices and water sources."
   },
-  "overview": "Cupriavidus is a genus of aerobic, motile, Gram-negative rods belonging to Burkholderiales. Many species tolerate or accumulate heavy metals and inhabit soil, freshwater, and industrial environments. While historically considered environmental organisms, several species have emerged as opportunistic human pathogens, especially in immunocompromised hosts or those with indwelling medical devices.",
-  "key_traits": [
-    "Gram-negative rods",
-    "Motile (polar flagella)",
-    "Oxidase variable (often weak or negative in clinical isolates)",
-    "Non-fermentative metabolism",
-    "Catalase positive",
-    "Nitrate reduction positive",
-    "Able to tolerate or accumulate heavy metals (species dependent)",
-    "Non-pigmented colonies",
-    "Grow on standard aerobic media"
-  ],
-  "ecology": "Widely distributed in water systems, soil, industrial effluents, metal-contaminated environments, and hospital water sources. Some species are known for extreme heavy-metal resistance.",
-  "pathogenicity": "Opportunistic infections including bacteremia, pneumonia, peritonitis, device-related infections, urinary tract infections, and soft tissue infections. Most clinically significant isolates belong to C. gilardii, C. pauculus, and rare isolates of C. metallidurans.",
-  "genus_level_biochemistry": {
-    "general_tendencies": [
-      "Non-fermenting, oxidative metabolism.",
-      "Nitrate reduction positive.",
-      "Oxidase negative or weak-positive reactions.",
-      "Motile Gram-negative rods.",
-      "Growth in low-nutrient and metal-rich environments."
+
+  "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"
     ],
-    "non_definitive_tests": [
-      "Oxidase results inconsistent and not reliable for speciation.",
-      "Biochemical patterns often overlap with Ralstonia and Burkholderia."
-    ]
-  },
-  "genus_differentiation": {
-    "from_close_genera": [
-      "Ralstonia typically oxidase positive; Cupriavidus more often oxidase negative or weak.",
-      "Burkholderia species typically show stronger oxidase positivity and broader carbon assimilation.",
-      "Pandoraea are non-motile or weakly motile and often involved in CF lung disease.",
-      "Delftia acidovorans shows DNase positivity and characteristic 'orange-peel' colony sheen."
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Non-pigmented"
     ],
-    "key_rag_filters": [
-      "Non-fermenter + oxidase variable + environmental/water isolate → Burkholderiales → consider Cupriavidus.",
-      "Metal-contaminated source → strongly suggests C. metallidurans.",
-      "Device-related infection with non-fermenter → C. gilardii or C. pauculus.",
-      "Weak oxidase reaction + no pigment + non-fermenter → narrows to Cupriavidus/Ralstonia."
-    ]
+    "Oxygen Requirement": "Aerobe",
+    "Growth Temperature": "20//37",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Negative",
+    "Urease": "Variable",
+    "Citrate": "Variable",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Negative",
+    "Nitrate Reduction": "Variable",
+    "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"
   },
-  "diagnostics": {
-    "typical_lab_findings": [
-      "Non-fermenting Gram-negative rods",
-      "NLF on MacConkey",
-      "Oxidase weak or negative",
-      "Motile",
-      "Non-pigmented colonies"
-    ],
-    "important_tests": [
-      "Oxidase (weak/variable)",
-      "Nitrate reduction",
-      "MALDI-TOF MS",
-      "Carbon assimilation profiles",
-      "16S rRNA or rpoB sequencing"
-    ],
-    "confirmation_methods": [
-      "MALDI-TOF MS (highly accurate for genus)",
-      "Whole-genome sequencing for species confirmation",
-      "rpoB or gyrB sequencing"
-    ]
+
+  "field_notes": {
+    "Oxidase": "Typically oxidase-positive, helping distinguish from many Enterobacterales.",
+    "Arginine dihydrolase": "Commonly positive and useful in non-fermenter differentiation.",
+    "Glucose Fermentation": "Non-fermentative metabolism is a key defining trait."
   },
-  "notes": "Cupriavidus species may be resistant to multiple antibiotics, including β-lactams and aminoglycosides.",
-  "references": [
-    "Burkholderiales taxonomy literature",
-    "Environmental microbiology of Cupriavidus",
-    "Cupriavidus clinical case series"
+
+  "key_differentiators": [
+    {
+      "field": "Oxidase",
+      "expected": "Positive",
+      "distinguishes_from": ["Acinetobacter"],
+      "notes": "Oxidase positivity separates Cupriavidus from oxidase-negative non-fermenters."
+    },
+    {
+      "field": "Arginine dihydrolase",
+      "expected": "Positive",
+      "distinguishes_from": ["Burkholderia"],
+      "notes": "Supports Cupriavidus identification among Betaproteobacteria."
+    },
+    {
+      "field": "Glucose Fermentation",
+      "expected": "Negative",
+      "distinguishes_from": ["Enterobacter", "Escherichia"],
+      "notes": "Non-fermentative metabolism excludes Enterobacterales."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Burkholderia",
+      "reason": "Overlapping non-fermentative profiles and environmental association."
+    },
+    {
+      "genus": "Ralstonia",
+      "reason": "Phylogenetic relatedness and similar biochemical reactions."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Oxidase negativity suggests Acinetobacter or other non-fermenters.",
+    "Strong glucose fermentation argues against Cupriavidus.",
+    "Growth failure under aerobic conditions is inconsistent."
+  ],
+
+  "recommended_next_tests": [
+    {
+      "test": "Oxidase test",
+      "reason": "Initial confirmation of non-fermentative oxidase-positive profile.",
+      "api_kit": "API 20 NE"
+    },
+    {
+      "test": "Arginine dihydrolase",
+      "reason": "Helpful discriminator among non-fermenters.",
+      "api_kit": "API 20 NE"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable genus- and species-level identification for environmental non-fermenters.",
+      "api_kit": "Not applicable"
+    }
+  ],
+
+  "supported_species": [
+    "gilardii",
+    "metallidurans",
+    "pauculus"
   ]
-}
+}