Update data/rag/knowledge_base/Comamonas/testosteroni.json

data/rag/knowledge_base/Comamonas/testosteroni.json

@@ -1,46 +1,125 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Comamonas",
-  "species": "testosteronii",
-  "full_name": "Comamonas testosteronii",
-  "clinical_significance": "Primarily an environmental organism involved in degradation of steroids such as testosterone. Rarely isolated from human clinical specimens. Most isolations represent colonization or contamination, though occasional opportunistic infections are reported in immunocompromised patients.",
-  "phenotype_profile": {
-    "morphology": "Motile Gram-negative rods with polar flagella.",
-    "culture": "Smooth, non-pigmented colonies on routine media. NLF on MacConkey.",
-    "biochemical": [
-      "Oxidase positive",
-      "Catalase positive",
-      "Non-fermentative",
-      "Indole negative",
-      "Nitrate reduction positive",
-      "ONPG negative",
-      "Urease negative",
-      "Motile"
-    ]
+  "species": "testosteroni",
+
+  "overview": {
+    "short": "Comamonas testosteroni is a Gram-negative, aerobic, non-fermentative rod primarily associated with environmental sources.",
+    "clinical_context": "Rare opportunistic pathogen occasionally isolated from bloodstream, respiratory, or wound infections."
   },
-  "differentiation": {
-    "from close species": [
-      "Less frequently pathogenic than C. kerstersii.",
-      "Distinguished by specific carbon assimilation patterns (e.g., steroid degradation).",
-      "MALDI-TOF MS required for reliable 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",
+      "Nutrient Agar"
     ],
-    "from other genera": [
-      "Oxidase positivity and motility with non-fermentative metabolism resembles Delftia but lacks DNase activity.",
-      "No pigment differentiates from Pseudomonas aeruginosa."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Non-pigmented"
+    ],
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "20//42",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "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": "Negative",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Negative",
+    "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": "Unknown",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Polar"
   },
-  "virulence_factors": [
-    "Environmental persistence",
-    "Biofilm formation in water systems (rare clinical relevance)"
+
+  "species_markers": [
+    {
+      "field": "Citrate",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Major discriminator from Comamonas kerstersii."
+    },
+    {
+      "field": "Nitrate Reduction",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Supports identification when combined with citrate positivity."
+    },
+    {
+      "field": "Environmental Source",
+      "value": "Common",
+      "importance": "medium",
+      "notes": "Frequently isolated from soil and water."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Comamonas kerstersii",
+      "reason": "Overlapping morphology and non-fermentative biochemistry."
+    },
+    {
+      "genus": "Achromobacter",
+      "reason": "Shared oxidase-positive, non-fermentative profile."
+    }
   ],
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "16S rRNA sequencing",
-    "Substrate assimilation testing (research)"
+
+  "when_to_question_identification": [
+    "Citrate negativity suggests Comamonas kerstersii.",
+    "Clinical isolation from intra-abdominal infections favors C. kerstersii.",
+    "Glucose fermentation excludes Comamonas species."
   ],
-  "treatment_notes": "Typically susceptible to fluoroquinolones, carbapenems, and TMP-SMX. Treatment only required for confirmed infections.",
-  "notes": "Most reported clinical isolates are incidental; pathogenicity generally low.",
-  "references": [
-    "Environmental Comamonas literature",
-    "Rare Comamonas infection case reports"
+
+  "recommended_next_tests": [
+    {
+      "test": "Citrate utilization",
+      "reason": "Primary biochemical discriminator.",
+      "api_kit": "API 20NE"
+    },
+    {
+      "test": "Nitrate reduction",
+      "reason": "Supports species-level separation.",
+      "api_kit": "API 20NE"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Definitive species identification.",
+      "api_kit": "Not applicable"
+    }
   ]
-}
+}