Update data/rag/knowledge_base/Campylobacter/coli.json

data/rag/knowledge_base/Campylobacter/coli.json

@@ -1,47 +1,102 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Campylobacter",
   "species": "coli",
-  "full_name": "Campylobacter coli",
-  "clinical_significance": "An important cause of bacterial gastroenteritis, similar to C. jejuni but generally milder. Often linked to pork, poultry, contaminated water, and animal contact. Can cause bloody diarrhea, fever, abdominal pain, and post-infectious sequelae such as GBS or reactive arthritis.",
-  "phenotype_profile": {
-    "morphology": "Curved Gram-negative rods; seagull-wing appearance; darting motility.",
-    "culture": "Grows at 42°C on selective media. Less fastidious than C. jejuni but similar colony morphology (moist, spreading).",
-    "biochemical": [
-      "Oxidase positive",
-      "Catalase positive",
-      "Hippurate hydrolysis negative (key differentiator)",
-      "ONPG negative",
-      "Indoxyl acetate positive",
-      "No growth in 6.5% NaCl",
-      "Microaerophilic"
-    ]
+
+  "overview": {
+    "short": "Campylobacter coli is a thermophilic, Gram-negative spiral bacterium causing gastroenteritis, particularly in agricultural settings.",
+    "clinical_context": "Often associated with pork and poultry exposure."
   },
-  "differentiation": {
-    "from close species": [
-      "Hippurate negative distinguishes C. coli from C. jejuni (positive).",
-      "Slightly broader rods compared to C. jejuni.",
-      "Environmental association stronger with pigs than poultry."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Spiral",
+    "Motility": "Positive",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Variable",
+    "Haemolysis Type": "Unknown",
+    "Media Grown On": [
+      "Campylobacter Agar",
+      "Blood Agar"
     ],
-    "from other genera": [
-      "Curved rod + 42°C growth + microaerophilic → Campylobacter, not Vibrio/Helicobacter."
-    ]
+    "Colony Morphology": [
+      "Small",
+      "Grey",
+      "Moist"
+    ],
+    "Oxygen Requirement": "Microaerophilic",
+    "Growth Temperature": "37//42",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Variable",
+    "DNase": "Negative",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Negative",
+    "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": "K/K",
+    "Colony Pattern": "Unknown",
+    "Pigment": "None",
+    "Motility Type": "Polar"
   },
-  "virulence_factors": [
-    "Cytolethal distending toxin (CDT)",
-    "Flagellar motility",
-    "Adhesins enabling intestinal colonization",
-    "LPS-triggered inflammation"
+
+  "species_markers": [
+    {
+      "field": "Hippurate Hydrolysis",
+      "value": "Negative",
+      "importance": "high",
+      "notes": "Primary discriminator from Campylobacter jejuni."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Campylobacter jejuni",
+      "reason": "Identical morphology and growth characteristics."
+    }
   ],
-  "confirmation_methods": [
-    "PCR (species-specific markers: ceuE)",
-    "Hippurate hydrolysis (negative)",
-    "MALDI-TOF MS",
-    "Growth at 42°C on selective media"
+
+  "when_to_question_identification": [
+    "Hippurate positivity suggests Campylobacter jejuni.",
+    "Failure to grow at 42 °C suggests a non-thermophilic species."
   ],
-  "treatment_notes": "Macrolides (azithromycin) preferred; fluoroquinolone resistance common. Severe infections may require IV therapy.",
-  "notes": "Accounts for approximately 10–25% of human Campylobacter disease depending on region.",
-  "references": [
-    "CDC Campylobacter statistics",
-    "Campylobacter coli genomics literature"
+
+  "recommended_next_tests": [
+    {
+      "test": "Hippurate hydrolysis",
+      "reason": "Differentiates C. coli from C. jejuni.",
+      "api_kit": "API Campy"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Reliable species confirmation."
+    }
   ]
-}
+}