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

data/rag/knowledge_base/Campylobacter/fetus.json

@@ -1,46 +1,106 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Campylobacter",
   "species": "fetus",
-  "full_name": "Campylobacter fetus",
-  "clinical_significance": "A cause of systemic infections including bacteremia, endocarditis, vascular infection, and meningitis, especially in immunocompromised or elderly patients. Unlike C. jejuni/coli, C. fetus rarely causes diarrhea. Zoonotic transmission occurs via livestock exposure.",
-  "phenotype_profile": {
-    "morphology": "Curved or spiral Gram-negative rods with characteristic S-shapes.",
-    "culture": "Grows at 25–37°C but NOT at 42°C (important differentiator). Requires microaerophilic environment but less thermophilic than jejuni/coli.",
-    "biochemical": [
-      "Oxidase positive",
-      "Catalase positive (strong)",
-      "Hippurate negative",
-      "ONPG negative",
-      "Hydrogen sulfide production on TSI slants (occasionally)",
-      "No growth in 6.5% NaCl"
-    ]
+
+  "overview": {
+    "short": "Campylobacter fetus is a non-thermophilic Campylobacter species associated with invasive infections.",
+    "clinical_context": "Causes bacteremia, meningitis, and pregnancy-related infections rather than gastroenteritis."
   },
-  "differentiation": {
-    "from close species": [
-      "Does NOT grow at 42°C (jejuni/coli do).",
-      "Causes bacteremia/systemic illness vs. enteritis in jejuni/coli.",
-      "Has a surface layer (S-layer) enabling serum resistance."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Spiral",
+    "Motility": "Positive",
+    "Capsule": "Positive",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar"
     ],
-    "from other genera": [
-      "Curved Gram-negative rod but microaerophilic; differentiates from Vibrio.",
-      "Serum resistance and systemic infection pattern unique among Campylobacter."
-    ]
+    "Colony Morphology": [
+      "Small",
+      "Grey",
+      "Smooth"
+    ],
+    "Oxygen Requirement": "Microaerophilic",
+    "Growth Temperature": "25//37",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Negative",
+    "Urease": "Negative",
+    "Citrate": "Negative",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "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": [
-    "Surface layer (S-layer) providing complement resistance",
-    "Flagellar motility",
-    "Adhesins facilitating vascular endothelium invasion"
+
+  "species_markers": [
+    {
+      "field": "Growth Temperature",
+      "value": "25//37",
+      "importance": "high",
+      "notes": "Lack of growth at 42 °C distinguishes C. fetus."
+    },
+    {
+      "field": "Capsule",
+      "value": "Positive",
+      "importance": "medium",
+      "notes": "Surface layer protein contributes to invasiveness."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Campylobacter jejuni",
+      "reason": "Similar morphology but different temperature tolerance."
+    }
   ],
-  "confirmation_methods": [
-    "PCR for C. fetus-specific markers (sapB2)",
-    "Inability to grow at 42°C",
-    "MALDI-TOF MS",
-    "16S or hsp60 sequencing"
+
+  "when_to_question_identification": [
+    "Robust growth at 42 °C argues against C. fetus.",
+    "Absence of invasive disease context weakens identification."
   ],
-  "treatment_notes": "Systemic infections require IV therapy; options include carbapenems, aminoglycosides, or ceftriaxone. Macrolides less effective than in jejuni/coli.",
-  "notes": "Important cause of bacteremia in elderly and immunocompromised patients; may cause fetal loss in livestock.",
-  "references": [
-    "Campylobacter fetus clinical reviews",
-    "Manual of Clinical Microbiology"
+
+  "recommended_next_tests": [
+    {
+      "test": "Growth temperature testing",
+      "reason": "Separates thermophilic from non-thermophilic Campylobacter."
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Accurate species identification."
+    }
   ]
-}
+}