Update data/rag/knowledge_base/Borrelia/afzelii.json

data/rag/knowledge_base/Borrelia/afzelii.json

@@ -1,44 +1,99 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Borrelia",
   "species": "afzelii",
-  "full_name": "Borrelia afzelii",
-  "clinical_significance": "One of the three main Borrelia burgdorferi sensu lato species causing Lyme borreliosis in Europe. Strongly associated with dermatologic manifestations, especially acrodermatitis chronica atrophicans and erythema migrans.",
-  "phenotype_profile": {
-    "morphology": "Loosely coiled spirochetes visible by dark-field microscopy or silver stain.",
-    "culture": "Grows in BSK medium; slower than B. burgdorferi sensu stricto. No growth on standard media.",
-    "biochemical": [
-      "Oxidase negative",
-      "Catalase negative",
-      "ONPG negative",
-      "Non-motile externally but highly motile via axial filaments",
-      "No NaCl tolerance",
-      "Microaerophilic"
-    ]
+
+  "overview": {
+    "short": "Borrelia afzelii is a Lyme disease–associated spirochete prevalent in Europe.",
+    "clinical_context": "Frequently associated with chronic cutaneous manifestations such as acrodermatitis chronica atrophicans."
   },
-  "differentiation": {
-    "from_close_species": [
-      "More dermatotropic than B. burgdorferi s.s. or B. garinii.",
-      "Less neuroinvasive than B. garinii.",
-      "Common in central/northern Europe with Ixodes ricinus ticks."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Spiral",
+    "Motility": "Positive",
+    "Capsule": "Negative",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Barbour-Stoenner-Kelly Agar"
     ],
-    "from_other_genera": [
-      "Spirochetal form excludes Anaplasma or Rickettsia.",
-      "Cannot be seen on routine blood film unlike relapsing fever Borrelia."
-    ]
+    "Colony Morphology": [
+      "Not visible on routine media"
+    ],
+    "Oxygen Requirement": "Microaerophilic",
+    "Growth Temperature": "30//34",
+    "Catalase": "Negative",
+    "Oxidase": "Negative",
+    "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": "Negative",
+    "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": "Axial Filaments"
   },
-  "virulence_factors": [
-    "Outer surface proteins (OspA/B/C) enabling tick and host colonization",
-    "Immune evasion through variable VlsE expression"
+
+  "species_markers": [
+    {
+      "field": "Geographic Distribution",
+      "value": "Europe",
+      "importance": "high",
+      "notes": "Predominantly European Lyme disease agent."
+    },
+    {
+      "field": "Clinical Manifestation",
+      "value": "Chronic cutaneous disease",
+      "importance": "medium",
+      "notes": "Skin involvement more common than neurologic disease."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Borrelia burgdorferi",
+      "reason": "Serologic cross-reactivity and overlapping Lyme disease features."
+    }
   ],
-  "confirmation_methods": [
-    "PCR of skin biopsy or CSF",
-    "Two-tier Lyme serology",
-    "BSK medium culture (research use only)"
+
+  "when_to_question_identification": [
+    "Neurologic-dominant disease may suggest other Borrelia species."
   ],
-  "treatment_notes": "Responds to doxycycline, amoxicillin, cefuroxime. Longer treatments needed for skin or neurologic involvement.",
-  "notes": "Major cause of acrodermatitis chronica atrophicans in Europe.",
-  "references": [
-    "European Lyme borreliosis guidelines",
-    "Borrelia burgdorferi s.l. comparative genomics"
+
+  "recommended_next_tests": [
+    {
+      "test": "PCR with species-specific primers",
+      "reason": "Differentiates European Lyme Borrelia species."
+    }
   ]
-}
+}