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

data/rag/knowledge_base/Borrelia/recurrentis.json

@@ -1,45 +1,103 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Borrelia",
   "species": "recurrentis",
-  "full_name": "Borrelia recurrentis",
-  "clinical_significance": "Causes louse-borne relapsing fever, a severe systemic illness characterized by recurrent high fevers, rigors, hepatosplenomegaly, and high-level spirochetemia. Transmitted by human body lice. Associated with overcrowding, war, famine, and refugee settings.",
-  "phenotype_profile": {
-    "morphology": "Long, loosely coiled spirochetes visible on peripheral blood smear during febrile episodes.",
-    "culture": "Extremely difficult to culture; rarely grown outside research laboratories.",
-    "biochemical": [
-      "Oxidase negative",
-      "Catalase negative",
-      "ONPG negative",
-      "Microaerophilic",
-      "Highly motile",
-      "No NaCl tolerance"
-    ]
+
+  "overview": {
+    "short": "Borrelia recurrentis is a spirochete responsible for louse-borne relapsing fever.",
+    "clinical_context": "Characterised by recurrent episodes of fever due to antigenic variation."
   },
-  "differentiation": {
-    "from close species": [
-      "Only Borrelia species regularly visible on Giemsa-stained blood smears.",
-      "Louse-borne (not tick-borne).",
-      "Higher relapse rate and more severe febrile episodes than tick-borne relapsing fever Borrelia."
+
+  "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": [
-      "Spirochete shape excludes Enterobacterales and most pathogens.",
-      "Peripheral smear visibility differentiates from Lyme Borrelia.",
-      "Clinical syndrome of relapsing fever is highly characteristic."
-    ]
+    "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": [
-      "Antigenic variation of surface proteins (Vmp proteins)",
-      "Immune evasion leading to relapsing fever cycles"
+
+  "species_markers": [
+    {
+      "field": "Clinical Pattern",
+      "value": "Relapsing fever",
+      "importance": "high",
+      "notes": "Recurring febrile episodes due to antigenic variation."
+    },
+    {
+      "field": "Vector",
+      "value": "Body louse",
+      "importance": "high",
+      "notes": "Distinct from tick-borne Borrelia species."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Borrelia (tick-borne species)",
+      "reason": "Shared spirochete morphology but differing clinical patterns."
+    }
   ],
-  "confirmation_methods": [
-    "Giemsa blood smear (shows spirochetes during fever)",
-    "PCR (species-level accuracy)",
-    "Serology (less reliable due to cross-reactivity)"
+
+  "when_to_question_identification": [
+    "Tick exposure without relapsing fever pattern suggests Lyme Borrelia."
   ],
-  "treatment_notes": "Tetracyclines are first-line. Jarisch–Herxheimer reaction is common after initiation of therapy.",
-  "notes": "Historically responsible for devastating epidemics; still present in resource-limited regions.",
-  "references": [
-    "WHO and CDC Relapsing Fever Guidelines",
-    "Relapsing fever pathogenesis studies"
+
+  "recommended_next_tests": [
+    {
+      "test": "Peripheral blood smear during fever",
+      "reason": "High spirochetemia allows direct visualisation."
+    },
+    {
+      "test": "PCR",
+      "reason": "Confirms species-level identification."
+    }
   ]
-}
+}