Update data/rag/knowledge_base/Bordetella/parapertussis.json

data/rag/knowledge_base/Bordetella/parapertussis.json

@@ -1,46 +1,95 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Bordetella",
   "species": "parapertussis",
-  "full_name": "Bordetella parapertussis",
-  "clinical_significance": "Causes a pertussis-like illness that is generally milder and shorter in duration than classical pertussis. Infects humans but can also infect sheep as a separate lineage (B. parapertussis ov).",
-  "phenotype_profile": {
-    "morphology": "Small Gram-negative coccobacilli, similar to B. pertussis.",
-    "culture": "Less fastidious than B. pertussis; can grow on blood agar. Grows on Regan-Lowe. Colonies gray-white and smooth.",
-    "biochemical": [
-      "Urease positive (different from B. pertussis)",
-      "Oxidase variable",
-      "Catalase positive",
-      "Non-motile",
-      "Nitrate reduction negative",
-      "ONPG negative"
-    ]
+
+  "overview": {
+    "short": "Bordetella parapertussis is a non-motile Gram-negative coccobacillus causing a pertussis-like respiratory illness.",
+    "clinical_context": "Human respiratory pathogen typically associated with milder disease than Bordetella pertussis."
   },
-  "differentiation": {
-    "from_close_species": [
-      "Urease positive differentiates it from B. pertussis.",
-      "Less fastidious, grows on blood agar unlike B. pertussis.",
-      "Negative for pertussis toxin genes (major distinction).",
-      "IS1001 PCR target used in identification."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Short Rods",
+    "Motility": "Negative",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Variable",
+    "Haemolysis Type": "Variable",
+    "Media Grown On": [
+      "Bordet-Gengou Agar",
+      "Regan-Lowe Agar"
     ],
-    "from_other_genera": [
-      "Distinctive growth pattern similar to Bordetella species but not others.",
-      "Non-motility separates from B. bronchiseptica."
-    ]
+    "Colony Morphology": [
+      "Small",
+      "Smooth"
+    ],
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "35//37",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Negative",
+    "Urease": "Positive",
+    "Citrate": "Negative",
+    "Methyl Red": "Unknown",
+    "VP": "Unknown",
+    "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": "None"
   },
-  "virulence_factors": [
-    "Lipooligosaccharide variants enabling immune evasion",
-    "Adhesins similar to B. pertussis but lacks PT toxin"
-  ],
-  "confirmation_methods": [
-    "PCR targeting IS1001",
-    "Culture characteristics",
-    "Urease positivity",
-    "MALDI-TOF MS"
+
+  "species_markers": [
+    {
+      "field": "Urease",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Key biochemical feature distinguishing from B. pertussis."
+    },
+    {
+      "field": "Haemolysis",
+      "value": "Variable",
+      "importance": "medium",
+      "notes": "Less consistent haemolysis compared to B. pertussis."
+    }
   ],
-  "treatment_notes": "Macrolides effective. Disease usually self-limited.",
-  "notes": "Does not produce pertussis toxin, contributing to milder disease.",
-  "references": [
-    "Pertussis-like illness literature",
-    "Bordetella molecular diagnostics research"
+
+  "recommended_next_tests": [
+    {
+      "test": "Urease test",
+      "reason": "Rapid biochemical differentiation.",
+      "api_kit": "API 20 NE"
+    },
+    {
+      "test": "PCR differentiation",
+      "reason": "Separates Bordetella species within the pertussis complex."
+    }
   ]
-}
+}