Update data/rag/knowledge_base/Burkholderia/cepacia.json

data/rag/knowledge_base/Burkholderia/cepacia.json

@@ -1,49 +1,116 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Burkholderia",
   "species": "cepacia",
-  "full_name": "Burkholderia cepacia complex (BCC)",
-  "clinical_significance": "A group of at least 20 genetically related species causing chronic lung infections in cystic fibrosis (CF) and chronic granulomatous disease patients. Known for multidrug resistance, biofilm formation, and the potentially fatal 'cepacia syndrome'—necrotizing pneumonia with bacteremia.",
-  "phenotype_profile": {
-    "morphology": "Gram-negative rods; motile.",
-    "culture": "Grows on blood agar, MacConkey, and selective BCC media (e.g., OFPBL). Colonies may be yellowish or variable.",
-    "biochemical": [
-      "Oxidase positive or variable",
-      "Catalase positive",
-      "Motile",
-      "ONPG negative",
-      "Lysine decarboxylase positive",
-      "Reduces nitrate variably",
-      "No growth in 6.5% NaCl"
-    ]
+
+  "overview": {
+    "short": "Burkholderia cepacia is a Gram-negative, motile, non-fermentative rod associated with opportunistic infections.",
+    "clinical_context": "Most significant in patients with cystic fibrosis or chronic granulomatous disease."
   },
-  "differentiation": {
-    "from close species": [
-      "Oxidase variable, unlike consistently positive Pseudomonas aeruginosa.",
-      "Highly drug-resistant patterns typical for BCC.",
-      "Selective media (OFPBL/PC) used for CF screening.",
-      "MALDI-TOF or recA sequencing required for species-level ID."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Positive",
+    "Capsule": "Variable",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "MacConkey Agar"
     ],
-    "from other genera": [
-      "Strong intrinsic resistance differentiates from most non-fermenters.",
-      "Growth on OFPBL medium differentiates from Pseudomonas/Acinetobacter."
-    ]
+    "Colony Morphology": [
+      "Smooth",
+      "Grey",
+      "Non-lactose fermenting"
+    ],
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "30//37",
+    "Catalase": "Positive",
+    "Oxidase": "Variable",
+    "Indole": "Negative",
+    "Urease": "Variable",
+    "Citrate": "Positive",
+    "Methyl Red": "Negative",
+    "VP": "Negative",
+    "H2S": "Negative",
+    "DNase": "Variable",
+    "ONPG": "Negative",
+    "Coagulase": "Negative",
+    "Gelatin Hydrolysis": "Variable",
+    "Esculin Hydrolysis": "Positive",
+    "Nitrate Reduction": "Variable",
+    "NaCl Tolerant (>=6%)": "Negative",
+    "Lipase Test": "Variable",
+    "Lysine Decarboxylase": "Negative",
+    "Ornithine Decarboxylase": "Negative",
+    "Ornitihine Decarboxylase": "Negative",
+    "Arginine dihydrolase": "Variable",
+    "Glucose Fermentation": "Negative",
+    "Lactose Fermentation": "Negative",
+    "Sucrose Fermentation": "Negative",
+    "Maltose Fermentation": "Negative",
+    "Mannitol Fermentation": "Variable",
+    "Sorbitol Fermentation": "Negative",
+    "Xylose Fermentation": "Variable",
+    "Rhamnose Fermentation": "Negative",
+    "Arabinose Fermentation": "Variable",
+    "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": [
-      "Biofilm formation",
-      "Quorum sensing systems",
-      "Cable pili and adhesins",
-      "Efflux pumps mediating MDR"
+
+  "species_markers": [
+    {
+      "field": "Esculin Hydrolysis",
+      "value": "Positive",
+      "importance": "medium",
+      "notes": "Supports identification within the Burkholderia cepacia complex."
+    },
+    {
+      "field": "Citrate",
+      "value": "Positive",
+      "importance": "medium",
+      "notes": "Common but not exclusive to B. cepacia."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "species": "Burkholderia multivorans",
+      "reason": "Part of the Burkholderia cepacia complex with overlapping profiles."
+    },
+    {
+      "species": "Burkholderia cenocepacia",
+      "reason": "Closely related genomically and biochemically."
+    }
   ],
-  "confirmation_methods": [
-    "MALDI-TOF MS",
-    "PCR or sequencing of recA gene",
-    "Selective CF media (OFPBL, BCSA)",
-    "Antimicrobial susceptibility testing to confirm MDR pattern"
+
+  "when_to_question_identification": [
+    "Non-motility argues against B. cepacia.",
+    "Strong oxidase positivity suggests Pseudomonas."
   ],
-  "treatment_notes": "Difficult to treat; susceptible agents include ceftazidime/avibactam, meropenem, minocycline, TMP-SMX, and sometimes chloramphenicol. Combination therapy may be required.",
-  "notes": "B. cepacia complex infections restrict CF lung transplant eligibility due to poor outcomes.",
-  "references": [
-    "CF Foundation BCC management guidelines",
-    "Burkholderia taxonomy and resistance studies"
+
+  "recommended_next_tests": [
+    {
+      "test": "Esculin hydrolysis",
+      "reason": "Helpful discriminator within the cepacia complex.",
+      "api_kit": "API 20 NE"
+    },
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Preferred method for species-level resolution."
+    },
+    {
+      "test": "Genomic sequencing",
+      "reason": "Recommended for definitive cepacia complex identification."
+    }
   ]
-}
+}