Update data/rag/knowledge_base/Bergeyella/genus.json

data/rag/knowledge_base/Bergeyella/genus.json

@@ -1,81 +1,121 @@
 {
+  "schema_version": "1.0",
+  "level": "genus",
   "genus": "Bergeyella",
-  "taxonomy": {
-    "family": "Weeksellaceae",
-    "order": "Flavobacteriales",
-    "class": "Flavobacteriia",
-    "phylum": "Bacteroidota"
+
+  "overview": {
+    "short": "Bergeyella species are fastidious, Gram-negative, non-motile short rods within the Flavobacteriaceae, most commonly associated with animal bite wounds.",
+    "clinical_context": "Primarily isolated from dog and cat bite infections, with rare cases of bacteremia and endocarditis."
   },
-  "overview": "Bergeyella is a genus of fastidious, oxidase-positive, non-motile Gram-negative rods within the family Weeksellaceae. Organisms in this genus are environmental or zoonotic, and rarely associated with human infection. Bergeyella zoohelcum is the only well-established species of clinical relevance, predominantly causing infections following dog or cat bites or licking.",
-  "key_traits": [
-    "Gram-negative rods (thin, fusiform or elongated)",
-    "Oxidase positive",
-    "Catalase positive or weak",
-    "Non-motile",
-    "Fastidious: poor growth on routine media",
-    "No growth or very weak growth on MacConkey agar",
-    "Indole negative",
-    "ONPG negative",
-    "Does not grow in 6.5% NaCl",
-    "Prefers blood or chocolate agar with CO₂"
-  ],
-  "ecology": "Found in the oral microbiota of dogs and cats. Human isolates are almost exclusively zoonotic in origin, typically following animal bites or licking of minor wounds.",
-  "pathogenicity": "Causes soft tissue infections, cellulitis, tenosynovitis, septic arthritis, and occasional bacteremia following dog or cat exposure. Infections are usually localized and treatable with β-lactam antibiotics.",
-  "genus_level_biochemistry": {
-    "general_tendencies": [
-      "Oxidase strongly positive.",
-      "Non-motile.",
-      "Indole negative.",
-      "ONPG negative.",
-      "Little to no growth on MacConkey.",
-      "No growth in high-salt conditions.",
-      "Slow growth—colonies appear after 48–72 hours."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Short Rods",
+    "Motility": "Negative",
+    "Capsule": "Negative",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "Chocolate Agar"
     ],
-    "non_definitive_tests": [
-      "Carbohydrate fermentation patterns are unreliable due to fastidious growth.",
-      "Hemolysis patterns vary and do not define the genus."
-    ]
-  },
-  "genus_differentiation": {
-    "from_close_genera": [
-      "Pasteurella multocida grows robustly on blood agar and is indole positive; Bergeyella is indole negative and slower growing.",
-      "Capnocytophaga are gliding motile and fusiform; Bergeyella is non-motile.",
-      "Weeksella species may appear similar but differ biochemically and ecologically.",
-      "Moraxella are oxidase positive but grow more readily and are diplococcoid.",
-      "Neisseria species are diplococci, not rods."
+    "Colony Morphology": [
+      "Small",
+      "Smooth",
+      "Grey"
     ],
-    "key_rag_filters": [
-      "Dog or cat exposure → strongly pushes toward Bergeyella zoohelcum or Pasteurella.",
-      "Oxidase positive + non-motile + poor MacConkey growth → favors Bergeyella.",
-      "Indole negative → pushes away from Pasteurella toward Bergeyella.",
-      "Fastidious slow growth → distinguishes from Pasteurella, Neisseria, Moraxella."
-    ]
+    "Oxygen Requirement": "Aerobic",
+    "Growth Temperature": "30//37",
+    "Catalase": "Positive",
+    "Oxidase": "Positive",
+    "Indole": "Positive",
+    "Urease": "Negative",
+    "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"
   },
-  "diagnostics": {
-    "typical_lab_findings": [
-      "Thin Gram-negative rods or fusiform cells",
-      "Slow-growing colonies on blood or chocolate agar",
-      "Oxidase positive, catalase variable",
-      "No/poor growth on MacConkey",
-      "Non-motile"
-    ],
-    "important_tests": [
-      "Oxidase test",
-      "Indole test",
-      "Growth characteristics on MacConkey",
-      "CO₂-enriched incubation",
-      "MALDI-TOF MS"
-    ],
-    "confirmation_methods": [
-      "MALDI-TOF MS (highly accurate for this genus)",
-      "16S rRNA sequencing",
-      "Clinical correlation with animal exposure"
-    ]
+
+  "field_notes": {
+    "Indole": "Indole positivity is a key clue separating Bergeyella from many other bite-associated organisms.",
+    "Growth": "Slow-growing and often missed on routine culture without prolonged incubation."
   },
-  "notes": "Part of the HACEK-adjacent group of fastidious Gram-negative rods but not included in HACEK. Zoonotic association is one of the strongest clues.",
-  "references": [
-    "Manual of Clinical Microbiology",
-    "Case reports of Bergeyella zoonotic infections",
-    "Flavobacteriales taxonomy reviews"
+
+  "key_differentiators": [
+    {
+      "field": "Indole",
+      "expected": "Positive",
+      "distinguishes_from": ["Capnocytophaga", "Pasteurella"],
+      "notes": "Indole positivity is unusual among many bite-associated Gram-negative rods."
+    },
+    {
+      "field": "Oxidase",
+      "expected": "Positive",
+      "distinguishes_from": ["Haemophilus"],
+      "notes": "Helps differentiate Bergeyella from oxidase-negative fastidious organisms."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Capnocytophaga",
+      "reason": "Shared association with animal bites and fastidious growth."
+    },
+    {
+      "genus": "Pasteurella",
+      "reason": "Similar clinical context and Gram-negative morphology."
+    }
+  ],
+
+  "when_to_question_identification": [
+    "Failure to recover organism after prolonged incubation.",
+    "Fermentative metabolism observed.",
+    "Motility detected."
+  ],
+
+  "recommended_next_tests": [
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Most reliable routine method for identifying Bergeyella.",
+      "api_kit": "Not applicable"
+    },
+    {
+      "test": "16S rRNA sequencing",
+      "reason": "Definitive identification for rare or atypical isolates."
+    }
+  ],
+
+  "supported_species": [
+    "zoohelcum"
   ]
-}
+}