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

data/rag/knowledge_base/Bergeyella/zoohelcum.json

@@ -1,50 +1,109 @@
 {
+  "schema_version": "1.0",
+  "level": "species",
   "genus": "Bergeyella",
   "species": "zoohelcum",
-  "full_name": "Bergeyella zoohelcum",
-  "clinical_significance": "A zoonotic pathogen found in the oral flora of dogs and cats. Causes soft-tissue infections, cellulitis, abscesses, septic arthritis, and bacteremia following animal bites or licks. Rare but important to recognize due to misidentification as Pasteurella or Capnocytophaga.",
-  "phenotype_profile": {
-    "morphology": "Slim, elongated Gram-negative rods; may be fusiform. Non-motile.",
-    "culture": "Slow-growing, translucent colonies on blood or chocolate agar after 48–72 hours. Very poor or no growth on MacConkey agar. Prefers CO₂.",
-    "biochemical": [
-      "Oxidase positive",
-      "Catalase weak or positive",
-      "Indole negative",
-      "ONPG negative",
-      "Non-motile",
-      "Does not grow in 6.5% NaCl",
-      "Urease negative",
-      "Nitrate reduction variable"
-    ]
+
+  "overview": {
+    "short": "Bergeyella zoohelcum is a fastidious Gram-negative rod primarily associated with animal bite wound infections.",
+    "clinical_context": "Most commonly isolated following dog or cat bites, occasionally causing soft tissue infection or bacteremia."
   },
-  "differentiation": {
-    "from_close_species": [
-      "Indole negative differentiates it from Pasteurella multocida.",
-      "Non-motility differentiates from Capnocytophaga (gliding).",
-      "Growth slower and more fastidious than Pasteurella.",
-      "Weeksella species grow more readily and have different environmental associations."
+
+  "expected_fields": {
+    "Gram Stain": "Negative",
+    "Shape": "Rods",
+    "Motility": "Negative",
+    "Capsule": "Negative",
+    "Spore Formation": "Negative",
+    "Haemolysis": "Negative",
+    "Haemolysis Type": "None",
+    "Media Grown On": [
+      "Blood Agar",
+      "Chocolate Agar"
     ],
-    "from_other_genera": [
-      "Oxidase positivity + poor MacConkey growth excludes Enterobacterales.",
-      "Slender rod morphology differentiates from Neisseria/Moraxella diplococci.",
-      "Zoonotic exposure is a strong clinical discriminator."
-    ]
+    "Colony Morphology": [
+      "Small",
+      "Smooth",
+      "Grey"
+    ],
+    "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"
   },
-  "virulence_factors": [
-    "Adhesion factors likely facilitating colonization of bite wounds",
-    "Unknown specific toxins; pathogenesis primarily opportunistic and due to inoculation into deep tissues"
+
+  "species_markers": [
+    {
+      "field": "Indole",
+      "value": "Positive",
+      "importance": "high",
+      "notes": "Unusual indole positivity among non-fermenting Gram-negative rods."
+    },
+    {
+      "field": "Clinical Association",
+      "value": "Animal bite",
+      "importance": "high",
+      "notes": "Strong epidemiological indicator for B. zoohelcum."
+    }
+  ],
+
+  "common_confusions": [
+    {
+      "genus": "Capnocytophaga",
+      "reason": "Shared association with animal bite wounds."
+    }
   ],
-  "confirmation_methods": [
-      "MALDI-TOF MS (best and most accurate method)",
-      "16S rRNA sequencing",
-      "Oxidase positivity + indole negativity + poor MacConkey growth",
-      "Clinical correlation with dog or cat exposure"
+
+  "when_to_question_identification": [
+    "Absence of animal exposure.",
+    "Fermentative carbohydrate metabolism.",
+    "Motility detected."
   ],
-  "treatment_notes": "Typically susceptible to β-lactams, including ampicillin, ceftriaxone, and amoxicillin–clavulanate. Resistant to macrolides in some reports. Empiric therapy for animal bites (amoxicillin–clavulanate) is effective.",
-  "notes": "Frequently misidentified by automated systems due to rarity. Should always be considered in slow-growing oxidase-positive rods from dog or cat bite wounds.",
-  "references": [
-    "Case studies involving B. zoohelcum infections",
-    "Manual of Clinical Microbiology",
-    "Zoonotic pathogen identification guidelines"
+
+  "recommended_next_tests": [
+    {
+      "test": "MALDI-TOF MS",
+      "reason": "Definitive identification of B. zoohelcum.",
+      "api_kit": "Bruker Biotyper or VITEK MS"
+    },
+    {
+      "test": "16S rRNA sequencing",
+      "reason": "Confirmation in rare or severe clinical cases."
+    }
   ]
-}
+}